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Protein

Histone deacetylase 1

Gene

HDAC1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes. Deacetylates SP proteins, SP1 and SP3, and regulates their function. Component of the BRG1-RB1-HDAC1 complex, which negatively regulates the CREST-mediated transcription in resting neurons. Upon calcium stimulation, HDAC1 is released from the complex and CREBBP is recruited, which facilitates transcriptional activation. Deacetylates TSHZ3 and regulates its transcriptional repressor activity. Deacetylates 'Lys-310' in RELA and thereby inhibits the transcriptional activity of NF-kappa-B. Deacetylates NR1D2 and abrogates the effect of KAT5-mediated relieving of NR1D2 transcription repression activity. Component of a RCOR/GFI/KDM1A/HDAC complex that suppresses, via histone deacetylase (HDAC) recruitment, a number of genes implicated in multilineage blood cell development. Involved in CIART-mediated transcriptional repression of the circadian transcriptional activator: CLOCK-ARNTL/BMAL1 heterodimer. Required for the transcriptional repression of circadian target genes, such as PER1, mediated by the large PER complex or CRY1 through histone deacetylation.7 Publications

Catalytic activityi

Hydrolysis of an N6-acetyl-lysine residue of a histone to yield a deacetylated histone.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei1411

GO - Molecular functioni

  • activating transcription factor binding Source: UniProtKB
  • core promoter sequence-specific DNA binding Source: CAFA
  • deacetylase activity Source: UniProtKB
  • DNA binding transcription factor activity Source: ProtInc
  • enzyme binding Source: UniProtKB
  • histone deacetylase activity Source: BHF-UCL
  • histone deacetylase binding Source: UniProtKB
  • NAD-dependent histone deacetylase activity (H3-K14 specific) Source: UniProtKB-EC
  • NF-kappaB binding Source: UniProtKB
  • p53 binding Source: CAFA
  • protein deacetylase activity Source: UniProtKB
  • protein N-terminus binding Source: MGI
  • repressing transcription factor binding Source: ParkinsonsUK-UCL
  • RNA polymerase II proximal promoter sequence-specific DNA binding Source: UniProtKB
  • RNA polymerase II repressing transcription factor binding Source: BHF-UCL
  • RNA polymerase II transcription factor binding Source: ParkinsonsUK-UCL
  • transcription corepressor activity Source: BHF-UCL
  • transcription factor binding Source: UniProtKB
  • transcription regulatory region DNA binding Source: ParkinsonsUK-UCL
  • transcription regulatory region sequence-specific DNA binding Source: UniProtKB

GO - Biological processi

  • ATP-dependent chromatin remodeling Source: UniProtKB
  • beta-catenin-TCF complex assembly Source: Reactome
  • blood coagulation Source: Reactome
  • chromatin organization Source: UniProtKB
  • chromatin remodeling Source: BHF-UCL
  • circadian regulation of gene expression Source: UniProtKB
  • embryonic digit morphogenesis Source: BHF-UCL
  • epidermal cell differentiation Source: BHF-UCL
  • eyelid development in camera-type eye Source: BHF-UCL
  • fungiform papilla formation Source: BHF-UCL
  • hair follicle placode formation Source: BHF-UCL
  • histone deacetylation Source: UniProtKB
  • histone H3 deacetylation Source: BHF-UCL
  • histone H4 deacetylation Source: BHF-UCL
  • methylation-dependent chromatin silencing Source: BHF-UCL
  • negative regulation by host of viral transcription Source: UniProtKB
  • negative regulation of androgen receptor signaling pathway Source: BHF-UCL
  • negative regulation of apoptotic process Source: BHF-UCL
  • negative regulation of canonical Wnt signaling pathway Source: ParkinsonsUK-UCL
  • negative regulation of gene expression Source: CACAO
  • negative regulation of transcription, DNA-templated Source: UniProtKB
  • negative regulation of transcription by RNA polymerase II Source: BHF-UCL
  • odontogenesis of dentin-containing tooth Source: BHF-UCL
  • positive regulation of cell proliferation Source: BHF-UCL
  • positive regulation of receptor biosynthetic process Source: BHF-UCL
  • positive regulation of transcription, DNA-templated Source: BHF-UCL
  • positive regulation of transcription by RNA polymerase II Source: BHF-UCL
  • protein deacetylation Source: UniProtKB
  • regulation of megakaryocyte differentiation Source: Reactome
  • transcription, DNA-templated Source: UniProtKB-KW

Keywordsi

Molecular functionChromatin regulator, Hydrolase, Repressor
Biological processBiological rhythms, Transcription, Transcription regulation

Enzyme and pathway databases

BRENDAi3.5.1.98 2681
ReactomeiR-HSA-1362277 Transcription of E2F targets under negative control by DREAM complex
R-HSA-1362300 Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1
R-HSA-1538133 G0 and Early G1
R-HSA-193670 p75NTR negatively regulates cell cycle via SC1
R-HSA-201722 Formation of the beta-catenin:TCF transactivating complex
R-HSA-2122947 NOTCH1 Intracellular Domain Regulates Transcription
R-HSA-2173795 Downregulation of SMAD2/3:SMAD4 transcriptional activity
R-HSA-2173796 SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription
R-HSA-2644606 Constitutive Signaling by NOTCH1 PEST Domain Mutants
R-HSA-2894862 Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants
R-HSA-3214815 HDACs deacetylate histones
R-HSA-3769402 Deactivation of the beta-catenin transactivating complex
R-HSA-427389 ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression
R-HSA-427413 NoRC negatively regulates rRNA expression
R-HSA-4551638 SUMOylation of chromatin organization proteins
R-HSA-4641265 Repression of WNT target genes
R-HSA-539107 Activation of E2F1 target genes at G1/S
R-HSA-6804758 Regulation of TP53 Activity through Acetylation
R-HSA-73762 RNA Polymerase I Transcription Initiation
R-HSA-8936459 RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function
R-HSA-8943724 Regulation of PTEN gene transcription
R-HSA-9018519 Estrogen-dependent gene expression
R-HSA-983231 Factors involved in megakaryocyte development and platelet production
SABIO-RKiQ13547
SIGNORiQ13547

Names & Taxonomyi

Protein namesi
Recommended name:
Histone deacetylase 1 (EC:3.5.1.98)
Short name:
HD1
Gene namesi
Name:HDAC1
Synonyms:RPD3L1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 1

Organism-specific databases

EuPathDBiHostDB:ENSG00000116478.11
HGNCiHGNC:4852 HDAC1
MIMi601241 gene
neXtProtiNX_Q13547

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi141H → A: Abolishes histone deacetylase activity. 1 Publication1
Mutagenesisi287F → Y: Abolishes interaction with CHFR; when associated with I-297. 1 Publication1
Mutagenesisi297M → I: Abolishes interaction with CHFR; when associated with Y-287. 1 Publication1
Mutagenesisi391 – 482Missing : Strongly decreases deacetylase activity, and disrupts interaction with NuRD and SIN3 complexes. Add BLAST92
Mutagenesisi421S → A: Strongly decreases deacetylase activity, and disrupts interaction with NuRD and SIN3 complexes. 1 Publication1
Mutagenesisi421S → D or E: Slightly decreases deacetylase activity. 1 Publication1
Mutagenesisi423S → A: Strongly decreases deacetylase activity, and disrupts interaction with NuRD and SIN3 complexes. 1 Publication1
Mutagenesisi423S → D or E: Decreases deacetylase activity. 1 Publication1
Mutagenesisi424E → A: Slightly decreases deacetylase activity, no effect on interaction with NuRD and SIN3 complexes. 1
Mutagenesisi425E → A: No effect on deacetylase activity, no effect on interaction with NuRD and SIN3 complexes. 1
Mutagenesisi426E → A: Decreases deacetylase activity, and disrupts interaction with NuRD and SIN3 complexes. 1

Organism-specific databases

DisGeNETi3065
OpenTargetsiENSG00000116478
PharmGKBiPA29226

Chemistry databases

ChEMBLiCHEMBL325
DrugBankiDB05015 Belinostat
DB05921 CRA-024781
DB05651 MGCD-0103
DB06603 Panobinostat
DB06176 Romidepsin
DB05223 SB939
DB02546 Vorinostat
GuidetoPHARMACOLOGYi2658

Polymorphism and mutation databases

BioMutaiHDAC1
DMDMi2498443

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001146871 – 482Histone deacetylase 1Add BLAST482

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei74N6-acetyllysine; alternateCombined sources1
Cross-linki74Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateBy similarity
Modified residuei220N6-acetyllysineCombined sources1
Modified residuei261S-nitrosocysteineBy similarity1
Modified residuei273S-nitrosocysteineBy similarity1
Modified residuei393PhosphoserineCombined sources1
Modified residuei406PhosphoserineBy similarity1
Modified residuei409PhosphoserineCombined sources1
Modified residuei421Phosphoserine; by CK2Combined sources1 Publication1
Modified residuei423Phosphoserine; by CK2Combined sources1 Publication1
Modified residuei432N6-methylated lysine; by EHMT21 Publication1
Cross-linki438Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki444Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO); alternate1 Publication
Cross-linki444Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateCombined sources
Cross-linki456Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Cross-linki457Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki473Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Cross-linki476Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO); alternate1 Publication
Cross-linki476Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateCombined sources
Cross-linki480Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources

Post-translational modificationi

Sumoylated on Lys-444 and Lys-476; which promotes enzymatic activity. Desumoylated by SENP1.3 Publications
Phosphorylation on Ser-421 and Ser-423 promotes enzymatic activity and interactions with NuRD and SIN3 complexes. Phosphorylated by CDK5.1 Publication
Ubiquitinated by CHFR, leading to its degradation by the proteasome. Ubiquitinated by KCTD11, leading to proteasomal degradation.2 Publications

Keywords - PTMi

Acetylation, Isopeptide bond, Methylation, Phosphoprotein, S-nitrosylation, Ubl conjugation

Proteomic databases

EPDiQ13547
PaxDbiQ13547
PeptideAtlasiQ13547
PRIDEiQ13547
ProteomicsDBi59529
TopDownProteomicsiQ13547

PTM databases

iPTMnetiQ13547
PhosphoSitePlusiQ13547
SwissPalmiQ13547

Expressioni

Tissue specificityi

Ubiquitous, with higher levels in heart, pancreas and testis, and lower levels in kidney and brain.

Gene expression databases

BgeeiENSG00000116478
CleanExiHS_HDAC1
ExpressionAtlasiQ13547 baseline and differential
GenevisibleiQ13547 HS

Organism-specific databases

HPAiCAB005017
CAB068191
HPA029693

Interactioni

Subunit structurei

Part of the core histone deacetylase (HDAC) complex composed of HDAC1, HDAC2, RBBP4 and RBBP7. The core complex associates with MTA2, MBD2, MBD3, MTA1L1, CHD3 and CHD4 to form the nucleosome remodeling and histone deacetylation (NuRD) complex, or with SIN3, SAP18 and SAP30 to form the SIN3 HDAC complex. Component of a BHC histone deacetylase complex that contains HDAC1, HDAC2, HMG20B/BRAF35, KDM1A, RCOR1/CoREST and PHF21A/BHC80. The BHC complex may also contain ZMYM2, ZNF217, ZMYM3, GSE1 and GTF2I. Component of a mSin3A corepressor complex that contains SIN3A, SAP130, SUDS3/SAP45, ARID4B/SAP180, HDAC1 and HDAC2. Found in a trimeric complex with APBB1 and TSHZ3; the interaction between HDAC1 and APBB1 is mediated by TSHZ3. Component of a RCOR/GFI/KDM1A/HDAC complex. Part of a complex composed of TRIM28, HDAC1, HDAC2 and EHMT2. Part of a complex containing at least CDYL, MIER1, MIER2, HDAC1 and HDAC2. The large PER complex involved in the histone deacetylation is composed of at least HDAC1, PER2, SFPQ and SIN3A. Associates with the 9-1-1 complex; interacts with HUS1. Found in a complex with DNMT3A and HDAC7. Interacts with the non-histone region of H2AFY. Interacts with TRIM28; the interaction recruits HDAC1 to E2F1 and inhibits its acetylation. Interacts with SP1; the interaction deacetylates SP1 and regulates its transcriptional activity. Interacts with SP3; the interaction deacetylates SP3 and regulates its transcriptional activity. In vitro, C(18) ceramides increase this interaction and the subsequent SP3 deacetylation and SP3-mediated repression of the TERT promoter. Interacts with TSHZ3 (via N-terminus); the interaction is direct. Interacts with APEX1; the interaction is not dependent on the acetylated status of APEX1. Interacts with C10orf90/FATS (via its N-terminal); the interaction prevents binding of HDAC1 to CDKN1A/p21 and facilitates the acetylation and stabilization of CDKN1A/p21. Interacts with CDKN1A/p21. Interacts with CDK5 complexed to CDK5R1 (p25). Interacts directly with GFI1 and GFI1B. Interacts with NR1D2 (via C-terminus). Interacts with TSC22D3 isoform 1; this interaction affects HDAC1 activity on MYOG promoter and thus inhibits MYOD1 transcriptional activity. Interacts with BAZ2A/TIP5, BANP, BCL6, BCOR, BHLHE40/DEC1, BRMS1, BRMS1L, CBFA2T3, CHFR, CIART, CRY1, DAXX, DDIT3/CHOP, DDX5, DNMT1, E4F1, EP300, HCFC1, HDAC9, INSM1, NFE4, NR4A2/NURR1, MIER1, KDM4A, KDM5B, KLF1, MINT, NRIP1, PCAF, PHB2, PRDM6, PRDM16, RB1, RERE, SAMSN1, SAP30L, SETDB1, SMAD3, SMARCA4/BRG1, SMYD2, SUV39H1, TGIF, TGIF2, TRAF6, UHRF1, UHRF2, ZMYND15, ZNF431 and ZNF541. Interacts with KDM5A (By similarity). Interacts with DNTTIP1 (PubMed:25653165). Identified in a histone deacetylase complex that contains DNTTIP1, HDAC1 and ELMSAN1; this complex assembles into a tetramer that contains four copies of each protein chain (PubMed:25653165). Interacts with CCAR2 (PubMed:21030595). Interacts with PPHLN1 (PubMed:17963697). Found in a complex with YY1, SIN3A and GON4L (By similarity). Interacts with CHD4 (PubMed:27616479). Found in a complex composed of at least SINHCAF, SIN3A, HDAC1, SAP30, RBBP4, OGT and TET1. Interacts with SIN3A (By similarity).By similarity46 Publications

Binary interactionsi

Show more details

GO - Molecular functioni

  • activating transcription factor binding Source: UniProtKB
  • enzyme binding Source: UniProtKB
  • histone deacetylase binding Source: UniProtKB
  • NF-kappaB binding Source: UniProtKB
  • p53 binding Source: CAFA
  • protein N-terminus binding Source: MGI
  • repressing transcription factor binding Source: ParkinsonsUK-UCL
  • RNA polymerase II repressing transcription factor binding Source: BHF-UCL
  • RNA polymerase II transcription factor binding Source: ParkinsonsUK-UCL
  • transcription factor binding Source: UniProtKB

Protein-protein interaction databases

BioGridi109315, 563 interactors
ComplexPortaliCPX-880 MBD2/NuRD nucleosome remodeling and deacetylase complex
CPX-922 MBD3/NuRD nucleosome remodeling and deacetylase complex
CORUMiQ13547
DIPiDIP-24184N
IntActiQ13547, 271 interactors
MINTiQ13547
STRINGi9606.ENSP00000362649

Chemistry databases

BindingDBiQ13547

Structurei

Secondary structure

1482
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi11 – 14Combined sources4
Helixi19 – 21Combined sources3
Helixi33 – 44Combined sources12
Turni45 – 47Combined sources3
Helixi48 – 50Combined sources3
Beta strandi51 – 56Combined sources6
Helixi61 – 64Combined sources4
Turni65 – 67Combined sources3
Helixi70 – 78Combined sources9
Turni83 – 86Combined sources4
Helixi88 – 94Combined sources7
Turni97 – 99Combined sources3
Helixi106 – 125Combined sources20
Beta strandi130 – 136Combined sources7
Beta strandi151 – 153Combined sources3
Helixi155 – 163Combined sources9
Turni164 – 166Combined sources3
Beta strandi170 – 174Combined sources5
Beta strandi176 – 178Combined sources3
Helixi181 – 186Combined sources6
Turni187 – 189Combined sources3
Beta strandi191 – 200Combined sources10
Beta strandi205 – 207Combined sources3
Helixi217 – 219Combined sources3
Beta strandi223 – 228Combined sources6
Helixi234 – 252Combined sources19
Beta strandi255 – 260Combined sources6
Helixi263 – 265Combined sources3
Helixi278 – 289Combined sources12
Beta strandi295 – 298Combined sources4
Helixi305 – 319Combined sources15
Helixi334 – 336Combined sources3
Turni338 – 340Combined sources3
Helixi356 – 371Combined sources16

3D structure databases

ProteinModelPortaliQ13547
SMRiQ13547
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni9 – 321Histone deacetylaseAdd BLAST313

Sequence similaritiesi

Phylogenomic databases

eggNOGiKOG1342 Eukaryota
COG0123 LUCA
GeneTreeiENSGT00910000144047
HOGENOMiHOG000225180
HOVERGENiHBG057112
InParanoidiQ13547
KOiK06067
OMAiMDTSKPK
OrthoDBiEOG091G067J
PhylomeDBiQ13547
TreeFamiTF106171

Family and domain databases

Gene3Di3.40.800.20, 1 hit
InterProiView protein in InterPro
IPR000286 His_deacetylse
IPR003084 His_deacetylse_1
IPR023801 His_deacetylse_dom
IPR037138 His_deacetylse_dom_sf
IPR023696 Ureohydrolase_dom_sf
PANTHERiPTHR10625 PTHR10625, 1 hit
PfamiView protein in Pfam
PF00850 Hist_deacetyl, 1 hit
PIRSFiPIRSF037913 His_deacetylse_1, 1 hit
PRINTSiPR01270 HDASUPER
PR01271 HISDACETLASE
SUPFAMiSSF52768 SSF52768, 1 hit

Sequencei

Sequence statusi: Complete.

Q13547-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAQTQGTRRK VCYYYDGDVG NYYYGQGHPM KPHRIRMTHN LLLNYGLYRK
60 70 80 90 100
MEIYRPHKAN AEEMTKYHSD DYIKFLRSIR PDNMSEYSKQ MQRFNVGEDC
110 120 130 140 150
PVFDGLFEFC QLSTGGSVAS AVKLNKQQTD IAVNWAGGLH HAKKSEASGF
160 170 180 190 200
CYVNDIVLAI LELLKYHQRV LYIDIDIHHG DGVEEAFYTT DRVMTVSFHK
210 220 230 240 250
YGEYFPGTGD LRDIGAGKGK YYAVNYPLRD GIDDESYEAI FKPVMSKVME
260 270 280 290 300
MFQPSAVVLQ CGSDSLSGDR LGCFNLTIKG HAKCVEFVKS FNLPMLMLGG
310 320 330 340 350
GGYTIRNVAR CWTYETAVAL DTEIPNELPY NDYFEYFGPD FKLHISPSNM
360 370 380 390 400
TNQNTNEYLE KIKQRLFENL RMLPHAPGVQ MQAIPEDAIP EESGDEDEDD
410 420 430 440 450
PDKRISICSS DKRIACEEEF SDSEEEGEGG RKNSSNFKKA KRVKTEDEKE
460 470 480
KDPEEKKEVT EEEKTKEEKP EAKGVKEEVK LA
Length:482
Mass (Da):55,103
Last modified:November 1, 1997 - v1
Checksum:i4D35B7C1ED7838D6
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti312W → R in BAA08909 (PubMed:8646880).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U50079 mRNA Translation: AAC50475.1
D50405 mRNA Translation: BAA08909.1
BC000301 mRNA Translation: AAH00301.1
CCDSiCCDS360.1
RefSeqiNP_004955.2, NM_004964.2
UniGeneiHs.88556

Genome annotation databases

EnsembliENST00000373548; ENSP00000362649; ENSG00000116478
GeneIDi3065
KEGGihsa:3065

Similar proteinsi

Entry informationi

Entry nameiHDAC1_HUMAN
AccessioniPrimary (citable) accession number: Q13547
Secondary accession number(s): Q92534
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1997
Last modified: July 18, 2018
This is version 217 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 1
    Human chromosome 1: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

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