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Protein

HLA class II histocompatibility antigen, DM beta chain

Gene

HLA-DMB

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

Functioni

Plays a critical role in catalyzing the release of class II-associated invariant chain peptide (CLIP) from newly synthesized MHC class II molecules and freeing the peptide binding site for acquisition of antigenic peptides. In B-cells, the interaction between HLA-DM and MHC class II molecules is regulated by HLA-DO.3 Publications

GO - Molecular functioni

  • MHC class II protein complex binding Source: UniProtKB

GO - Biological processi

  • antigen processing and presentation of exogenous peptide antigen via MHC class II Source: UniProtKB
  • immune response Source: InterPro
  • MHC class II protein complex assembly Source: UniProtKB
  • peptide antigen assembly with MHC class II protein complex Source: UniProtKB
  • positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell Source: UniProtKB
  • positive regulation of T cell proliferation Source: UniProtKB

Keywordsi

Biological processImmunity

Enzyme and pathway databases

ReactomeiR-HSA-2132295 MHC class II antigen presentation
SIGNORiP28068

Names & Taxonomyi

Protein namesi
Recommended name:
HLA class II histocompatibility antigen, DM beta chain
Alternative name(s):
MHC class II antigen DMB
Really interesting new gene 7 protein
Gene namesi
Name:HLA-DMB
Synonyms:DMB, RING7
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 6

Organism-specific databases

EuPathDBiHostDB:ENSG00000242574.8
HGNCiHGNC:4935 HLA-DMB
MIMi142856 gene
neXtProtiNX_P28068

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

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini19 – 218LumenalSequence analysisAdd BLAST200
Transmembranei219 – 239HelicalSequence analysisAdd BLAST21
Topological domaini240 – 263CytoplasmicSequence analysisAdd BLAST24

Keywords - Cellular componenti

Endosome, Lysosome, Membrane, MHC II

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi248Y → A: Abolishes targeting to endosomes and results in relocalization to the cell membrane. 1 Publication1
Mutagenesisi251L → A: Abolishes targeting to endosomes and results in relocalization to the cell membrane. 1 Publication1

Organism-specific databases

DisGeNETi3109
PharmGKBiPA35059

Polymorphism and mutation databases

BioMutaiHLA-DMB
DMDMi133160

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 18Sequence analysisAdd BLAST18
ChainiPRO_000001896019 – 263HLA class II histocompatibility antigen, DM beta chainAdd BLAST245

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi29 ↔ 97
Glycosylationi110N-linked (GlcNAc...) asparagine1 Publication1
Disulfide bondi135 ↔ 192

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

PaxDbiP28068
PeptideAtlasiP28068
PRIDEiP28068

PTM databases

iPTMnetiP28068
PhosphoSitePlusiP28068

Expressioni

Gene expression databases

BgeeiENSG00000242574
CleanExiHS_HLA-DMB
ExpressionAtlasiP28068 baseline and differential
GenevisibleiP28068 HS

Organism-specific databases

HPAiHPA012298

Interactioni

Subunit structurei

Heterodimer of an alpha chain (DMA) and a beta chain (DMB).2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
HLA-DMAQ6ICR95EBI-2877138,EBI-16027071

Protein-protein interaction databases

BioGridi109354, 11 interactors
DIPiDIP-6185N
IntActiP28068, 10 interactors
MINTiP28068
STRINGi9606.ENSP00000398890

Structurei

Secondary structure

1263
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi22 – 32Combined sources11
Beta strandi33 – 35Combined sources3
Beta strandi37 – 46Combined sources10
Beta strandi49 – 55Combined sources7
Turni56 – 59Combined sources4
Beta strandi60 – 63Combined sources4
Beta strandi67 – 69Combined sources3
Helixi70 – 81Combined sources12
Helixi84 – 91Combined sources8
Helixi93 – 109Combined sources17
Beta strandi116 – 121Combined sources6
Beta strandi128 – 143Combined sources16
Beta strandi146 – 151Combined sources6
Beta strandi154 – 156Combined sources3
Beta strandi170 – 172Combined sources3
Beta strandi174 – 182Combined sources9
Beta strandi190 – 195Combined sources6
Beta strandi199 – 201Combined sources3
Beta strandi203 – 207Combined sources5
Helixi212 – 214Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1HDMX-ray2.50B19-218[»]
2BC4X-ray2.27B/D19-218[»]
4FQXX-ray2.60D19-211[»]
4GBXX-ray3.00D19-211[»]
4I0PX-ray3.20B/F21-211[»]
ProteinModelPortaliP28068
SMRiP28068
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP28068

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini114 – 208Ig-like C1-typeAdd BLAST95

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni19 – 112Beta-1Add BLAST94
Regioni113 – 207Beta-2Add BLAST95
Regioni208 – 218Connecting peptideSequence analysisAdd BLAST11

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi248 – 251YXXZ motif4

Domaini

The YXXZ (Tyr-Xaa-Xaa-Zaa, where Zaa is a hydrophobic residue) motif mediates the targeting to the lysosomal compartments.

Sequence similaritiesi

Belongs to the MHC class II family.Curated

Keywords - Domaini

Immunoglobulin domain, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG410IFNH Eukaryota
ENOG410YU9X LUCA
HOVERGENiHBG007327
InParanoidiP28068
KOiK06752
OrthoDBiEOG091G0G84
PhylomeDBiP28068
TreeFamiTF335727

Family and domain databases

Gene3Di2.60.40.10, 1 hit
3.10.320.10, 1 hit
InterProiView protein in InterPro
IPR007110 Ig-like_dom
IPR036179 Ig-like_dom_sf
IPR013783 Ig-like_fold
IPR003006 Ig/MHC_CS
IPR003597 Ig_C1-set
IPR011162 MHC_I/II-like_Ag-recog
IPR014745 MHC_II_a/b_N
IPR000353 MHC_II_b_N
PfamiView protein in Pfam
PF07654 C1-set, 1 hit
PF00969 MHC_II_beta, 1 hit
SMARTiView protein in SMART
SM00407 IGc1, 1 hit
SM00921 MHC_II_beta, 1 hit
SUPFAMiSSF48726 SSF48726, 1 hit
SSF54452 SSF54452, 1 hit
PROSITEiView protein in PROSITE
PS50835 IG_LIKE, 1 hit
PS00290 IG_MHC, 1 hit

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P28068-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MITFLPLLLG LSLGCTGAGG FVAHVESTCL LDDAGTPKDF TYCISFNKDL
60 70 80 90 100
LTCWDPEENK MAPCEFGVLN SLANVLSQHL NQKDTLMQRL RNGLQNCATH
110 120 130 140 150
TQPFWGSLTN RTRPPSVQVA KTTPFNTREP VMLACYVWGF YPAEVTITWR
160 170 180 190 200
KNGKLVMPHS SAHKTAQPNG DWTYQTLSHL ALTPSYGDTY TCVVEHIGAP
210 220 230 240 250
EPILRDWTPG LSPMQTLKVS VSAVTLGLGL IIFSLGVISW RRAGHSSYTP
260
LPGSNYSEGW HIS
Length:263
Mass (Da):28,943
Last modified:August 1, 1992 - v1
Checksum:i9B50F6CC22B3A4BA
GO

Polymorphismi

The following alleles of DMB are known: DMB*01:01, DMB*01:02, DMB*01:03, DMB*01:04 (DMB3.4), DMB*01:05, DMB*01:06, and DMB*01:07. The sequence shown is that of DMB*01:01.

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_05036028T → A in allele DMB*01:07. Corresponds to variant dbSNP:rs17583782Ensembl.1
Natural variantiVAR_01675245S → F in allele DMB*01:06. Corresponds to variant dbSNP:rs41560814Ensembl.1
Natural variantiVAR_05036149D → V in allele DMB*01:07. Corresponds to variant dbSNP:rs17617333Ensembl.1
Natural variantiVAR_05036271S → N in allele DMB*01:07. Corresponds to variant dbSNP:rs17617321Ensembl.1
Natural variantiVAR_016753162A → E in allele DMB*01:02 and allele DMB*01:06. Corresponds to variant dbSNP:rs2071555Ensembl.1
Natural variantiVAR_016754162A → V in allele DMB*01:04 and allele DMB*01:05. Corresponds to variant dbSNP:rs2071555Ensembl.1
Natural variantiVAR_016755197I → T in allele DMB*01:03, allele DMB*01:04 and allele DMB*01:06. 1 PublicationCorresponds to variant dbSNP:rs1042337Ensembl.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z23139 mRNA Translation: CAA80670.1
U15085 mRNA Translation: AAB60387.1
X76776 Genomic DNA Translation: CAA54171.1
X87344 Genomic DNA Translation: CAA60782.1
AY645722 mRNA Translation: AAV97947.1
AL662845 Genomic DNA No translation available.
AL645941 Genomic DNA No translation available.
AL935042 Genomic DNA No translation available.
BX088556 Genomic DNA No translation available.
BX927138 Genomic DNA No translation available.
CR936913 Genomic DNA No translation available.
CR759798 Genomic DNA No translation available.
CR752645 Genomic DNA No translation available.
CH471081 Genomic DNA Translation: EAX03657.1
BC027175 mRNA Translation: AAH27175.1
Z24750 Genomic DNA No translation available.
Z24751 Genomic DNA No translation available.
U00700 Genomic DNA Translation: AAA03296.1
U16762 Genomic DNA Translation: AAC50514.1
AF134890 Genomic DNA Translation: AAD30279.1
AF072680 Genomic DNA Translation: AAC26112.1
CCDSiCCDS4760.1
PIRiI37533
RefSeqiNP_002109.2, NM_002118.4
UniGeneiHs.351279

Genome annotation databases

EnsembliENST00000383231; ENSP00000372718; ENSG00000241674
ENST00000395312; ENSP00000378723; ENSG00000242092
ENST00000412948; ENSP00000413471; ENSG00000241296
ENST00000418107; ENSP00000398890; ENSG00000242574
ENST00000424822; ENSP00000414817; ENSG00000234154
ENST00000428420; ENSP00000393646; ENSG00000239329
ENST00000440078; ENSP00000411321; ENSG00000226264
ENST00000450897; ENSP00000408453; ENSG00000242386
GeneIDi3109
KEGGihsa:3109
UCSCiuc003ocl.2 human

Keywords - Coding sequence diversityi

Polymorphism

Similar proteinsi

Entry informationi

Entry nameiDMB_HUMAN
AccessioniPrimary (citable) accession number: P28068
Secondary accession number(s): O77936
, Q13012, Q29751, Q58ZE2, Q5SNZ8, Q5STC4, Q9XRX2
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 1, 1992
Last sequence update: August 1, 1992
Last modified: May 23, 2018
This is version 176 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

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