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P05534 - 1A24_HUMAN

UniProt

P05534 - 1A24_HUMAN

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Protein

HLA class I histocompatibility antigen, A-24 alpha chain

Gene

HLA-A

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in the presentation of foreign antigens to the immune system.

GO - Molecular functioni

  1. beta-2-microglobulin binding Source: UniProtKB
  2. peptide antigen binding Source: UniProtKB
  3. receptor binding Source: GO_Central
  4. TAP binding Source: UniProtKB

GO - Biological processi

  1. antigen processing and presentation of exogenous peptide antigen via MHC class I Source: Reactome
  2. antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent Source: Reactome
  3. antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent Source: Reactome
  4. antigen processing and presentation of peptide antigen via MHC class I Source: Reactome
  5. cytokine-mediated signaling pathway Source: Reactome
  6. interferon-gamma-mediated signaling pathway Source: Reactome
  7. positive regulation of T cell mediated cytotoxicity Source: InterPro
  8. regulation of immune response Source: Reactome
  9. type I interferon signaling pathway Source: Reactome
  10. viral process Source: UniProtKB-KW
Complete GO annotation...

Keywords - Biological processi

Host-virus interaction, Immunity

Enzyme and pathway databases

ReactomeiREACT_111168. Endosomal/Vacuolar pathway.
REACT_111178. ER-Phagosome pathway.
REACT_11152. Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell.
REACT_25078. Interferon gamma signaling.
REACT_25162. Interferon alpha/beta signaling.
REACT_75795. Antigen Presentation: Folding, assembly and peptide loading of class I MHC.

Names & Taxonomyi

Protein namesi
Recommended name:
HLA class I histocompatibility antigen, A-24 alpha chain
Alternative name(s):
Aw-24
HLA class I histocompatibility antigen, A-9 alpha chain
MHC class I antigen A*24
Gene namesi
Name:HLA-A
Synonyms:HLAA
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo
ProteomesiUP000005640: Unplaced

Organism-specific databases

HGNCiHGNC:4931. HLA-A.

Subcellular locationi

Membrane; Single-pass type I membrane protein

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini25 – 308284ExtracellularSequence AnalysisAdd
BLAST
Transmembranei309 – 33224HelicalSequence AnalysisAdd
BLAST
Topological domaini333 – 36533CytoplasmicSequence AnalysisAdd
BLAST

GO - Cellular componenti

  1. cell surface Source: UniProtKB
  2. early endosome membrane Source: Reactome
  3. endoplasmic reticulum Source: UniProtKB
  4. ER to Golgi transport vesicle membrane Source: Reactome
  5. extracellular vesicular exosome Source: UniProtKB
  6. Golgi apparatus Source: UniProtKB
  7. Golgi membrane Source: Reactome
  8. integral component of lumenal side of endoplasmic reticulum membrane Source: Reactome
  9. MHC class I protein complex Source: UniProtKB
  10. phagocytic vesicle membrane Source: Reactome
  11. plasma membrane Source: Reactome
Complete GO annotation...

Keywords - Cellular componenti

Membrane, MHC I

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2424Add
BLAST
Chaini25 – 365341HLA class I histocompatibility antigen, A-24 alpha chainPRO_0000018818Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi110 – 1101N-linked (GlcNAc...)1 Publication
Disulfide bondi125 ↔ 1881 PublicationPROSITE-ProRule annotation
Disulfide bondi227 ↔ 2831 PublicationPROSITE-ProRule annotation
Modified residuei356 – 3561Phosphoserine1 Publication

Post-translational modificationi

Polyubiquitinated in a post ER compartment by interaction with human herpesvirus 8 MIR1 protein. This targets the protein for rapid degradation via the ubiquitin system (By similarity).By similarity

Keywords - PTMi

Disulfide bond, Glycoprotein, Phosphoprotein, Ubl conjugation

Proteomic databases

MaxQBiP05534.
PaxDbiP05534.
PRIDEiP05534.

Expressioni

Gene expression databases

CleanExiHS_HLA-A.
GenevestigatoriP05534.

Interactioni

Subunit structurei

Heterodimer of an alpha chain and a beta chain (beta-2-microglobulin). Interacts with human herpesvirus 8 MIR1 protein (By similarity).By similarity

Structurei

Secondary structure

1
365
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi27 – 3610Combined sources
Beta strandi41 – 433Combined sources
Beta strandi45 – 528Combined sources
Beta strandi55 – 617Combined sources
Beta strandi64 – 663Combined sources
Beta strandi70 – 734Combined sources
Helixi74 – 763Combined sources
Helixi81 – 10929Combined sources
Beta strandi113 – 1153Combined sources
Beta strandi118 – 12710Combined sources
Beta strandi133 – 14210Combined sources
Beta strandi145 – 1506Combined sources
Beta strandi157 – 1593Combined sources
Helixi162 – 17312Combined sources
Helixi176 – 18510Combined sources
Helixi187 – 19812Combined sources
Helixi200 – 2034Combined sources
Beta strandi210 – 23526Combined sources
Beta strandi238 – 2436Combined sources
Beta strandi246 – 2483Combined sources
Helixi249 – 2513Combined sources
Beta strandi252 – 2543Combined sources
Beta strandi261 – 2633Combined sources
Beta strandi265 – 27410Combined sources
Helixi278 – 2803Combined sources
Beta strandi281 – 2866Combined sources
Beta strandi290 – 2923Combined sources
Beta strandi294 – 2974Combined sources
Beta strandi298 – 3003Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2BCKX-ray2.80A/D25-300[»]
3I6LX-ray2.40D25-298[»]
3NFNX-ray2.39A25-298[»]
3QZWX-ray2.80A/D25-298[»]
3VXMX-ray2.50A25-298[»]
3VXNX-ray1.95A25-298[»]
3VXOX-ray2.61A/D25-298[»]
3VXPX-ray2.50A/D25-298[»]
3VXRX-ray2.40A25-298[»]
3VXSX-ray1.80A25-298[»]
3VXUX-ray2.70A/F25-298[»]
3W0WX-ray2.60A25-298[»]
3WL9X-ray1.66A25-298[»]
3WLBX-ray2.00A25-298[»]
4F7MX-ray2.40A/D25-298[»]
4F7PX-ray1.90A25-298[»]
4F7TX-ray1.70A/D25-298[»]
ProteinModelPortaliP05534.
SMRiP05534. Positions 25-298.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP05534.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini209 – 29587Ig-like C1-typeAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni25 – 11490Alpha-1Add
BLAST
Regioni115 – 20692Alpha-2Add
BLAST
Regioni207 – 29892Alpha-3Add
BLAST
Regioni299 – 30810Connecting peptide

Sequence similaritiesi

Belongs to the MHC class I family.Curated
Contains 1 Ig-like C1-type (immunoglobulin-like) domain.Curated

Keywords - Domaini

Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiNOG42056.
HOVERGENiHBG016709.
PhylomeDBiP05534.

Family and domain databases

Gene3Di2.60.40.10. 1 hit.
3.30.500.10. 1 hit.
InterProiIPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR003006. Ig/MHC_CS.
IPR003597. Ig_C1-set.
IPR011161. MHC_I-like_Ag-recog.
IPR011162. MHC_I/II-like_Ag-recog.
IPR027648. MHC_I_a.
IPR001039. MHC_I_a_a1/a2.
IPR010579. MHC_I_a_C.
[Graphical view]
PfamiPF07654. C1-set. 1 hit.
PF00129. MHC_I. 1 hit.
PF06623. MHC_I_C. 1 hit.
[Graphical view]
PRINTSiPR01638. MHCCLASSI.
SMARTiSM00407. IGc1. 1 hit.
[Graphical view]
SUPFAMiSSF54452. SSF54452. 1 hit.
PROSITEiPS50835. IG_LIKE. 1 hit.
PS00290. IG_MHC. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

P05534-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MAVMAPRTLV LLLSGALALT QTWAGSHSMR YFSTSVSRPG RGEPRFIAVG 
        60         70         80         90        100
YVDDTQFVRF DSDAASQRME PRAPWIEQEG PEYWDEETGK VKAHSQTDRE 
       110        120        130        140        150
NLRIALRYYN QSEAGSHTLQ MMFGCDVGSD GRFLRGYHQY AYDGKDYIAL 
       160        170        180        190        200
KEDLRSWTAA DMAAQITKRK WEAAHVAEQQ RAYLEGTCVD GLRRYLENGK 
       210        220        230        240        250
ETLQRTDPPK THMTHHPISD HEATLRCWAL GFYPAEITLT WQRDGEDQTQ 
       260        270        280        290        300
DTELVETRPA GDGTFQKWAA VVVPSGEEQR YTCHVQHEGL PKPLTLRWEP 
       310        320        330        340        350
SSQPTVPIVG IIAGLVLLGA VITGAVVAAV MWRRNSSDRK GGSYSQAASS 
       360 
DSAQGSDVSL TACKV
Length:365
Mass (Da):40,689
Last modified:June 27, 2003 - v2
Checksum:iD33684D126F98EC3
GO

Polymorphismi

The following alleles of A-24 are known: A*2401, A*24:02, A*24:03, A*24:06, A*24:08 (A9HH), A*24:10 (A*24JV), A*24:13 (A*24YM), A*24:14 (A*24SA) and A*24:29. Allele A*24:02 is represented in all major racial groups. Allele A*24:06 and allele A*24:13 are found in the Australian Aboriginal population. Allele A*24:14 is found in individuals of South American descent. The sequence shown is that of A*24:02.

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti5 – 51A → G in allele A*2401.
VAR_004354
Natural varianti27 – 271H → Q in allele A*24:08.
Corresponds to variant rs41541319 [ dbSNP | Ensembl ].		VAR_004355
Natural varianti86 – 861E → G in allele A*24:08.
VAR_004356
Natural varianti89 – 891G → R in allele A*24:08 and allele A*24:29.
VAR_004357
Natural varianti119 – 1191L → V in allele A*24:14.
VAR_015765
Natural varianti121 – 1211M → R in allele A*24:14.
VAR_015766
Natural varianti123 – 1231F → Y in allele A*24:14.
VAR_015767
Natural varianti131 – 1311G → W in allele A*24:14.
VAR_015768
Natural varianti180 – 1801Q → L in allele A*24:13.
VAR_015769
Natural varianti180 – 1801Q → W in allele A*24:06; requires 2 nucleotide substitutions. 1 Publication
VAR_004358
Natural varianti187 – 1871T → R in allele A*24:10.
VAR_015770
Natural varianti190 – 1912DG → EW in allele A*24:03 and allele A*24:10.
VAR_004359
Natural varianti205 – 2051R → H.
Corresponds to variant rs17185861 [ dbSNP | Ensembl ].		VAR_056263
Natural varianti206 – 2061T → A in allele A*2401.
VAR_004360

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M15497 Genomic DNA. Translation: AAA59611.1.
M64740 mRNA. Translation: AAA59600.1.
M64741 Genomic DNA. Translation: AAA59601.1.
Z72422 Genomic DNA. Translation: CAA96532.1.
D83516 mRNA. Translation: BAA11936.1.
U37111, U37110 Genomic DNA. Translation: AAA83264.1.
U37113, U37112 Genomic DNA. Translation: AAA83265.1.
AH004915 Genomic DNA. Translation: AAB40048.1.
AH005378 Genomic DNA. Translation: AAB60651.1.
PIRiI54416.
UniGeneiHs.181244.
Hs.713441.

Genome annotation databases

EnsembliENST00000431930; ENSP00000406366; ENSG00000229215.
ENST00000443552; ENSP00000404678; ENSG00000224320.

Polymorphism databases

DMDMi32363482.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M15497 Genomic DNA. Translation: AAA59611.1.
M64740 mRNA. Translation: AAA59600.1.
M64741 Genomic DNA. Translation: AAA59601.1.
Z72422 Genomic DNA. Translation: CAA96532.1.
D83516 mRNA. Translation: BAA11936.1.
U37111, U37110 Genomic DNA. Translation: AAA83264.1.
U37113, U37112 Genomic DNA. Translation: AAA83265.1.
AH004915 Genomic DNA. Translation: AAB40048.1.
AH005378 Genomic DNA. Translation: AAB60651.1.
PIRiI54416.
UniGeneiHs.181244.
Hs.713441.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2BCKX-ray2.80A/D25-300[»]
3I6LX-ray2.40D25-298[»]
3NFNX-ray2.39A25-298[»]
3QZWX-ray2.80A/D25-298[»]
3VXMX-ray2.50A25-298[»]
3VXNX-ray1.95A25-298[»]
3VXOX-ray2.61A/D25-298[»]
3VXPX-ray2.50A/D25-298[»]
3VXRX-ray2.40A25-298[»]
3VXSX-ray1.80A25-298[»]
3VXUX-ray2.70A/F25-298[»]
3W0WX-ray2.60A25-298[»]
3WL9X-ray1.66A25-298[»]
3WLBX-ray2.00A25-298[»]
4F7MX-ray2.40A/D25-298[»]
4F7PX-ray1.90A25-298[»]
4F7TX-ray1.70A/D25-298[»]
ProteinModelPortaliP05534.
SMRiP05534. Positions 25-298.
ModBaseiSearch...
MobiDBiSearch...

Polymorphism databases

DMDMi32363482.

Proteomic databases

MaxQBiP05534.
PaxDbiP05534.
PRIDEiP05534.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000431930; ENSP00000406366; ENSG00000229215.
ENST00000443552; ENSP00000404678; ENSG00000224320.

Organism-specific databases

GeneCardsiGC06P030186.
GC06Pi29846.
GC06Pj29898.
H-InvDBHIX0165910.
HIX0165954.
HIX0166079.
HIX0166152.
HIX0166432.
HIX0166685.
HIX0166954.
HGNCiHGNC:4931. HLA-A.
MIMi142800. gene.
neXtProtiNX_P05534.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG42056.
HOVERGENiHBG016709.
PhylomeDBiP05534.

Enzyme and pathway databases

ReactomeiREACT_111168. Endosomal/Vacuolar pathway.
REACT_111178. ER-Phagosome pathway.
REACT_11152. Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell.
REACT_25078. Interferon gamma signaling.
REACT_25162. Interferon alpha/beta signaling.
REACT_75795. Antigen Presentation: Folding, assembly and peptide loading of class I MHC.

Miscellaneous databases

ChiTaRSiHLA-A. human.
EvolutionaryTraceiP05534.
PROiP05534.
SOURCEiSearch...

Gene expression databases

CleanExiHS_HLA-A.
GenevestigatoriP05534.

Family and domain databases

Gene3Di2.60.40.10. 1 hit.
3.30.500.10. 1 hit.
InterProiIPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR003006. Ig/MHC_CS.
IPR003597. Ig_C1-set.
IPR011161. MHC_I-like_Ag-recog.
IPR011162. MHC_I/II-like_Ag-recog.
IPR027648. MHC_I_a.
IPR001039. MHC_I_a_a1/a2.
IPR010579. MHC_I_a_C.
[Graphical view]
PfamiPF07654. C1-set. 1 hit.
PF00129. MHC_I. 1 hit.
PF06623. MHC_I_C. 1 hit.
[Graphical view]
PRINTSiPR01638. MHCCLASSI.
SMARTiSM00407. IGc1. 1 hit.
[Graphical view]
SUPFAMiSSF54452. SSF54452. 1 hit.
PROSITEiPS50835. IG_LIKE. 1 hit.
PS00290. IG_MHC. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The HLA-AW24 gene: sequence, surroundings and comparison with the HLA-A2 and HLA-A3 genes."
    N'Guyen C., Sodoyer R., Trucy J., Strachan T., Jordan B.R.
    Immunogenetics 21:479-489(1985) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ALLELE A*2401).
  2. Jordan B.R.
    Submitted (JUL-1988) to the EMBL/GenBank/DDBJ databases
    Cited for: SEQUENCE REVISION.
  3. "Molecular definition of an elusive third HLA-A9 molecule: HLA-A9.3."
    Little A.-M., Madrigal J.A., Parham P.
    Immunogenetics 35:41-45(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA] (ALLELES A*24:02 AND A*24:03).
  4. Cited for: NUCLEOTIDE SEQUENCE (ALLELE A*24:02).
  5. "An intronic mutation responsible for a low level of expression of an HLA-A*24 allele."
    Laforet M., Froelich N., Parissiadis A., Bausinger H., Pfeiffer B., Tongio M.M.
    Tissue Antigens 50:340-346(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ALLELE A*24:02).
  6. "Sequence analysis of a serological subtype, HLA-A9HH, observed in Japanese and the confirmatory sequence of A*2408."
    Kashiwase K., Tokunaga K., Ishikawa Y., Qiu L., Furuya M., Sawanaka K., Akaza T., Tadokoro K., Juji T.
    MHC 3:9-14(1996)
    Cited for: NUCLEOTIDE SEQUENCE (ALLELE A*24:08).
    Tissue: Blood.
  7. "Confirmation of the sequence of HLA-A*2429 allele found in a potential bone marrow donor."
    Dunn P.
    Submitted (JAN-2003) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 26-337 (ALLELE A*24:29).
  8. "A novel HLA-A*24 (A*2410) identified in a Javanese population."
    Gao X., Matheson B.
    Tissue Antigens 48:711-713(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 26-206 (ALLELE A*24:10).
    Tissue: Blood.
  9. "Three newly identified A*24 alleles: A*2406, A*2413 and A*2414."
    Gao X., Lester S., Matheson B., Boettcher B., McCluskey J.
    Tissue Antigens 50:192-196(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 26-206 (ALLELES A*24:06; A*24:13 AND A*24:14).
    Tissue: Blood.
  10. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-356, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Platelet.
  11. "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
    Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
    Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  12. "Glycoproteomics analysis of human liver tissue by combination of multiple enzyme digestion and hydrazide chemistry."
    Chen R., Jiang X., Sun D., Han G., Wang F., Ye M., Wang L., Zou H.
    J. Proteome Res. 8:651-661(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: GLYCOSYLATION [LARGE SCALE ANALYSIS] AT ASN-110.
    Tissue: Liver.
  13. "Plasticity of human CD8alphaalpha binding to peptide-HLA-A*2402."
    Shi Y., Qi J., Iwamoto A., Gao G.F.
    Mol. Immunol. 48:2198-2202(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.39 ANGSTROMS) OF 25-298 (ALLELE A*24:02) IN COMPLEX WITH B2M AND CD8, DISULFIDE BONDS.
  14. Cited for: VARIANT [LARGE SCALE ANALYSIS] TRP-180, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
+Additional computationally mapped references.

Entry informationi

Entry namei1A24_HUMAN
AccessioniPrimary (citable) accession number: P05534
Secondary accession number(s): P30448
, P30449, Q29908, Q29909, Q29910, Q95355
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1988
Last sequence update: June 27, 2003
Last modified: February 4, 2015
This is version 153 of the entry and version 2 of the sequence. [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 6
    Human chromosome 6: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.