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Protein

HLA class II histocompatibility antigen, DM beta chain

Gene

HLA-DMB

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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
Complete GO annotation...

Keywords - Biological processi

Immunity

Enzyme and pathway databases

BioCyciZFISH:ENSG00000112091-MONOMER.
ReactomeiR-HSA-2132295. MHC class II antigen presentation.

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

HGNCiHGNC:4935. HLA-DMB.

Subcellular locationi

Topology

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

GO - Cellular componenti

Complete GO annotation...

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.
OpenTargetsiENSG00000226264.
ENSG00000239329.
ENSG00000241674.
ENSG00000242092.
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...)1 Publication1
Disulfide bondi135 ↔ 192

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

PaxDbiP28068.
PeptideAtlasiP28068.
PRIDEiP28068.

PTM databases

iPTMnetiP28068.
PhosphoSitePlusiP28068.

Expressioni

Gene expression databases

BgeeiENSG00000226264.
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

GO - Molecular functioni

  • MHC class II protein complex binding Source: UniProtKB

Protein-protein interaction databases

BioGridi109354. 10 interactors.
DIPiDIP-6185N.
IntActiP28068. 7 interactors.
MINTiMINT-1539801.
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/D19-256[»]
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.
OMAiDCATHTQ.
OrthoDBiEOG091G0G84.
PhylomeDBiP28068.
TreeFamiTF335727.

Family and domain databases

Gene3Di2.60.40.10. 1 hit.
3.10.320.10. 1 hit.
InterProiIPR007110. Ig-like_dom.
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.
[Graphical view]
PfamiPF07654. C1-set. 1 hit.
PF00969. MHC_II_beta. 1 hit.
[Graphical view]
SMARTiSM00407. IGc1. 1 hit.
SM00921. MHC_II_beta. 1 hit.
[Graphical view]
SUPFAMiSSF48726. SSF48726. 1 hit.
SSF54452. 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.

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 rs17583782dbSNPEnsembl.1
Natural variantiVAR_01675245S → F in allele DMB*01:06. Corresponds to variant rs41560814dbSNPEnsembl.1
Natural variantiVAR_05036149D → V in allele DMB*01:07. Corresponds to variant rs17617333dbSNPEnsembl.1
Natural variantiVAR_05036271S → N in allele DMB*01:07. Corresponds to variant rs17617321dbSNPEnsembl.1
Natural variantiVAR_016753162A → E in allele DMB*01:02 and allele DMB*01:06. Corresponds to variant rs2071555dbSNPEnsembl.1
Natural variantiVAR_016754162A → V in allele DMB*01:04 and allele DMB*01:05. Corresponds to variant rs2071555dbSNPEnsembl.1
Natural variantiVAR_016755197I → T in allele DMB*01:03, allele DMB*01:04 and allele DMB*01:06. 1 PublicationCorresponds to variant rs1042337dbSNPEnsembl.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. Translation: CAI17490.1.
AL645941 Genomic DNA. Translation: CAI18108.1.
AL935042 Genomic DNA. Translation: CAI18685.1.
BX088556 Genomic DNA. Translation: CAM26271.1.
BX927138 Genomic DNA. Translation: CAQ08457.1.
CR936913 Genomic DNA. Translation: CAQ08780.1.
CR759798 Genomic DNA. Translation: CAQ09462.1.
CR752645 Genomic DNA. Translation: CAQ09834.1.
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

Cross-referencesi

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. Translation: CAI17490.1.
AL645941 Genomic DNA. Translation: CAI18108.1.
AL935042 Genomic DNA. Translation: CAI18685.1.
BX088556 Genomic DNA. Translation: CAM26271.1.
BX927138 Genomic DNA. Translation: CAQ08457.1.
CR936913 Genomic DNA. Translation: CAQ08780.1.
CR759798 Genomic DNA. Translation: CAQ09462.1.
CR752645 Genomic DNA. Translation: CAQ09834.1.
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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1HDMX-ray2.50B19-218[»]
2BC4X-ray2.27B/D19-256[»]
4FQXX-ray2.60D19-211[»]
4GBXX-ray3.00D19-211[»]
4I0PX-ray3.20B/F21-211[»]
ProteinModelPortaliP28068.
SMRiP28068.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi109354. 10 interactors.
DIPiDIP-6185N.
IntActiP28068. 7 interactors.
MINTiMINT-1539801.
STRINGi9606.ENSP00000398890.

PTM databases

iPTMnetiP28068.
PhosphoSitePlusiP28068.

Polymorphism and mutation databases

BioMutaiHLA-DMB.
DMDMi133160.

Proteomic databases

PaxDbiP28068.
PeptideAtlasiP28068.
PRIDEiP28068.

Protocols and materials databases

DNASUi3109.
Structural Biology KnowledgebaseSearch...

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.

Organism-specific databases

CTDi3109.
DisGeNETi3109.
GeneCardsiHLA-DMB.
H-InvDBHIX0166396.
HIX0207613.
HIX0207705.
HIX0207762.
HGNCiHGNC:4935. HLA-DMB.
HPAiHPA012298.
MIMi142856. gene.
neXtProtiNX_P28068.
OpenTargetsiENSG00000226264.
ENSG00000239329.
ENSG00000241674.
ENSG00000242092.
PharmGKBiPA35059.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IFNH. Eukaryota.
ENOG410YU9X. LUCA.
HOVERGENiHBG007327.
InParanoidiP28068.
KOiK06752.
OMAiDCATHTQ.
OrthoDBiEOG091G0G84.
PhylomeDBiP28068.
TreeFamiTF335727.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000112091-MONOMER.
ReactomeiR-HSA-2132295. MHC class II antigen presentation.

Miscellaneous databases

ChiTaRSiHLA-DMB. human.
EvolutionaryTraceiP28068.
GeneWikiiHLA-DMB.
GenomeRNAii3109.
PROiP28068.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000226264.
CleanExiHS_HLA-DMB.
ExpressionAtlasiP28068. baseline and differential.
GenevisibleiP28068. HS.

Family and domain databases

Gene3Di2.60.40.10. 1 hit.
3.10.320.10. 1 hit.
InterProiIPR007110. Ig-like_dom.
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.
[Graphical view]
PfamiPF07654. C1-set. 1 hit.
PF00969. MHC_II_beta. 1 hit.
[Graphical view]
SMARTiSM00407. IGc1. 1 hit.
SM00921. MHC_II_beta. 1 hit.
[Graphical view]
SUPFAMiSSF48726. SSF48726. 1 hit.
SSF54452. SSF54452. 1 hit.
PROSITEiPS50835. IG_LIKE. 1 hit.
PS00290. IG_MHC. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDMB_HUMAN
AccessioniPrimary (citable) accession number: P28068
Secondary accession number(s): O77936
, Q13012, Q29751, Q58ZE2, Q5SNZ8, Q5STC4, Q9XRX2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1992
Last sequence update: August 1, 1992
Last modified: November 2, 2016
This is version 164 of the entry and version 1 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

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 one 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.