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Crystal structure of DR11 presenting the gag293 epitope

Source organisms:
Biochemical function: T cell receptor binding
Biological process: antigen processing and presentation
Cellular component: MHC class II protein complex

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EC 3.4.23.16: HIV-1 retropepsin

Reaction catalysed:
Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro.
Alternative Name(s):
  • Gag protease
  • HIV aspartyl protease
  • HIV proteinase
  • HIV-1 protease
  • HIV-2 protease
  • Human immunodeficiency virus type 1 protease
  • Retroproteinase

EC 3.1.26.13: Retroviral ribonuclease H

Reaction catalysed:
Endohydrolysis of RNA in RNA/DNA hybrids. Three different cleavage modes: 1. sequence-specific internal cleavage of RNA. Human immunodeficiency virus type 1 and Moloney murine leukemia virus enzymes prefer to cleave the RNA strand one nucleotide away from the RNA-DNA junction. 2. RNA 5'-end directed cleavage 13-19 nucleotides from the RNA end. 3. DNA 3'-end directed cleavage 15-20 nucleotides away from the primer terminus.
Systematic name:
-
Alternative Name(s):
  • HIV RNase H
  • RT/RNase H
  • Retroviral reverse transcriptase RNaseH

EC 3.1.13.2: Exoribonuclease H

Reaction catalysed:
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
Systematic name:
-

EC 2.7.7.7: DNA-directed DNA polymerase

Reaction catalysed:
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Systematic name:
Deoxynucleoside-triphosphate:DNA deoxynucleotidyltransferase (DNA-directed)
Alternative Name(s):
  • DNA duplicase
  • DNA nucleotidyltransferase
  • DNA nucleotidyltransferase (DNA-directed)
  • DNA polymerase
  • DNA polymerase I
  • DNA polymerase II
  • DNA polymerase III
  • DNA polymerase alpha
  • DNA polymerase beta
  • DNA polymerase gamma
  • DNA replicase
  • DNA-dependent DNA polymerase
  • Deoxynucleate polymerase
  • Deoxyribonucleate nucleotidyltransferase
  • Deoxyribonucleic acid duplicase
  • Deoxyribonucleic acid polymerase
  • Deoxyribonucleic duplicase
  • Deoxyribonucleic polymerase
  • Deoxyribonucleic polymerase I
  • Duplicase
  • Klenow fragment
  • Sequenase
  • Taq DNA polymerase
  • Taq Pol I
  • Tca DNA polymerase

EC 2.7.7.49: RNA-directed DNA polymerase

Reaction catalysed:
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Systematic name:
Deoxynucleoside-triphosphate:DNA deoxynucleotidyltransferase (RNA-directed)
Alternative Name(s):
  • DNA nucleotidyltransferase (RNA-directed)
  • RNA revertase
  • RNA-dependent DNA polymerase
  • RNA-dependent deoxyribonucleate nucleotidyltransferase
  • RNA-instructed DNA polymerase
  • RT
  • Reverse transcriptase
  • Revertase

GO terms

Sequence families

Pfam Protein families (Pfam)
PF07654
Domain description: Immunoglobulin C1-set domain
Occurring in:
  1. HLA class II histocompatibility antigen, DR alpha chain
  2. HLA class II histocompatibility antigen, DRB1 beta chain
The deposited structure of PDB entry 6cpl contains 1 copy of Pfam domain PF07654 (Immunoglobulin C1-set domain) in HLA class II histocompatibility antigen, DR alpha chain. Showing 1 copy in chain A.
The deposited structure of PDB entry 6cpl contains 1 copy of Pfam domain PF07654 (Immunoglobulin C1-set domain) in HLA class II histocompatibility antigen, DRB1 beta chain. Showing 1 copy in chain B.

PF00969
Domain description: Class II histocompatibility antigen, beta domain
Occurring in:
  1. HLA class II histocompatibility antigen, DRB1 beta chain
The deposited structure of PDB entry 6cpl contains 1 copy of Pfam domain PF00969 (Class II histocompatibility antigen, beta domain) in HLA class II histocompatibility antigen, DRB1 beta chain. Showing 1 copy in chain B.

PF00993
Domain description: Class II histocompatibility antigen, alpha domain
Occurring in:
  1. HLA class II histocompatibility antigen, DR alpha chain
The deposited structure of PDB entry 6cpl contains 1 copy of Pfam domain PF00993 (Class II histocompatibility antigen, alpha domain) in HLA class II histocompatibility antigen, DR alpha chain. Showing 1 copy in chain A.

InterPro InterPro annotations
IPR003597
Domain description: Immunoglobulin C1-set
Occurring in:
  1. HLA class II histocompatibility antigen, DR alpha chain
  2. HLA class II histocompatibility antigen, DRB1 beta chain
IPR000353
Domain description: MHC class II, beta chain, N-terminal
Occurring in:
  1. HLA class II histocompatibility antigen, DRB1 beta chain
IPR003006
Domain description: Immunoglobulin/major histocompatibility complex, conserved site
Occurring in:
  1. HLA class II histocompatibility antigen, DR alpha chain
  2. HLA class II histocompatibility antigen, DRB1 beta chain
IPR007110
Domain description: Immunoglobulin-like domain
Occurring in:
  1. HLA class II histocompatibility antigen, DR alpha chain
  2. HLA class II histocompatibility antigen, DRB1 beta chain
IPR036179
Domain description: Immunoglobulin-like domain superfamily
Occurring in:
  1. HLA class II histocompatibility antigen, DR alpha chain
  2. HLA class II histocompatibility antigen, DRB1 beta chain
IPR013783
Domain description: Immunoglobulin-like fold
Occurring in:
  1. HLA class II histocompatibility antigen, DR alpha chain
  2. HLA class II histocompatibility antigen, DRB1 beta chain
IPR001003
Domain description: MHC class II, alpha chain, N-terminal
Occurring in:
  1. HLA class II histocompatibility antigen, DR alpha chain
IPR011162
Domain description: MHC classes I/II-like antigen recognition protein
Occurring in:
  1. HLA class II histocompatibility antigen, DR alpha chain
  2. HLA class II histocompatibility antigen, DRB1 beta chain
IPR014745
Domain description: MHC class II, alpha/beta chain, N-terminal
Occurring in:
  1. HLA class II histocompatibility antigen, DR alpha chain
  2. HLA class II histocompatibility antigen, DRB1 beta chain
IPR008916
Domain description: Retrovirus capsid, C-terminal
Occurring in:
  1. Capsid protein p24

Structure domains

CATH CATH domains
2.60.40.10
Class: Mainly Beta
Architecture: Sandwich
Topology: Immunoglobulin-like
Homology: Immunoglobulins
Occurring in:
  1. HLA class II histocompatibility antigen, DR alpha chain
  2. HLA class II histocompatibility antigen, DRB1 beta chain
The deposited structure of PDB entry 6cpl contains 1 copy of CATH domain 2.60.40.10 (Immunoglobulin-like) in HLA class II histocompatibility antigen, DR alpha chain. Showing 1 copy in chain A.
The deposited structure of PDB entry 6cpl contains 1 copy of CATH domain 2.60.40.10 (Immunoglobulin-like) in HLA class II histocompatibility antigen, DRB1 beta chain. Showing 1 copy in chain B.
3.10.320.10
Class: Alpha Beta
Architecture: Roll
Topology: Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homology: Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Occurring in:
  1. HLA class II histocompatibility antigen, DR alpha chain
  2. HLA class II histocompatibility antigen, DRB1 beta chain
The deposited structure of PDB entry 6cpl contains 1 copy of CATH domain 3.10.320.10 (Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1) in HLA class II histocompatibility antigen, DR alpha chain. Showing 1 copy in chain A.
The deposited structure of PDB entry 6cpl contains 1 copy of CATH domain 3.10.320.10 (Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1) in HLA class II histocompatibility antigen, DRB1 beta chain. Showing 1 copy in chain B.

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