4ZFZ

Crystal structure of rhesus macaque MHC class I molecule Mamu-B*098 complexed with myristoylated 5-mer lipopeptide derived from SIV Nef protein

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	C1 set domains-like	8070468	4000202	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Immunoglobulin (Ig) domain-like	8070469	3000071	SCOP2 (2022-06-29)
E	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8070469	3000071	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8070469	3000071	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8070469	3000071	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	C1-set_2	e4zfzA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_2	ECOD (1.6)
A	MHC_I	e4zfzA2	A: a+b two layers	X: MHC antigen-recognition domain (From Topology)	H: MHC antigen-recognition domain (From Topology)	T: MHC antigen-recognition domain	F: MHC_I	ECOD (1.6)
D	C1-set_2	e4zfzD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_2	ECOD (1.6)
D	MHC_I	e4zfzD2	A: a+b two layers	X: MHC antigen-recognition domain (From Topology)	H: MHC antigen-recognition domain (From Topology)	T: MHC antigen-recognition domain	F: MHC_I	ECOD (1.6)
G	C1-set_2	e4zfzG1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_2	ECOD (1.6)
G	MHC_I	e4zfzG2	A: a+b two layers	X: MHC antigen-recognition domain (From Topology)	H: MHC antigen-recognition domain (From Topology)	T: MHC antigen-recognition domain	F: MHC_I	ECOD (1.6)
J	C1-set_2	e4zfzJ1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_2	ECOD (1.6)
J	MHC_I	e4zfzJ2	A: a+b two layers	X: MHC antigen-recognition domain (From Topology)	H: MHC antigen-recognition domain (From Topology)	T: MHC antigen-recognition domain	F: MHC_I	ECOD (1.6)
B	C1-set_2	e4zfzB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_2	ECOD (1.6)
E	C1-set_2	e4zfzE1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_2	ECOD (1.6)
H	C1-set_2	e4zfzH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_2	ECOD (1.6)
K	C1-set_2	e4zfzK1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.500.10	Alpha Beta	2-Layer Sandwich	Murine Class I Major Histocompatibility Complex, H2-DB	Chain A, domain 1	CATH (4.3.0)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D	3.30.500.10	Alpha Beta	2-Layer Sandwich	Murine Class I Major Histocompatibility Complex, H2-DB	Chain A, domain 1	CATH (4.3.0)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
G	3.30.500.10	Alpha Beta	2-Layer Sandwich	Murine Class I Major Histocompatibility Complex, H2-DB	Chain A, domain 1	CATH (4.3.0)
G	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
J	3.30.500.10	Alpha Beta	2-Layer Sandwich	Murine Class I Major Histocompatibility Complex, H2-DB	Chain A, domain 1	CATH (4.3.0)
J	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
H	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
K	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
A, D, G, J	Major histocompatibility I (MH1)	I-ALPHA	Macaca mulatta (Rhesus monkey)	MH1-A*02	G-DOMAIN G-ALPHA1, G-DOMAIN G-ALPHA2	MH	MH1-ALPHA_B2M	IMGT (202434-0)
B, E, H, K	Major histocompatibility I (MH1)	B2M	Macaca mulatta (Rhesus monkey)	B2M*01	C-LIKE-DOMAIN C-LIKE	MH	MH1-ALPHA_B2M	IMGT (202434-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D, G, J	PF00129	Class I Histocompatibility antigen, domains alpha 1 and 2 (MHC_I)	Class I Histocompatibility antigen, domains alpha 1 and 2	-	Domain
A, D, G, J	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	Domain
B, E, H, K	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D, G, J	Major histocompatibility complex class I	protein binding binding signaling receptor binding antigen binding peptide antigen binding peptide binding cation binding ion binding metal ion binding small molecule binding	response to stimulus immune response immune system process antigen processing and presentation antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway antigen processing and presentation of endogenous peptide antigen antigen processing and presentation of peptide antigen via MHC class I antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent antigen processing and presentation of peptide antigen antigen processing and presentation of endogenous antigen antigen processing and presentation of endogenous peptide antigen via MHC class I antigen processing and presentation of endogenous peptide antigen via MHC class Ib antigen processing and presentation of peptide antigen via MHC class Ib antigen processing and presentation via MHC class Ib response to stimulus immune response immune system process antigen processing and presentation antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway antigen processing and presentation of endogenous peptide antigen antigen processing and presentation of peptide antigen via MHC class I antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent antigen processing and presentation of peptide antigen antigen processing and presentation of endogenous antigen antigen processing and presentation of endogenous peptide antigen via MHC class I antigen processing and presentation of endogenous peptide antigen via MHC class Ib antigen processing and presentation of peptide antigen via MHC class Ib antigen processing and presentation via MHC class Ib adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity regulation of immune effector process T cell mediated immunity positive regulation of leukocyte mediated immunity regulation of cellular process positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of lymphocyte mediated immunity positive regulation of biological process positive regulation of response to stimulus regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of immune response positive regulation of leukocyte mediated cytotoxicity leukocyte mediated immunity regulation of immune system process positive regulation of immune effector process positive regulation of adaptive immune response positive regulation of immune system process positive regulation of cellular process regulation of T cell mediated immunity T cell mediated cytotoxicity regulation of biological process positive regulation of T cell mediated cytotoxicity regulation of adaptive immune response biological regulation regulation of leukocyte mediated cytotoxicity leukocyte mediated cytotoxicity adaptive immune response immune effector process regulation of leukocyte mediated immunity regulation of T cell mediated cytotoxicity regulation of lymphocyte mediated immunity regulation of response to stimulus positive regulation of T cell mediated immunity regulation of immune response regulation of cell killing cellular process positive regulation of cell killing cell killing	cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane MHC class I protein complex MHC protein complex protein-containing complex plasma membrane protein complex membrane protein complex membrane-bounded organelle intracellular anatomical structure cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane MHC class I protein complex MHC protein complex protein-containing complex plasma membrane protein complex membrane protein complex membrane-bounded organelle intracellular anatomical structure organelle subcompartment lumenal side of endoplasmic reticulum membrane intracellular membrane-bounded organelle endomembrane system lumenal side of membrane endoplasmic reticulum subcompartment intracellular organelle organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum cytoplasm organelle membrane endoplasmic reticulum membrane intracellular vesicle phagocytic vesicle phagocytic vesicle membrane cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane endocytic vesicle membrane vesicle endocytic vesicle endosome membrane endosome recycling endosome recycling endosome membrane early endosome early endosome membrane extracellular region extracellular space transport vesicle transport vesicle membrane coated vesicle membrane COPII-coated ER to Golgi transport vesicle ER to Golgi transport vesicle membrane coated vesicle
B, E, H, K	Beta-2-microglobulin	binding antigen binding peptide antigen binding peptide binding protein-containing complex binding MHC protein complex binding MHC class II protein complex binding	regulation of biological process response to stimulus immune response biological regulation positive regulation of biological process positive regulation of response to stimulus positive regulation of immune response regulation of response to stimulus immune system process regulation of immune response regulation of immune system process positive regulation of immune system process peptide antigen assembly with MHC class II protein complex protein-containing complex organization regulation of biological process response to stimulus immune response biological regulation positive regulation of biological process positive regulation of response to stimulus positive regulation of immune response regulation of response to stimulus immune system process regulation of immune response regulation of immune system process positive regulation of immune system process peptide antigen assembly with MHC class II protein complex protein-containing complex organization peptide antigen assembly with MHC protein complex MHC class II protein complex assembly cellular component organization cellular component biogenesis antigen processing and presentation antigen processing and presentation of peptide or polysaccharide antigen via MHC class II cellular component assembly protein-containing complex assembly antigen processing and presentation of peptide antigen via MHC class II cellular process MHC protein complex assembly cellular component organization or biogenesis antigen processing and presentation of peptide antigen antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen antigen processing and presentation of exogenous antigen antigen processing and presentation of peptide antigen via MHC class I multicellular organismal process regulation of cellular process regulation of leukocyte activation regulation of cell activation positive regulation of leukocyte cell-cell adhesion lymphocyte activation leukocyte cell-cell adhesion leukocyte activation positive regulation of cell-cell adhesion positive regulation of lymphocyte activation positive regulation of cell activation cell adhesion cell-cell adhesion T cell activation positive regulation of leukocyte activation regulation of multicellular organismal process regulation of cell-cell adhesion positive regulation of cellular process positive regulation of T cell activation positive regulation of cell adhesion regulation of cell adhesion cell activation regulation of T cell activation regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process regulation of lymphocyte activation	vacuolar membrane membrane-bounded organelle intracellular anatomical structure membrane lytic vacuole vacuole cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle lytic vacuole membrane bounding membrane of organelle organelle lysosomal membrane cytoplasm vacuolar membrane membrane-bounded organelle intracellular anatomical structure membrane lytic vacuole vacuole cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle lytic vacuole membrane bounding membrane of organelle organelle lysosomal membrane cytoplasm organelle membrane lysosome extracellular region MHC protein complex cell periphery MHC class II protein complex protein-containing complex plasma membrane protein complex plasma membrane membrane protein complex MHC class I protein complex endosome membrane endosome intracellular vesicle late endosome membrane endomembrane system cytoplasmic vesicle membrane cytoplasmic vesicle vesicle membrane late endosome vesicle
C, F, I, L	5-mer lipopeptide from Protein Nef	binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding organic cyclic compound binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding organic cyclic compound binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding	symbiont-mediated perturbation of host defense response response to host defenses biological process involved in interspecies interaction between organisms response to stimulus response to other organism response to defenses of other organism modulation by virus of host process response to external stimulus virus-mediated perturbation of host defense response biological process involved in interaction with host response to biotic stimulus biological process involved in symbiotic interaction modulation by symbiont of host process viral process symbiont-mediated perturbation of host defense response response to host defenses biological process involved in interspecies interaction between organisms response to stimulus response to other organism response to defenses of other organism modulation by virus of host process response to external stimulus virus-mediated perturbation of host defense response biological process involved in interaction with host response to biotic stimulus biological process involved in symbiotic interaction modulation by symbiont of host process viral process response to host response to external biotic stimulus modulation of process of another organism modulation by virus of host cellular process	membrane cellular anatomical entity host cell plasma membrane host cellular component host cell part host cell membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D, G, J	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, D, G, J	IPR050208	Antigen-presenting and immune regulatory MHC class I-related	Family
A, D, G, J	IPR003597	Immunoglobulin C1-set	Domain
A, D, G, J	IPR010579	MHC class I, alpha chain, C-terminal	Domain
A, D, G, J	IPR011161	MHC class I-like antigen recognition-like	Domain
A, D, G, J	IPR011162	MHC classes I/II-like antigen recognition protein	Homologous Superfamily
A, D, G, J	IPR001039	MHC class I alpha chain, alpha1 alpha2 domains	Domain
A, D, G, J	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
A, D, G, J	IPR037055	MHC class I-like antigen recognition-like superfamily	Homologous Superfamily
A, D, G, J	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, D, G, J	IPR007110	Immunoglobulin-like domain	Domain
B, E, H, K	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B, E, H, K	IPR050160	Major Histocompatibility Complex/Immunoglobulin	Family
B, E, H, K	IPR003597	Immunoglobulin C1-set	Domain
B, E, H, K	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B, E, H, K	IPR015707	Beta-2-Microglobulin	Family
B, E, H, K	IPR007110	Immunoglobulin-like domain	Domain
B, E, H, K	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
C, F, I, L	IPR001558	HIV negative factor Nef	Family
C, F, I, L	IPR027481	HIV-1 Nef protein, core domain superfamily	Homologous Superfamily