2NYZ | pdb_00002nyz

Viral Chemokine Binding Protein M3 From Murine Gammaherpesvirus68 In Complex With The C- Chemokine XCL1

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2nyza1	All beta proteins	Viral chemokine binding protein m3	Viral chemokine binding protein m3	Viral chemokine binding protein m3	Viral chemokine binding protein m3	Murine herpesvirus 68 (Murid gammaherpesvirus 4 ) [TaxId: 33708 ],	SCOPe (2.08)
B	d2nyzb1	All beta proteins	Viral chemokine binding protein m3	Viral chemokine binding protein m3	Viral chemokine binding protein m3	Viral chemokine binding protein m3	Murine herpesvirus 68 (Murid gammaherpesvirus 4 ) [TaxId: 33708 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Viral chemokine binding protein m3	8043647	3001430	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Viral chemokine binding protein m3	8043647	3001430	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		e2nyzA1	A: jelly-roll	X: Double-stranded beta-helix	H: Double-stranded beta-helix	T: Histone	F:	ECOD (20:10:01)
B		e2nyzB1	A: PBZ domain	X: PBZ domain	H: PBZ domain	T: TPR_COPA_B	F:	ECOD (20:10:01)
C [auth D]		e2nyzD1	A: MocoBD/DmpA-related	X: MocoBD/DmpA-related	H: Retrovirus capsid protein-C	T: Ldh_1_C	F:	ECOD (20:10:01)
D [auth E]		e2nyzE1	A: MocoBD/DmpA-related	X: MocoBD/DmpA-related	H: Retrovirus capsid protein-C	T: Ldh_1_C	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.40.1330	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
A	2.60.40.1340	Mainly Beta	Sandwich	Immunoglobulin-like	Chemokine-binding protein M3-like	CATH (4.3.0)
B	2.60.40.1330	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
B	2.60.40.1340	Mainly Beta	Sandwich	Immunoglobulin-like	Chemokine-binding protein M3-like	CATH (4.3.0)
C [auth D]	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
D [auth E]	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF09213	M3 (M3)	M3	Members of this family of viral chemokine binding proteins adopt a structure consisting of two different beta-sandwich domains of partial topological similarity to immunoglobulin-like folds. They bind with the CC-chemokine MCP-1, acting as cytokine d ...	Members of this family of viral chemokine binding proteins adopt a structure consisting of two different beta-sandwich domains of partial topological similarity to immunoglobulin-like folds. They bind with the CC-chemokine MCP-1, acting as cytokine decoy receptors [1].	Domain
C [auth D], D [auth E]	PF00048	Small cytokines (intecrine/chemokine), interleukin-8 like (IL8)	Small cytokines (intecrine/chemokine), interleukin-8 like	Includes a number of secreted growth factors and interferons involved in mitogenic, chemotactic, and inflammatory activity. Structure contains two highly conserved disulfide bonds.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Hypothetical protein GAMMAHV.M3	protein binding binding chemokine binding cytokine binding	-	-
C [auth D], D [auth E]	Lymphotactin	protein binding binding signaling receptor binding cytokine receptor binding G protein-coupled receptor binding chemokine receptor binding CCR chemokine receptor binding molecular function activator activity signaling receptor activator activity chemokine activity molecular function regulator activity cytokine activity signaling receptor regulator activity receptor ligand activity protein binding binding signaling receptor binding cytokine receptor binding G protein-coupled receptor binding chemokine receptor binding CCR chemokine receptor binding molecular function activator activity signaling receptor activator activity chemokine activity molecular function regulator activity cytokine activity signaling receptor regulator activity receptor ligand activity identical protein binding protein homodimerization activity protein dimerization activity	regulation of transforming growth factor beta production multicellular organismal process regulation of cellular process positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process regulation of cytokine production cytokine production regulation of multicellular organismal process positive regulation of macromolecule metabolic process transforming growth factor beta production positive regulation of cellular process regulation of biosynthetic process regulation of transforming growth factor beta production multicellular organismal process regulation of cellular process positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process regulation of cytokine production cytokine production regulation of multicellular organismal process positive regulation of macromolecule metabolic process transforming growth factor beta production positive regulation of cellular process regulation of biosynthetic process regulation of biological process biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression positive regulation of multicellular organismal process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process positive regulation of transforming growth factor beta production positive regulation of cytokine production regulation of metabolic process cellular response to stimulus positive regulation of locomotion regulation of cell motility response to stimulus regulation of B cell chemotaxis positive regulation of chemotaxis positive regulation of cell migration regulation of lymphocyte chemotaxis taxis cell migration regulation of immune system process regulation of mononuclear cell migration positive regulation of immune system process chemotaxis regulation of leukocyte chemotaxis positive regulation of lymphocyte migration regulation of leukocyte migration lymphocyte migration response to external stimulus positive regulation of leukocyte chemotaxis leukocyte migration regulation of response to stimulus response to chemical regulation of locomotion B cell chemotaxis regulation of response to external stimulus lymphocyte chemotaxis regulation of lymphocyte migration positive regulation of lymphocyte chemotaxis positive regulation of response to stimulus positive regulation of response to external stimulus positive regulation of cell motility regulation of cell migration positive regulation of mononuclear cell migration cell motility positive regulation of B cell chemotaxis locomotion cell chemotaxis positive regulation of leukocyte migration regulation of chemotaxis cellular response to chemical stimulus immune system process mononuclear cell migration leukocyte chemotaxis adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of immune effector process lymphocyte mediated immunity T cell mediated immunity positive regulation of leukocyte mediated immunity T cell cytokine production positive regulation of immune response T-helper 1 cell cytokine production leukocyte mediated immunity positive regulation of adaptive immune response positive regulation of T cell cytokine production regulation of T cell mediated immunity regulation of cytokine production involved in immune response immune response regulation of adaptive immune response T-helper 1 type immune response regulation of T-helper 1 type immune response immune effector process regulation of leukocyte mediated immunity positive regulation of production of molecular mediator of immune response regulation of immune response regulation of production of molecular mediator of immune response 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 T-helper 1 cell cytokine production regulation of T-helper 1 cell cytokine production regulation of T cell cytokine production CD4-positive, alpha-beta T cell cytokine production regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of immune effector process cytokine production involved in immune response production of molecular mediator of immune response positive regulation of T-helper 1 type immune response adaptive immune response regulation of lymphocyte mediated immunity positive regulation of T cell mediated immunity positive regulation of cytokine production involved in immune response positive regulation of cell population proliferation CD8-positive, alpha-beta T cell activation regulation of alpha-beta T cell activation regulation of leukocyte activation CD8-positive, alpha-beta T cell proliferation positive regulation of alpha-beta T cell proliferation regulation of cell activation positive regulation of CD8-positive, alpha-beta T cell activation positive regulation of cell activation T cell activation alpha-beta T cell proliferation lymphocyte proliferation positive regulation of leukocyte activation positive regulation of CD8-positive, alpha-beta T cell proliferation alpha-beta T cell activation regulation of leukocyte proliferation positive regulation of T cell activation cell population proliferation regulation of CD8-positive, alpha-beta T cell proliferation positive regulation of lymphocyte proliferation positive regulation of T cell proliferation positive regulation of alpha-beta T cell activation mononuclear cell proliferation regulation of cell population proliferation regulation of leukocyte cell-cell adhesion positive regulation of leukocyte proliferation positive regulation of leukocyte cell-cell adhesion lymphocyte activation leukocyte cell-cell adhesion leukocyte proliferation leukocyte activation positive regulation of cell-cell adhesion positive regulation of lymphocyte activation regulation of alpha-beta T cell proliferation cell adhesion cell-cell adhesion positive regulation of mononuclear cell proliferation regulation of cell-cell adhesion T cell proliferation regulation of lymphocyte proliferation positive regulation of cell adhesion regulation of cell adhesion cell activation regulation of T cell activation regulation of T cell proliferation regulation of mononuclear cell proliferation regulation of CD8-positive, alpha-beta T cell activation regulation of lymphocyte activation negative regulation of biological process negative regulation of interleukin-2 production negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of interleukin-2 production negative regulation of metabolic process interleukin-2 production negative regulation of cytokine production negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of multicellular organismal process natural killer cell chemotaxis positive regulation of natural killer cell chemotaxis regulation of natural killer cell chemotaxis response to interleukin-4 response to peptide response to cytokine cellular response to cytokine stimulus cellular response to interleukin-4 neutrophil chemotaxis neutrophil migration granulocyte migration granulocyte chemotaxis myeloid leukocyte migration signaling cell-cell signaling cell communication positive regulation of granzyme B production granzyme B production regulation of granzyme B production negative regulation of lymphocyte activation negative regulation of cell adhesion regulation of T-helper 1 cell activation CD4-positive, alpha-beta T cell activation T-helper 1 cell activation negative regulation of cell activation regulation of CD4-positive, alpha-beta T cell activation negative regulation of CD4-positive, alpha-beta T cell activation negative regulation of T cell activation negative regulation of immune system process negative regulation of leukocyte cell-cell adhesion negative regulation of cell-cell adhesion negative regulation of alpha-beta T cell activation negative regulation of T-helper 1 cell activation negative regulation of leukocyte activation positive regulation of CD4-positive, alpha-beta T cell proliferation regulation of CD4-positive, alpha-beta T cell proliferation positive regulation of CD4-positive, alpha-beta T cell activation CD4-positive, alpha-beta T cell proliferation interleukin-10 production regulation of interleukin-10 production positive regulation of interleukin-10 production regulation of type II interferon production type II interferon production negative regulation of type II interferon production regulation of granzyme A production granzyme A production positive regulation of granzyme A production positive regulation of leukocyte mediated cytotoxicity T cell mediated cytotoxicity positive regulation of T cell mediated cytotoxicity regulation of leukocyte mediated cytotoxicity leukocyte mediated cytotoxicity regulation of T cell mediated cytotoxicity regulation of cell killing positive regulation of cell killing cell killing positive regulation of DNA-templated transcription RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II primary metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription negative regulation of RNA metabolic process T-helper 2 cell cytokine production type 2 immune response regulation of T-helper 2 cell cytokine production regulation of type 2 immune response positive regulation of T-helper 2 cell cytokine production positive regulation of type 2 immune response cellular response to endogenous stimulus cellular response to growth factor stimulus response to transforming growth factor beta cellular response to transforming growth factor beta stimulus response to endogenous stimulus response to growth factor positive regulation of thymocyte migration thymocyte migration regulation of thymocyte migration positive regulation of T cell migration regulation of T cell migration T cell migration cell surface receptor signaling pathway response to chemokine cytokine-mediated signaling pathway cellular response to chemokine chemokine-mediated signaling pathway G protein-coupled receptor signaling pathway signal transduction negative regulation of T-helper 1 type immune response negative regulation of response to stimulus negative regulation of immune response negative regulation of adaptive immune response negative regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of neutrophil chemotaxis positive regulation of granulocyte chemotaxis regulation of neutrophil chemotaxis regulation of neutrophil migration regulation of granulocyte chemotaxis positive regulation of neutrophil migration mature natural killer cell chemotaxis regulation of immunoglobulin production in mucosal tissue positive regulation of immunoglobulin mediated immune response regulation of B cell mediated immunity positive regulation of immunoglobulin production in mucosal tissue B cell mediated immunity mucosal immune response organ or tissue specific immune response immunoglobulin production immunoglobulin production involved in immunoglobulin-mediated immune response positive regulation of B cell mediated immunity regulation of immunoglobulin mediated immune response immunoglobulin production in mucosal tissue positive regulation of immunoglobulin production immunoglobulin mediated immune response regulation of immunoglobulin production regulation of defense response defense response regulation of inflammatory response response to stress regulation of response to stress inflammatory response humoral immune response biological process involved in interspecies interaction between organisms response to other organism defense response to symbiont antimicrobial humoral response response to biotic stimulus antimicrobial humoral immune response mediated by antimicrobial peptide defense response to other organism response to external biotic stimulus calcium ion transmembrane import into cytosol transport monoatomic ion transmembrane transport establishment of localization calcium ion transport metal ion transport monoatomic cation transmembrane transport transmembrane transport release of sequestered calcium ion into cytosol localization monoatomic ion transport monoatomic cation transport calcium ion transmembrane transport negative regulation of lymphocyte mediated immunity negative regulation of cytokine production involved in immune response negative regulation of immune effector process negative regulation of production of molecular mediator of immune response negative regulation of T cell mediated immunity negative regulation of T cell cytokine production negative regulation of leukocyte mediated immunity response to virus regulation of calcium ion transport regulation of localization positive regulation of cation transmembrane transport positive regulation of calcium ion transport regulation of monoatomic ion transmembrane transport regulation of calcium ion transmembrane transport positive regulation of monoatomic ion transport positive regulation of calcium ion transmembrane transport positive regulation of transmembrane transport positive regulation of monoatomic ion transmembrane transport positive regulation of release of sequestered calcium ion into cytosol regulation of metal ion transport regulation of transport regulation of release of sequestered calcium ion into cytosol regulation of monoatomic ion transport regulation of transmembrane transport positive regulation of transport regulation of monoatomic cation transmembrane transport positive regulation of T cell chemotaxis regulation of T cell chemotaxis T cell chemotaxis negative regulation of lymphocyte proliferation negative regulation of T cell proliferation negative regulation of leukocyte proliferation negative regulation of mononuclear cell proliferation negative regulation of cell population proliferation negative regulation of alpha-beta T cell proliferation negative regulation of CD4-positive, alpha-beta T cell proliferation	cellular anatomical structure extracellular region extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR015950	Chemokine-binding M3, subdomain 1, viral	Homologous Superfamily
A, B	IPR015951	Chemokine-binding M3, subdomain 2, viral	Homologous Superfamily
A, B	IPR015296	Chemokine-binding M3, viral	Family
A, B	IPR036323	Chemokine-binding M3 superfamily	Homologous Superfamily
C [auth D], D [auth E]	IPR001811	Chemokine interleukin-8-like domain	Domain
C [auth D], D [auth E]	IPR008105	C chemokine	Family
C [auth D], D [auth E]	IPR036048	Chemokine interleukin-8-like superfamily	Homologous Superfamily
C [auth D], D [auth E]	IPR039809	Chemokine beta/gamma/delta	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth D], D [auth E]	Pharos: P47992	psoriasis vascular disease

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.