7YGG

Crystal structure of human CD47 in complex with engineered SIRPa.D1(N80A)

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF07686	e7yggA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
B	PF07686	e7yggB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
C	PF08204	e7yggC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF08204	ECOD (1.6)
D	PF08204	e7yggD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF08204	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain
C, D	PF08204	CD47 immunoglobulin-like domain (V-set_CD47)	CD47 immunoglobulin-like domain	This family represents the CD47 leukocyte antigen V-set like Ig domain [1,2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	SIRPA protein	protein antigen binding protein binding binding antigen binding protein phosphatase binding phosphatase binding enzyme binding SH3 domain binding protein domain specific binding cell adhesion molecule binding cell adhesion mediator activity cell-cell adhesion mediator activity GTPase regulator activity enzyme regulator activity protein antigen binding protein binding binding antigen binding protein phosphatase binding phosphatase binding enzyme binding SH3 domain binding protein domain specific binding cell adhesion molecule binding cell adhesion mediator activity cell-cell adhesion mediator activity GTPase regulator activity enzyme regulator activity nucleoside-triphosphatase regulator activity molecular function regulator activity protein binding involved in heterotypic cell-cell adhesion protein tyrosine kinase binding kinase binding protein kinase binding	multicellular organismal process regulation of tumor necrosis factor production regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process negative regulation of tumor necrosis factor production organic substance metabolic process cytokine production organic substance biosynthetic process regulation of cytokine production negative regulation of cellular process regulation of multicellular organismal process negative regulation of macromolecule metabolic process multicellular organismal process regulation of tumor necrosis factor production regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process negative regulation of tumor necrosis factor production organic substance metabolic process cytokine production organic substance biosynthetic process regulation of cytokine production negative regulation of cellular process regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process cellular metabolic process negative regulation of metabolic process biological regulation tumor necrosis factor superfamily cytokine production regulation of cellular metabolic process negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process tumor necrosis factor production negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression regulation of tumor necrosis factor superfamily cytokine production biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of tumor necrosis factor superfamily cytokine production metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process negative regulation of multicellular organismal process regulation of metabolic process interleukin-6 production regulation of interleukin-6 production negative regulation of interleukin-6 production leukocyte migration immune system process mononuclear cell migration cellular extravasation myeloid leukocyte migration cell migration cell motility monocyte extravasation regulation of protein modification process regulation of protein phosphorylation negative regulation of phosphate metabolic process regulation of primary metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process negative regulation of protein modification process protein metabolic process protein modification process phosphorus metabolic process negative regulation of protein metabolic process organonitrogen compound metabolic process protein phosphorylation phosphorylation regulation of protein metabolic process primary metabolic process negative regulation of protein phosphorylation macromolecule modification negative regulation of phosphorus metabolic process regulation of phosphorylation regulation of phosphorus metabolic process negative regulation of phosphorylation regulation of defense response response to stimulus regulation of response to external stimulus negative regulation of inflammatory response defense response negative regulation of response to stimulus response to external stimulus regulation of inflammatory response regulation of response to stimulus response to stress negative regulation of response to external stimulus regulation of response to stress negative regulation of defense response inflammatory response regulation of type II interferon production type II interferon production cellular response to stimulus response to organic substance biological process involved in interspecies interaction between organisms response to lipid response to other organism cellular response to lipopolysaccharide response to oxygen-containing compound cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound response to biotic stimulus cellular response to biotic stimulus cellular response to chemical stimulus response to chemical response to bacterium cellular response to lipid cellular response to organic substance response to external biotic stimulus response to molecule of bacterial origin signaling negative regulation of signaling negative regulation of intracellular signal transduction regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication regulation of intracellular signal transduction intracellular signaling cassette signal transduction regulation of signaling regulation of MAPK cascade negative regulation of signal transduction negative regulation of ERK1 and ERK2 cascade MAPK cascade regulation of cell communication ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade negative regulation of MAPK cascade regulation of localization import into cell positive regulation of cellular component organization regulation of cellular component organization transport positive regulation of biological process vesicle-mediated transport cellular component organization localization positive regulation of endocytosis phagocytosis cellular component organization or biogenesis positive regulation of cellular process regulation of endocytosis regulation of transport regulation of phagocytosis regulation of vesicle-mediated transport establishment of localization positive regulation of phagocytosis positive regulation of transport endocytosis regulation of nitric oxide biosynthetic process negative regulation of nitric oxide metabolic process reactive nitrogen species metabolic process nitric oxide metabolic process nitric oxide biosynthetic process negative regulation of nitric oxide biosynthetic process regulation of nitric oxide metabolic process negative regulation of type I interferon production regulation of interferon-beta production interferon-beta production type I interferon production negative regulation of interferon-beta production regulation of type I interferon production negative regulation of JNK cascade JNK cascade regulation of JNK cascade cellular response to oxidative stress cellular response to chemical stress cellular response to hydrogen peroxide response to reactive oxygen species response to inorganic substance response to hydrogen peroxide response to oxidative stress cellular response to reactive oxygen species cellular response to stress chemokine (C-C motif) ligand 5 production negative regulation of chemokine production negative regulation of chemokine (C-C motif) ligand 5 production regulation of chemokine production chemokine production regulation of chemokine (C-C motif) ligand 5 production response to type II interferon response to cytokine cellular response to type II interferon innate immune response cellular response to cytokine stimulus immune response defense response to symbiont defense response to other organism cell adhesion negative regulation of transport negative regulation of endocytosis negative regulation of phagocytosis negative regulation of cellular component organization I-kappaB phosphorylation canonical NF-kappaB signal transduction negative regulation of I-kappaB phosphorylation regulation of I-kappaB phosphorylation interleukin-1 production regulation of interleukin-1 beta production regulation of interleukin-1 production interleukin-1 beta production cellular response to interleukin-12 response to interleukin-12 cellular response to interleukin-1 response to interleukin-1 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-cell adhesion T cell activation positive regulation of leukocyte activation regulation of immune system process regulation of cell-cell adhesion positive regulation of immune system 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 negative regulation of macrophage inflammatory protein 1 alpha production macrophage inflammatory protein-1 alpha production regulation of macrophage inflammatory protein 1 alpha production regulation of cytokine production involved in inflammatory response negative regulation of cytokine production involved in inflammatory response production of molecular mediator involved in inflammatory response cytokine production involved in inflammatory response	membrane-bounded organelle intracellular anatomical structure tertiary granule membrane membrane intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle endomembrane system tertiary granule intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane cytoplasmic vesicle membrane-bounded organelle intracellular anatomical structure tertiary granule membrane membrane intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle endomembrane system tertiary granule intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle organelle membrane secretory granule membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cell surface cell periphery plasma membrane ficolin-1-rich granule membrane ficolin-1-rich granule
C, D	Leukocyte surface antigen CD47	molecular transducer activity signaling receptor activity thrombospondin receptor activity cell adhesion molecule binding protein binding binding cell adhesion mediator activity cell-cell adhesion mediator activity protein binding involved in heterotypic cell-cell adhesion	positive regulation of locomotion regulation of cell motility regulation of cellular process positive regulation of monocyte extravasation positive regulation of biological process positive regulation of cell migration monocyte extravasation positive regulation of cell motility cellular extravasation myeloid leukocyte migration regulation of cell migration positive regulation of mononuclear cell migration cell migration regulation of immune system process positive regulation of locomotion regulation of cell motility regulation of cellular process positive regulation of monocyte extravasation positive regulation of biological process positive regulation of cell migration monocyte extravasation positive regulation of cell motility cellular extravasation myeloid leukocyte migration regulation of cell migration positive regulation of mononuclear cell migration cell migration regulation of immune system process cell motility regulation of mononuclear cell migration positive regulation of immune system process locomotion positive regulation of cellular process regulation of biological process regulation of leukocyte migration biological regulation positive regulation of leukocyte migration leukocyte migration immune system process regulation of locomotion mononuclear cell migration regulation of monocyte extravasation cellular process regulation of cellular extravasation positive regulation of cellular extravasation regulation of defense response response to stimulus regulation of response to external stimulus defense response response to external stimulus regulation of inflammatory response positive regulation of response to stimulus positive regulation of response to external stimulus positive regulation of inflammatory response regulation of response to stimulus regulation of response to stress response to stress positive regulation of defense response inflammatory response developmental process multicellular organismal process blood vessel morphogenesis tube development angiogenesis vasculature development circulatory system development multicellular organism development anatomical structure morphogenesis tube morphogenesis anatomical structure development anatomical structure formation involved in morphogenesis blood vessel development system development apoptotic process cell death programmed cell death cellular response to stimulus integrin-mediated signaling pathway cell surface receptor signaling pathway signaling cell communication signal transduction regulation of type II interferon production type II interferon production cellular biosynthetic process organic substance metabolic process cytokine production organic substance biosynthetic process regulation of cytokine production regulation of multicellular organismal process regulation of biosynthetic process cellular metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process positive regulation of cell adhesion regulation of cell adhesion positive regulation of cell-cell adhesion cell adhesion cell-cell adhesion regulation of cell-cell adhesion regulation of localization import into cell positive regulation of cellular component organization regulation of cellular component organization transport vesicle-mediated transport cellular component organization localization positive regulation of endocytosis phagocytosis cellular component organization or biogenesis regulation of endocytosis regulation of transport regulation of phagocytosis regulation of vesicle-mediated transport establishment of localization positive regulation of phagocytosis positive regulation of transport endocytosis regulation of tumor necrosis factor production tumor necrosis factor superfamily cytokine production tumor necrosis factor production regulation of tumor necrosis factor superfamily cytokine production interleukin-10 production regulation of interleukin-10 production regulation of nitric oxide biosynthetic process reactive nitrogen species metabolic process nitric oxide metabolic process nitric oxide biosynthetic process regulation of nitric oxide metabolic process cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation response to organic substance biological process involved in interspecies interaction between organisms response to type II interferon response to cytokine cellular response to type II interferon response to biotic stimulus innate immune response cellular response to cytokine stimulus response to external biotic stimulus cellular response to organic substance immune response response to other organism defense response to symbiont cellular response to chemical stimulus response to chemical defense response to other organism negative regulation of biological process negative regulation of transport negative regulation of endocytosis negative regulation of phagocytosis negative regulation of cellular process negative regulation of cellular component organization immune response-regulating cell surface receptor signaling pathway regulation of signal transduction regulation of Fc receptor mediated stimulatory signaling pathway immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of signaling immune response-activating cell surface receptor signaling pathway Fc receptor mediated stimulatory signaling pathway regulation of cell communication regulation of immune response activation of immune response interleukin-6 production regulation of interleukin-6 production regulation of interleukin-12 production interleukin-12 production cellular response to interleukin-12 response to interleukin-12 cellular response to interleukin-1 response to interleukin-1 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 lymphocyte activation positive regulation of cell activation T cell activation positive regulation of leukocyte activation positive regulation of T cell activation cell activation regulation of T cell activation regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process regulation of lymphocyte activation positive regulation of organelle organization regulation of cytoskeleton organization regulation of actin filament-based process regulation of actin filament bundle assembly cellular component biogenesis cellular component assembly positive regulation of actin filament bundle assembly actin filament bundle organization positive regulation of stress fiber assembly actin filament-based process stress fiber assembly regulation of actin filament organization actin cytoskeleton organization actomyosin structure organization positive regulation of cellular component biogenesis positive regulation of cytoskeleton organization actin filament organization regulation of cellular component biogenesis positive regulation of supramolecular fiber organization regulation of organelle organization regulation of stress fiber assembly organelle organization contractile actin filament bundle assembly regulation of actomyosin structure organization actin filament bundle assembly regulation of actin cytoskeleton organization regulation of supramolecular fiber organization supramolecular fiber organization cytoskeleton organization ATP transport nitrogen compound transport organic anion transport nucleotide transport purine ribonucleotide transport organic substance transport carbohydrate derivative transport purine nucleotide transport adenine nucleotide transport ATP export nucleobase-containing compound transport organophosphate ester transport	membrane-bounded organelle intracellular anatomical structure tertiary granule membrane membrane intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle endomembrane system tertiary granule intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane cytoplasmic vesicle membrane-bounded organelle intracellular anatomical structure tertiary granule membrane membrane intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle endomembrane system tertiary granule intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle organelle membrane secretory granule membrane specific granule membrane specific granule extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cell surface cell periphery plasma membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, B	IPR003599	Immunoglobulin subtype	Domain
A, B	IPR003597	Immunoglobulin C1-set	Domain
A, B	IPR013106	Immunoglobulin V-set domain	Domain
A, B	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B	IPR007110	Immunoglobulin-like domain	Domain
C, D	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C, D	IPR013270	CD47 immunoglobulin-like	Domain
C, D	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C, D	IPR037805	Leukocyte surface antigen CD47, IgV	Domain
C, D	IPR007110	Immunoglobulin-like domain	Domain
C, D	IPR006704	Leukocyte surface antigen CD47	Family
C, D	IPR013147	CD47-like, transmembrane	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P78324	primitive neuroectodermal tumor ulcerative colitis atypical teratoid rhabdoid tumor Condition, Preneoplastic interstitial cystitis lung adenocarcinoma malignant glioma non-small cell lung carcinoma precancerous condition psoriasis breast cancer gastric carcinoma invasive ductal breast carcinoma lung cancer malignant mesothelioma primitive neuroectodermal tumor ulcerative colitis atypical teratoid rhabdoid tumor Condition, Preneoplastic interstitial cystitis lung adenocarcinoma malignant glioma non-small cell lung carcinoma precancerous condition psoriasis breast cancer gastric carcinoma invasive ductal breast carcinoma lung cancer malignant mesothelioma osteosarcoma subependymal giant cell astrocytoma breast carcinoma glioblastoma large cell medulloblastoma lung carcinoma medulloblastoma ovarian cancer
C, D	Pharos: Q08722	malignant pancreatic neoplasm oligodendroglioma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia primitive neuroectodermal tumor astrocytic tumor Tourette syndrome bipolar disorder cystic fibrosis Emery-Dreifuss muscular dystrophy juvenile dermatomyositis lung cancer malignant glioma medulloblastoma osteosarcoma malignant pancreatic neoplasm oligodendroglioma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia primitive neuroectodermal tumor astrocytic tumor Tourette syndrome bipolar disorder cystic fibrosis Emery-Dreifuss muscular dystrophy juvenile dermatomyositis lung cancer malignant glioma medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous carcinoma Pick disease psoriasis atopic eczema ulcerative colitis breast cancer dermatomyositis glioblastoma large cell medulloblastoma lymphoplasmacytic lymphoma malignant mesothelioma non-small cell lung carcinoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm plasma cell myeloma Sjogren syndrome atypical teratoid rhabdoid tumor cancer Duchenne muscular dystrophy invasive ductal breast carcinoma lung adenocarcinoma malignant ependymoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C, D	PCA	Parent Component: GLN RESID: AA0031 PSI-MOD : 2-pyrrolidone-5-carboxylic acid (Gln) MOD:00040 , 2-pyrrolidone-5-carboxylic acid (Glu) MOD:00420

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 R01GM133198.