7SK4

Cryo-EM structure of ACKR3 in complex with chemokine N-terminal mutant CXCL12_LRHQ, an intracellular Fab, and an extracellular Fab

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Interleukin 8-like chemokines	8043051	3001955	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)
C	PF07686	e7sk4C1	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)
D	PF07686	e7sk4D1	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)
E	PF07686	e7sk4E1	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)
F	PF07686	e7sk4F1	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)
A	PF00001	e7sk4A1	A: alpha bundles	X: Family A G protein-coupled receptor-like (From Topology)	H: Family A G protein-coupled receptor-like (From Topology)	T: Family A G protein-coupled receptor-like	F: PF00001	ECOD (1.6)
B	PF00048	e7sk4B1	A: beta barrels	X: IL8-related (From Homology)	H: IL8-related	T: IL8	F: PF00048	ECOD (1.6)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C	Light Chain	IGKV1	Kappa	stromal cell-derived factor 1	SAbDab (2024-04-26)
D	Heavy Chain	IGHV3	-	stromal cell-derived factor 1	SAbDab (2024-04-26)
E	Light Chain	IGKV1	Kappa	atypical chemokine receptor 3	SAbDab (2024-04-26)
F	Heavy Chain	IGHV3	-	atypical chemokine receptor 3	SAbDab (2024-04-26)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00001	7 transmembrane receptor (rhodopsin family) (7tm_1)	7 transmembrane receptor (rhodopsin family)	-	Family
B	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
C	CID25 Fab light chain	-	-	-
D	CID25 Fab heavy chain	-	-	-
E	CID24 Fab light chain	-	-	-
F	CID24 Fab heavy chain	-	-	-
A	Atypical chemokine receptor 3	molecular transducer activity coreceptor activity signaling receptor activity G protein-coupled chemoattractant receptor activity C-C chemokine receptor activity chemokine receptor activity G protein-coupled receptor activity transmembrane signaling receptor activity cytokine receptor activity immune receptor activity cargo receptor activity scavenger receptor activity C-X-C chemokine receptor activity C-C chemokine binding molecular transducer activity coreceptor activity signaling receptor activity G protein-coupled chemoattractant receptor activity C-C chemokine receptor activity chemokine receptor activity G protein-coupled receptor activity transmembrane signaling receptor activity cytokine receptor activity immune receptor activity cargo receptor activity scavenger receptor activity C-X-C chemokine receptor activity C-C chemokine binding protein binding binding chemokine binding cytokine binding C-X-C chemokine binding	positive regulation of cytosolic calcium ion concentration biological regulation regulation of biological quality developmental process multicellular organismal process parasympathetic nervous system development nervous system development multicellular organism development nerve development cranial nerve development central nervous system development preganglionic parasympathetic fiber development anatomical structure development oculomotor nerve development positive regulation of cytosolic calcium ion concentration biological regulation regulation of biological quality developmental process multicellular organismal process parasympathetic nervous system development nervous system development multicellular organism development nerve development cranial nerve development central nervous system development preganglionic parasympathetic fiber development anatomical structure development oculomotor nerve development autonomic nervous system development system development cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus positive regulation of ERK1 and ERK2 cascade regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of biological process regulation of signaling positive regulation of MAPK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade regulation of response to stimulus MAPK cascade regulation of cell communication cellular process ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade positive regulation of signaling localization import into cell receptor internalization transport receptor-mediated endocytosis endocytosis establishment of localization vesicle-mediated transport blood vessel morphogenesis tube development angiogenesis vasculature development circulatory system development anatomical structure morphogenesis tube morphogenesis anatomical structure formation involved in morphogenesis blood vessel development immune response immune system process response to organic substance cell surface receptor signaling pathway response to cytokine response to chemokine cytokine-mediated signaling pathway cellular response to chemokine chemokine-mediated signaling pathway cellular response to chemical stimulus response to chemical G protein-coupled receptor signaling pathway cellular response to cytokine stimulus cellular response to organic substance positive regulation of locomotion regulation of cell motility positive regulation of mesenchymal stem cell migration positive regulation of cell migration regulation of mesenchymal stem cell migration regulation of locomotion mesenchymal stem cell migration positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion calcium-mediated signaling cell chemotaxis chemotaxis response to external stimulus taxis cellular developmental process vasculogenesis cell differentiation negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation negative regulation of cellular process negative regulation of biological process cell adhesion negative regulation of signaling negative regulation of intracellular signal transduction regulation of cellular response to stress regulation of intrinsic apoptotic signaling pathway in response to DNA damage regulation of programmed cell death regulation of intrinsic apoptotic signaling pathway negative regulation of cell communication cellular response to stress response to stress negative regulation of apoptotic signaling pathway regulation of response to stress intrinsic apoptotic signaling pathway in response to DNA damage intrinsic apoptotic signaling pathway negative regulation of response to stimulus negative regulation of programmed cell death regulation of apoptotic process cell death negative regulation of signal transduction negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage apoptotic signaling pathway negative regulation of intrinsic apoptotic signaling pathway negative regulation of apoptotic process DNA damage response apoptotic process programmed cell death regulation of apoptotic signaling pathway	cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane clathrin-coated pit endomembrane system membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle intracellular membrane-bounded organelle cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane clathrin-coated pit endomembrane system membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle intracellular membrane-bounded organelle early endosome endosome intracellular vesicle cytoplasmic vesicle cytoplasm vesicle recycling endosome
B	Stromal cell-derived factor 1	protein binding binding molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity cytokine receptor binding G protein-coupled receptor binding chemokine receptor binding chemokine activity cytokine activity protein binding binding molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity cytokine receptor binding G protein-coupled receptor binding chemokine receptor binding chemokine activity cytokine activity CXCR chemokine receptor binding cell adhesion molecule binding protein-containing complex binding integrin binding	cellular response to stimulus response to organic substance response to stimulus response to chemokine response to cytokine cellular response to chemokine cellular response to chemical stimulus response to chemical cellular response to cytokine stimulus cellular process cellular response to organic substance cellular component organization cellular component biogenesis cellular component assembly cellular response to stimulus response to organic substance response to stimulus response to chemokine response to cytokine cellular response to chemokine cellular response to chemical stimulus response to chemical cellular response to cytokine stimulus cellular process cellular response to organic substance cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly integrin activation cellular component organization or biogenesis response to mechanical stimulus response to abiotic stimulus response to external stimulus response to ultrasound regulation of biological process regulation of cellular process cell surface receptor signaling pathway chemokine (C-X-C motif) ligand 12 signaling pathway signaling biological regulation cytokine-mediated signaling pathway chemokine-mediated signaling pathway cell communication G protein-coupled receptor signaling pathway signal transduction developmental process multicellular organismal process head development forebrain development animal organ development brain development nervous system development multicellular organism development telencephalon cell migration central nervous system development forebrain cell migration anatomical structure development cell migration telencephalon development cell motility system development inorganic ion homeostasis intracellular calcium ion homeostasis homeostatic process calcium ion homeostasis cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis defense response response to stress regulation of cytoskeleton organization regulation of cellular component organization regulation of actin filament-based process regulation of cellular component size actin filament-based process regulation of biological quality actin polymerization or depolymerization regulation of actin filament organization actin cytoskeleton organization regulation of actin polymerization or depolymerization actin filament organization regulation of organelle organization organelle organization regulation of actin filament length regulation of actin cytoskeleton organization regulation of supramolecular fiber organization supramolecular fiber organization cytoskeleton organization regulation of anatomical structure size chemotaxis taxis locomotion detection of external stimulus system process detection of stimulus involved in sensory perception of pain nervous system process sensory perception of temperature stimulus sensory perception of pain detection of temperature stimulus involved in sensory perception response to temperature stimulus detection of abiotic stimulus detection of stimulus sensory perception detection of temperature stimulus detection of stimulus involved in sensory perception detection of temperature stimulus involved in sensory perception of pain cell chemotaxis positive regulation of monocyte chemotaxis positive regulation of locomotion regulation of cell motility regulation of response to external stimulus positive regulation of biological process positive regulation of chemotaxis positive regulation of cell migration regulation of monocyte chemotaxis positive regulation of response to stimulus positive regulation of response to external stimulus positive regulation of cell motility regulation of cell migration myeloid leukocyte migration positive regulation of mononuclear cell migration regulation of immune system process regulation of mononuclear cell migration positive regulation of immune system process positive regulation of cellular process regulation of leukocyte chemotaxis regulation of leukocyte migration positive regulation of leukocyte migration positive regulation of leukocyte chemotaxis regulation of chemotaxis monocyte chemotaxis leukocyte migration regulation of response to stimulus immune system process regulation of locomotion mononuclear cell migration leukocyte chemotaxis regulation of calcium ion import regulation of calcium ion transport regulation of localization positive regulation of calcium ion transport positive regulation of calcium ion import transport regulation of transport regulation of monoatomic ion transport establishment of localization calcium ion transport metal ion transport localization positive regulation of transport positive regulation of monoatomic ion transport monoatomic ion transport calcium ion import monoatomic cation transport regulation of metal ion transport regulation of lymphocyte migration positive regulation of lymphocyte migration positive regulation of T cell migration lymphocyte migration regulation of T cell migration T cell migration cell adhesion response to decreased oxygen levels response to hypoxia response to oxygen levels negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of biological process regulation of cellular response to stress regulation of signal transduction regulation of intrinsic apoptotic signaling pathway in response to DNA damage regulation of programmed cell death regulation of intrinsic apoptotic signaling pathway intracellular signal transduction negative regulation of cell communication cellular response to stress regulation of intracellular signal transduction negative regulation of apoptotic signaling pathway regulation of response to stress negative regulation of cellular process intrinsic apoptotic signaling pathway in response to DNA damage intrinsic apoptotic signaling pathway regulation of signaling negative regulation of response to stimulus negative regulation of programmed cell death regulation of apoptotic process cell death negative regulation of signal transduction negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage apoptotic signaling pathway negative regulation of intrinsic apoptotic signaling pathway negative regulation of apoptotic process DNA damage response regulation of cell communication apoptotic process programmed cell death regulation of apoptotic signaling pathway adult locomotory behavior behavior adult behavior locomotory behavior response to hormone response to endogenous stimulus response to organonitrogen compound response to peptide hormone response to oxygen-containing compound response to nitrogen compound detection of mechanical stimulus involved in sensory perception of pain detection of mechanical stimulus involved in sensory perception sensory perception of mechanical stimulus detection of mechanical stimulus positive chemotaxis positive regulation of positive chemotaxis induction of positive chemotaxis regulation of positive chemotaxis immune response axon extension positive regulation of nervous system development regulation of growth axonogenesis developmental growth cell projection organization regulation of cell differentiation regulation of neurogenesis neuron projection development regulation of cell development positive regulation of axon extension involved in axon guidance positive regulation of developmental process cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation positive regulation of cell projection organization positive regulation of developmental growth neuron projection extension involved in neuron projection guidance regulation of cell projection organization positive regulation of cell development developmental growth involved in morphogenesis generation of neurons positive regulation of multicellular organismal process regulation of neuron projection development positive regulation of cellular component organization cellular developmental process regulation of developmental process plasma membrane bounded cell projection morphogenesis cell development cell growth cell morphogenesis regulation of axon extension regulation of nervous system development neurogenesis regulation of axon extension involved in axon guidance regulation of extent of cell growth positive regulation of cell differentiation regulation of axonogenesis positive regulation of neurogenesis regulation of multicellular organismal process axon extension involved in axon guidance positive regulation of axon extension positive regulation of axonogenesis regulation of anatomical structure morphogenesis regulation of cell size neuron projection extension regulation of multicellular organismal development regulation of developmental growth plasma membrane bounded cell projection organization developmental cell growth growth axon guidance positive regulation of cell growth axon development regulation of cell growth cell morphogenesis involved in neuron differentiation anatomical structure morphogenesis positive regulation of growth neuron projection guidance neuron development regulation of plasma membrane bounded cell projection organization CXCL12-activated CXCR4 signaling pathway C-X-C chemokine receptor CXCR4 signaling pathway negative regulation of locomotion regulation of leukocyte adhesion to vascular endothelial cell leukocyte cell-cell adhesion negative regulation of cell adhesion leukocyte tethering or rolling negative regulation of leukocyte tethering or rolling cell-cell adhesion negative regulation of cellular extravasation cellular extravasation regulation of cell-cell adhesion negative regulation of cell migration regulation of cell adhesion negative regulation of leukocyte adhesion to vascular endothelial cell regulation of leukocyte tethering or rolling negative regulation of leukocyte migration negative regulation of leukocyte cell-cell adhesion negative regulation of immune system process leukocyte adhesion to vascular endothelial cell negative regulation of cell-cell adhesion regulation of leukocyte cell-cell adhesion negative regulation of cell motility regulation of cellular extravasation monoamine transport nitrogen compound transport regulation of catecholamine secretion organic hydroxy compound transport positive regulation of secretion by cell dopamine transport positive regulation of amine transport secretion by cell regulation of secretion by cell catecholamine transport positive regulation of secretion signal release secretion organic substance transport positive regulation of catecholamine secretion export from cell cell-cell signaling dopamine secretion positive regulation of dopamine secretion regulation of secretion catecholamine secretion amine transport regulation of amine transport regulation of dopamine secretion vasculature development regulation of vasculature development circulatory system development positive regulation of vasculature development regulation of leukocyte apoptotic process dendritic cell apoptotic process negative regulation of dendritic cell apoptotic process leukocyte apoptotic process negative regulation of leukocyte apoptotic process regulation of dendritic cell apoptotic process positive regulation of cell adhesion positive regulation of neuron differentiation regulation of neuron differentiation biological process involved in interspecies interaction between organisms response to other organism response to external biotic stimulus response to virus response to biotic stimulus neuron migration animal organ regeneration regeneration cell population proliferation positive regulation of cell population proliferation endothelial cell proliferation positive regulation of epithelial cell proliferation regulation of endothelial cell proliferation regulation of cell population proliferation positive regulation of endothelial cell proliferation regulation of epithelial cell proliferation epithelial cell proliferation circulatory system process blood circulation	cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle extracellular matrix external encapsulating structure collagen-containing extracellular matrix

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001416	Atypical chemokine receptor 3	Family
A	IPR000276	G protein-coupled receptor, rhodopsin-like	Family
A	IPR017452	GPCR, rhodopsin-like, 7TM	Domain
A	IPR047143	G-protein coupled estrogen receptor 1-like	Family
B	IPR001811	Chemokine interleukin-8-like domain	Domain
B	IPR036048	Chemokine interleukin-8-like superfamily	Homologous Superfamily
B	IPR039809	Chemokine beta/gamma/delta	Family
B	IPR033899	CXC Chemokine domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P25106	rheumatoid arthritis Liver Cirrhosis, Experimental carcinoma sarcomatoid carcinoma kidney disease colorectal cancer hepatocellular carcinoma malignant ependymoma adenoma pancreatic intraductal papillary-mucinous carcinoma astrocytic tumor pituitary cancer breast cancer tuberculosis colorectal carcinoma rheumatoid arthritis Liver Cirrhosis, Experimental carcinoma sarcomatoid carcinoma kidney disease colorectal cancer hepatocellular carcinoma malignant ependymoma adenoma pancreatic intraductal papillary-mucinous carcinoma astrocytic tumor pituitary cancer breast cancer tuberculosis colorectal carcinoma ductal breast carcinoma in situ gastric carcinoma invasive ductal breast carcinoma lung adenocarcinoma malignant mesothelioma oligodendroglioma adrenal cortex carcinoma pancreatic intraductal papillary-mucinous neoplasm atopic eczema polycystic ovary syndrome breast carcinoma ulcerative colitis facioscapulohumeral muscular dystrophy glioblastoma lung cancer medulloblastoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia atypical teratoid rhabdoid tumor psoriasis breast fibroadenoma sinusitis undifferentiated carcinoma dermatomyositis gastric cancer
B	Pharos: P48061	breast cancer breast carcinoma HIV infectious disease prostate cancer malignant mesothelioma Neoplasm Metastasis dermatitis coronary artery disease pancreatic intraductal papillary-mucinous carcinoma hematologic disease periodontitis limb-girdle muscular dystrophy Sjogren syndrome lung adenocarcinoma adenoma breast cancer breast carcinoma HIV infectious disease prostate cancer malignant mesothelioma Neoplasm Metastasis dermatitis coronary artery disease pancreatic intraductal papillary-mucinous carcinoma hematologic disease periodontitis limb-girdle muscular dystrophy Sjogren syndrome lung adenocarcinoma adenoma lung disease atopic eczema MALT lymphoma breast fibroadenoma medulloblastoma ovarian cancer glioblastoma pancreatic intraductal papillary-mucinous neoplasm hepatocellular carcinoma interstitial cystitis periodontitis, chronic, adult ischemic disease subependymal giant cell astrocytoma lung cancer adrenal cortex carcinoma lymphoplasmacytic lymphoma atypical teratoid rhabdoid tumor cancer myocardial infarction non-small cell lung carcinoma Duchenne muscular dystrophy pancreatic ductal adenocarcinoma heart disease pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia invasive ductal breast carcinoma Pick disease large cell medulloblastoma susceptibility to HIV infection lung carcinoma Alzheimer disease malignant colon neoplasm autoimmune disease malignant pancreatic neoplasm breast disease chronic periodontitis cystic fibrosis osteosarcoma ductal breast carcinoma in situ

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B	OPM	Transmembrane	Alpha-helical polytopic	Rhodopsin-like receptors and pumps	G-protein coupled receptors, family A

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	G Protein-Coupled Receptors: Class A	Atypical chemokine receptor 3 (ACKR3) in complex with chemokine CXCL12, intracellular Fab, and extracellular Fab

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.