5YHL | pdb_00005yhl

Crystal structure of the human prostaglandin E receptor EP4 in complex with Fab and an antagonist Br-derivative

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Class A (rhodopsin) G protein-coupled receptor-like	8091247	4001858	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	G protein-coupled receptor-like	8091248	3000473	SCOP2 (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	7tm_1_3	e5yhlA1	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: 7tm_1_3	ECOD (1.6)
B [auth H]	V-set_8	e5yhlH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
B [auth H]	C1-set_1	e5yhlH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
C [auth L]	C1-set_4	e5yhlL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
C [auth L]	V-set	e5yhlL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)

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
B [auth H]	Antibody Fab Fragment	VH-CH1	Mus musculus (house mouse)	IGHV1S13501, IGHJ301, IGHG2A01, IGHG2A02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202549-0)
C [auth L]	Antibody Fab Fragment	L-KAPPA	Mus musculus (house mouse)	IGKV14-11101, IGKJ401, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202549-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth H]	Heavy Chain	IGHV1	-	prostaglandin e2 receptor ep4 subtype	SAbDab (2025-12-19)
C [auth L]	Light Chain	IGKV14	Kappa	prostaglandin e2 receptor ep4 subtype	SAbDab (2025-12-19)

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)	This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GC ...	This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Prostaglandin E2 receptor EP4 subtype	prostaglandin E receptor activity prostanoid receptor activity molecular transducer activity G protein-coupled receptor activity transmembrane signaling receptor activity signaling receptor activity icosanoid receptor activity prostaglandin receptor activity	positive regulation of cytosolic calcium ion concentration biological regulation regulation of biological quality multicellular organismal process cellular developmental process response to stimulus cell development mononuclear cell differentiation lymphocyte activation lymphocyte differentiation cell activation involved in immune response CD4-positive, alpha-beta T cell differentiation CD4-positive, alpha-beta T cell differentiation involved in immune response alpha-beta T cell differentiation involved in immune response positive regulation of cytosolic calcium ion concentration biological regulation regulation of biological quality multicellular organismal process cellular developmental process response to stimulus cell development mononuclear cell differentiation lymphocyte activation lymphocyte differentiation cell activation involved in immune response CD4-positive, alpha-beta T cell differentiation CD4-positive, alpha-beta T cell differentiation involved in immune response alpha-beta T cell differentiation involved in immune response leukocyte activation alpha-beta T cell differentiation T cell activation involved in immune response alpha-beta T cell activation involved in immune response T cell activation cell differentiation CD4-positive, alpha-beta T cell activation leukocyte activation involved in immune response anatomical structure development alpha-beta T cell activation T cell differentiation lymphocyte activation involved in immune response developmental process T-helper cell differentiation immune response hemopoiesis cell activation T cell differentiation involved in immune response immune effector process immune system process cellular process leukocyte differentiation regulation of defense response regulation of biological process regulation of response to external stimulus defense response positive regulation of biological process 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 regulation of cytoskeleton organization regulation of cellular process regulation of cellular component organization regulation of actin filament-based process regulation of actin filament bundle assembly cellular component biogenesis cellular component organization cellular component assembly actin filament bundle organization actin filament-based process cellular component organization or biogenesis stress fiber assembly regulation of actin filament organization actin cytoskeleton organization actomyosin structure organization actin filament organization regulation of cellular component biogenesis regulation of organelle organization regulation of stress fiber assembly organelle organization contractile actin filament bundle assembly regulation of actomyosin structure organization regulation of actin cytoskeleton organization actin filament bundle assembly regulation of supramolecular fiber organization supramolecular fiber organization cytoskeleton organization cellular response to stimulus signaling intracellular signal transduction cell communication intracellular signaling cassette MAPK cascade ERK1 and ERK2 cascade signal transduction multicellular organism development skeletal system development animal organ development bone development system development negative regulation of inflammatory response negative regulation of response to stimulus negative regulation of biological process negative regulation of response to external stimulus negative regulation of defense response adenylate cyclase-modulating G protein-coupled receptor signaling pathway G protein-coupled receptor signaling pathway response to ketone response to prostaglandin response to lipid response to endogenous stimulus response to alcohol cellular response to prostaglandin stimulus response to oxygen-containing compound cellular response to oxygen-containing compound cellular response to endogenous stimulus cellular response to prostaglandin E stimulus cellular response to chemical stimulus cellular response to alcohol response to hormone response to chemical cellular response to lipid response to prostaglandin E cellular response to ketone cellular response to hormone stimulus adenylate cyclase-activating G protein-coupled receptor signaling pathway negative regulation of cellular process cytokine production regulation of cytokine production regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of metabolic process negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process negative regulation of multicellular organismal process regulation of metabolic process response to mechanical stimulus response to abiotic stimulus negative regulation of locomotion regulation of cell motility negative regulation of eosinophil migration eosinophil migration eosinophil extravasation negative regulation of cellular extravasation cellular extravasation myeloid leukocyte migration regulation of cell migration cell migration regulation of immune system process cell motility negative regulation of eosinophil extravasation negative regulation of cell migration locomotion regulation of leukocyte migration regulation of eosinophil extravasation granulocyte migration regulation of eosinophil migration leukocyte migration negative regulation of leukocyte migration negative regulation of immune system process regulation of locomotion negative regulation of cell motility regulation of cellular extravasation cellular response to mechanical stimulus cellular response to abiotic stimulus cellular response to external stimulus cellular response to environmental stimulus JNK cascade adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of gene expression positive regulation of multicellular organismal process positive regulation of cytokine production negative regulation of cellular component organization protein-containing complex organization negative regulation of protein-containing complex assembly negative regulation of integrin activation regulation of protein-containing complex assembly protein-containing complex assembly regulation of integrin activation integrin activation	cellular anatomical structure membrane cell periphery plasma membrane
B [auth H]	Heavy chain of Fab fragment	-	-	-
C [auth L]	Light chain of Fab fragment	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR008365	Prostanoid receptor	Family
A	IPR000276	G protein-coupled receptor, rhodopsin-like	Family
A	IPR017452	GPCR, rhodopsin-like, 7TM	Domain
A	IPR001244	Prostaglandin DP receptor	Family
A	IPR001758	Prostanoid EP4 receptor	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P35408	ankylosing spondylitis Chloracne endometriosis lymphoma Sjogren syndrome esophageal adenocarcinoma Gaucher disease invasive ductal breast carcinoma acute myeloid leukemia lung cancer adrenal cortex carcinoma malignant colon neoplasm medulloblastoma ovarian cancer breast cancer ankylosing spondylitis Chloracne endometriosis lymphoma Sjogren syndrome esophageal adenocarcinoma Gaucher disease invasive ductal breast carcinoma acute myeloid leukemia lung cancer adrenal cortex carcinoma malignant colon neoplasm medulloblastoma ovarian cancer breast cancer pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia dermatomyositis pilocytic astrocytoma gastric carcinoma glioblastoma juvenile dermatomyositis adenoma lung carcinoma malignant ependymoma non-small cell lung carcinoma ovarian cyst breast carcinoma pancreatic intraductal papillary-mucinous carcinoma corpus luteum cyst physiological sexual disorder Duchenne muscular dystrophy gastric cardia carcinoma lung adenocarcinoma adrenal cortex adenoma malignant pancreatic neoplasm osteosarcoma bipolar disorder pancreatic intraductal papillary-mucinous neoplasm cystic fibrosis Emery-Dreifuss muscular dystrophy

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

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

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	G Protein-Coupled Receptors: Class A	prostaglandin EP₄ receptor in complex with agonist ONO-AE3-208

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.