5GMJ | pdb_00005gmj

Crystal Structure of GRASP55 GRASP domain in complex with JAM-B C-terminus

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
A	SCOP2B Superfamily	PDZ domain-like	8092754	3000388	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PDZ domain-like	8092755	3000388	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PDZ domain-like	8092755	3000388	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PDZ domain-like	8092754	3000388	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	GRASP55_65	e5gmjA1	A: beta barrels	X: PDZ domain (From Topology)	H: PDZ domain (From Topology)	T: PDZ domain	F: GRASP55_65	ECOD (1.6)
B	GRASP55_65	e5gmjB2	A: beta barrels	X: PDZ domain (From Topology)	H: PDZ domain (From Topology)	T: PDZ domain	F: GRASP55_65	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.30.42.10	Mainly Beta	Roll	Pdz3 Domain	PDZ domain	CATH (4.3.0)
B	2.30.42.10	Mainly Beta	Roll	Pdz3 Domain	PDZ domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF04495	GRASP55/65 PDZ-like domain (GRASP55_65)	GRASP55/65 PDZ-like domain	GRASP55 (Golgi re-assembly stacking protein of 55 kDa) and GRASP65 (a 65 kDa) protein are highly homologous. GRASP55 is a component of the Golgi stacking machinery. GRASP65, an N-ethylmaleimide- sensitive membrane protein required for the stacking of ...	GRASP55 (Golgi re-assembly stacking protein of 55 kDa) and GRASP65 (a 65 kDa) protein are highly homologous. GRASP55 is a component of the Golgi stacking machinery. GRASP65, an N-ethylmaleimide- sensitive membrane protein required for the stacking of Golgi cisternae in a cell-free system [1]. This region appears to be related to the PDZ domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Golgi reassembly-stacking protein 2	-	developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation cellular developmental process cell differentiation cellular process cellular component organization organelle organization cellular component organization or biogenesis developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation cellular developmental process cell differentiation cellular process cellular component organization organelle organization cellular component organization or biogenesis protein localization establishment of protein localization cellular localization protein localization to cell periphery establishment of protein localization to membrane protein localization to plasma membrane establishment of protein localization to plasma membrane localization within membrane protein localization to membrane establishment of localization localization cellular macromolecule localization macromolecule localization cellular component biogenesis cellular component assembly organelle assembly cellular response to stimulus cellular response to stress response to stimulus response to stress response to endoplasmic reticulum stress	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system Golgi membrane membrane bounding membrane of organelle organelle membrane organelle subcompartment membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system Golgi membrane membrane bounding membrane of organelle organelle membrane organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane
C, D	Junctional adhesion molecule B	cell adhesion molecule binding protein-containing complex binding protein binding binding integrin binding signaling receptor binding	leukocyte tethering or rolling leukocyte cell-cell adhesion leukocyte migration cell adhesion cell-cell adhesion immune system process leukocyte adhesion to vascular endothelial cell cellular extravasation cell migration cellular process cell motility developmental process spermatid development spermatid differentiation leukocyte tethering or rolling leukocyte cell-cell adhesion leukocyte migration cell adhesion cell-cell adhesion immune system process leukocyte adhesion to vascular endothelial cell cellular extravasation cell migration cellular process cell motility developmental process spermatid development spermatid differentiation sexual reproduction cellular developmental process spermatogenesis reproductive process multicellular organismal reproductive process cell development cellular process involved in reproduction in multicellular organism developmental process involved in reproduction gamete generation male gamete generation cell differentiation anatomical structure development germ cell development hematopoietic stem cell migration hematopoietic stem cell migration to bone marrow multicellular organismal process negative regulation of nervous system process system process regulation of cellular process regulation of developmental process regulation of myelination regulation of system process negative regulation of biological process regulation of nervous system development multicellular organism development axon ensheathment ensheathment of neurons negative regulation of cellular process regulation of multicellular organismal process system development regulation of biological process regulation of multicellular organismal development nervous system process biological regulation nervous system development regulation of nervous system process myelination negative regulation of myelination negative regulation of multicellular organismal process positive regulation of locomotion regulation of cell motility positive regulation of biological process regulation of lymphocyte migration positive regulation of cell migration positive regulation of cell motility positive regulation of mononuclear cell migration regulation of cell migration regulation of immune system process regulation of mononuclear cell migration positive regulation of immune system process locomotion positive regulation of cellular process positive regulation of lymphocyte migration regulation of leukocyte migration lymphocyte migration positive regulation of leukocyte migration regulation of locomotion mononuclear cell migration regulation of cell adhesion negative regulation of cell adhesion	somatodendritic compartment cellular anatomical structure cell surface cell-cell junction apical junction complex bicellular tight junction tight junction anchoring junction cell junction cell periphery plasma membrane membrane protein-containing complex protein complex involved in cell adhesion

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR007583	GRASP55/65	Family
A, B	IPR036034	PDZ superfamily	Homologous Superfamily
A, B	IPR024958	GRASP-type PDZ domain	Domain
C, D	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C, D	IPR003598	Immunoglobulin subtype 2	Domain
C, D	IPR042625	Junctional adhesion molecule B	Family
C, D	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C, D	IPR013106	Immunoglobulin V-set domain	Domain
C, D	IPR003599	Immunoglobulin domain subtype	Domain
C, D	IPR007110	Immunoglobulin-like domain	Domain

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.