1OLZ | pdb_00001olz

The ligand-binding face of the semaphorins revealed by the high resolution crystal structure of SEMA4D

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)
B	d1olzb1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	I set domains	Semaphorin 4d Ig-like domain	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1olzb2	All beta proteins	7-bladed beta-propeller	Sema domain	Sema domain	Semaphorin 4d	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1olzb3	Small proteins	Trefoil/Plexin domain-like	Plexin repeat	Plexin repeat	Semaphorin 4d	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1olza1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	I set domains	Semaphorin 4d Ig-like domain	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1olza2	All beta proteins	7-bladed beta-propeller	Sema domain	Sema domain	Semaphorin 4d	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1olza3	Small proteins	Trefoil/Plexin domain-like	Plexin repeat	Plexin repeat	Semaphorin 4d	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054793	3000071	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Plexin repeat-like	8037643	3000415	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Sema domain-like	8037641	3000180	SCOP2B (2022-06-29)
A	SCOP2 Family	Sema domain-like	8025262	4000934	SCOP2 (2022-06-29)
A	SCOP2 Family	Plexin repeat-like	8025264	4001807	SCOP2 (2022-06-29)
A	SCOP2 Family	I set domains	8054792	4007543	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Sema domain-like	8037641	3000180	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Plexin repeat-like	8037643	3000415	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Immunoglobulin (Ig) domain-like	8054793	3000071	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)
B	Copper-bind	e1olzB1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: Copper-bind	ECOD (develop294)
B	DPPIV_N	e1olzB2	A: alpha bundles	X: Cloacin translocation domain	H: Cloacin translocation domain	T: Cloacin translocation domain	F: DPPIV_N	ECOD (develop294)
B	Ectatomin	e1olzB3	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Ectatomin	ECOD (develop294)
A	Ig_3	e1olzA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ig_3	ECOD (develop294)
A	Sema	e1olzA2	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: Sema	ECOD (develop294)
A	PSI	e1olzA3	A: few secondary structure elements	X: Trefoil/Plexin domain-like	H: Trefoil/Plexin domain-like	T: Trefoil/Plexin domain-like	F: PSI	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
B	3.30.1680.10	Alpha Beta	2-Layer Sandwich	ligand-binding face of the semaphorins, domain 2	ligand-binding face of the semaphorins, domain 2	CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
A	3.30.1680.10	Alpha Beta	2-Layer Sandwich	ligand-binding face of the semaphorins, domain 2	ligand-binding face of the semaphorins, domain 2	CATH (4.3.0)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01437	Plexin repeat (PSI)	Plexin repeat	-	Family
A, B	PF01403	Sema domain (Sema)	Sema domain	-	Repeat
A, B	PF00047	Immunoglobulin domain (ig)	Immunoglobulin domain	Members of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases. Immunoglobulin-like domains may be involved in protein-prote ...	Members of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases. Immunoglobulin-like domains may be involved in protein-protein and protein-ligand interactions.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	SEMAPHORIN 4D	protein binding binding semaphorin receptor binding signaling receptor binding identical protein binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity molecular function activator activity molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity neuropilin binding protein binding binding semaphorin receptor binding signaling receptor binding identical protein binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity molecular function activator activity molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity neuropilin binding chemorepellent activity	cell adhesion cell-cell adhesion cellular process leukocyte cell-cell adhesion leukocyte aggregation cellular component organization regulation of biological process regulation of cellular component organization regulation of cellular process cell projection organization regulation of cell projection organization biological regulation cellular component organization or biogenesis chemotaxis cell adhesion cell-cell adhesion cellular process leukocyte cell-cell adhesion leukocyte aggregation cellular component organization regulation of biological process regulation of cellular component organization regulation of cellular process cell projection organization regulation of cell projection organization biological regulation cellular component organization or biogenesis chemotaxis negative chemotaxis response to stimulus taxis response to chemical response to external stimulus locomotion multicellular organismal process positive regulation of nervous system development regulation of growth axonogenesis regulation of cellular component size developmental growth regulation of cell differentiation regulation of neurogenesis neuron projection development regulation of cell development positive regulation of developmental process multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation anatomical structure development positive regulation of cell projection organization regulation of biological quality positive regulation of developmental growth system development developmental process positive regulation of collateral sprouting positive regulation of cell development nervous system development developmental growth involved in morphogenesis generation of neurons positive regulation of multicellular organismal process regulation of neuron projection development regulation of collateral sprouting positive regulation of cellular component organization cellular developmental process regulation of developmental process plasma membrane bounded cell projection morphogenesis positive regulation of biological process cell development cell growth cell morphogenesis regulation of nervous system development neurogenesis regulation of extent of cell growth positive regulation of cell differentiation regulation of axonogenesis positive regulation of neurogenesis regulation of multicellular organismal process positive regulation of cellular process regulation of anatomical structure morphogenesis positive regulation of axonogenesis regulation of cell size regulation of multicellular organismal development collateral sprouting regulation of developmental growth plasma membrane bounded cell projection organization developmental cell growth growth positive regulation of cell growth axon development regulation of cell growth cell morphogenesis involved in neuron differentiation positive regulation of growth anatomical structure morphogenesis neuron development regulation of plasma membrane bounded cell projection organization regulation of anatomical structure size negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process regulation of cell adhesion negative regulation of cell adhesion immune response immune system process negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process apoptotic process programmed cell death regulation of osteoblast differentiation negative regulation of osteoblast differentiation negative regulation of developmental process osteoblast differentiation ossification negative regulation of cell differentiation bone trabecula morphogenesis trabecula morphogenesis positive regulation of molecular function regulation of molecular function positive regulation of hydrolase activity regulation of catalytic activity regulation of hydrolase activity positive regulation of catalytic activity regulation of GTPase activity positive regulation of GTPase activity cellular response to stimulus positive regulation of cell communication small GTPase-mediated signal transduction positive regulation of signal transduction signaling regulation of small GTPase mediated signal transduction regulation of signal transduction intracellular signal transduction Rho protein signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction regulation of signaling positive regulation of intracellular signal transduction regulation of Rho protein signal transduction positive regulation of Rho protein signal transduction regulation of response to stimulus regulation of cell communication positive regulation of small GTPase mediated signal transduction positive regulation of signaling regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction phosphatidylinositol 3-kinase/protein kinase B signal transduction stem cell development neural crest cell differentiation animal organ development neural crest cell development mesenchyme development tissue development mesenchymal cell migration stem cell differentiation ameboidal-type cell migration cell migration mesenchymal cell differentiation cell motility neural crest cell migration regulation of cell shape regulation of cell morphogenesis cellular component biogenesis cellular component assembly cell junction assembly regulation of synapse structure or activity synapse organization regulation of synapse assembly positive regulation of inhibitory synapse assembly inhibitory synapse assembly positive regulation of cellular component biogenesis regulation of cellular component biogenesis regulation of cell junction assembly regulation of synapse organization positive regulation of cell junction assembly cell junction organization synapse assembly regulation of inhibitory synapse assembly positive regulation of synapse assembly cell surface receptor signaling pathway semaphorin-plexin signaling pathway bone maturation developmental maturation skeletal system development anatomical structure maturation ossification involved in bone maturation animal organ maturation bone development axon guidance neuron projection guidance positive regulation of locomotion regulation of cell motility positive regulation of cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration dendrite development regulation of dendrite morphogenesis dendrite morphogenesis regulation of dendrite development positive regulation of phosphorylation regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of phosphate metabolic process positive regulation of metabolic process positive regulation of protein modification process phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of protein phosphorylation phosphorus metabolic process protein modification process protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation regulation of protein metabolic process macromolecule modification regulation of phosphorus metabolic process regulation of phosphorylation	cell periphery postsynapse cellular anatomical structure postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region synaptic membrane ciliary transition zone membrane-bounded organelle cell projection organelle cell periphery postsynapse cellular anatomical structure postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region synaptic membrane ciliary transition zone membrane-bounded organelle cell projection organelle cilium plasma membrane bounded cell projection protein-containing complex semaphorin receptor complex receptor complex extracellular region extracellular space intracellular anatomical structure intracellular membraneless organelle intracellular organelle ciliary basal body microtubule organizing center cytoskeleton membraneless organelle microtubule cytoskeleton centrosome nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen GABA-ergic synapse

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, B	IPR003599	Immunoglobulin domain subtype	Domain
A, B	IPR013151	Immunoglobulin-like beta-sandwich domain	Domain
A, B	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B	IPR036352	Sema domain superfamily	Homologous Superfamily
A, B	IPR007110	Immunoglobulin-like domain	Domain
A, B	IPR003598	Immunoglobulin subtype 2	Domain
A, B	IPR016201	PSI domain	Domain
A, B	IPR027231	Semaphorin	Family
A, B	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A, B	IPR002165	Plexin repeat	Repeat
A, B	IPR001627	Sema domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q92854	Sjogren syndrome astrocytic tumor diabetes mellitus large cell medulloblastoma malignant glioma oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm primitive neuroectodermal tumor subependymal giant cell astrocytoma atypical teratoid rhabdoid tumor glioblastoma lung cancer medulloblastoma osteosarcoma Pick disease Sjogren syndrome astrocytic tumor diabetes mellitus large cell medulloblastoma malignant glioma oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm primitive neuroectodermal tumor subependymal giant cell astrocytoma atypical teratoid rhabdoid tumor glioblastoma lung cancer medulloblastoma osteosarcoma Pick disease psoriasis ulcerative colitis cleft lip invasive ductal breast carcinoma malignant ependymoma metabolic syndrome X pancreatic intraductal papillary-mucinous carcinoma pilocytic astrocytoma

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.