1OLZ

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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
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)
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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	I set domains	8054792	4007543	SCOP2 (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 Superfamily	Immunoglobulin (Ig) domain-like	8054793	3000071	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)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	I-set_3	e1olzA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set_3	ECOD (1.6)
A	Sema	e1olzA2	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: Sema	ECOD (1.6)
A	PSI_1	e1olzA3	A: few secondary structure elements	X: Trefoil/Plexin domain-like (From Topology)	H: Trefoil/Plexin domain-like (From Topology)	T: Trefoil/Plexin domain-like	F: PSI_1	ECOD (1.6)
B	I-set_3	e1olzB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set_3	ECOD (1.6)
B	Sema	e1olzB2	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: Sema	ECOD (1.6)
B	PSI_1	e1olzB3	A: few secondary structure elements	X: Trefoil/Plexin domain-like (From Topology)	H: Trefoil/Plexin domain-like (From Topology)	T: Trefoil/Plexin domain-like	F: PSI_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)

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-prot ...	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	molecular transducer activity signaling receptor activity protein binding binding signaling receptor binding molecular function activator activity molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity semaphorin receptor binding chemorepellent activity identical protein binding transmembrane signaling receptor activity	cell adhesion cell-cell adhesion cellular process leukocyte cell-cell adhesion leukocyte aggregation response to stimulus immune response immune system process regulation of biological process regulation of cellular process negative regulation of programmed cell death regulation of apoptotic process biological regulation negative regulation of biological process cell adhesion cell-cell adhesion cellular process leukocyte cell-cell adhesion leukocyte aggregation response to stimulus immune response immune system process regulation of biological process regulation of cellular process negative regulation of programmed cell death regulation of apoptotic process biological regulation negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process apoptotic process programmed cell death developmental process regulation of osteoblast differentiation multicellular organismal process regulation of developmental process cellular developmental process negative regulation of osteoblast differentiation negative regulation of developmental process regulation of cell differentiation osteoblast differentiation ossification cell differentiation negative regulation of cell differentiation anatomical structure morphogenesis bone trabecula morphogenesis anatomical structure development 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 negative regulation of locomotion developmental growth cell projection organization negative regulation of chemotaxis neuron projection development regulation of cell development multicellular organism development cell projection morphogenesis neuron differentiation regulation of biological quality system development chemotaxis regulation of cell projection organization response to external stimulus generation of neurons negative regulation of axonogenesis negative regulation of developmental growth regulation of response to stimulus negative regulation of multicellular organismal process regulation of neuron projection development regulation of cellular component organization regulation of response to external stimulus plasma membrane bounded cell projection morphogenesis cell development cell growth neurogenesis negative regulation of neurogenesis regulation of axon extension involved in axon guidance regulation of extent of cell growth negative regulation of nervous system development regulation of anatomical structure morphogenesis locomotion neuron projection extension regulation of developmental growth developmental cell growth growth axon development negative regulation of axon extension regulation of chemotaxis regulation of cell growth cell morphogenesis involved in neuron differentiation negative regulation of cell development neuron projection guidance neuron development axon extension regulation of growth axonogenesis regulation of cellular component size regulation of neurogenesis negative regulation of growth neuron projection morphogenesis taxis neuron projection extension involved in neuron projection guidance negative regulation of cellular component organization negative regulation of axon extension involved in axon guidance negative regulation of cell growth nervous system development developmental growth involved in morphogenesis response to chemical regulation of locomotion negative regulation of response to external stimulus cell morphogenesis regulation of axon extension cellular component organization regulation of nervous system development regulation of axonogenesis regulation of multicellular organismal process cellular component organization or biogenesis axon extension involved in axon guidance negative regulation of cell projection organization regulation of cell size regulation of multicellular organismal development plasma membrane bounded cell projection organization negative regulation of response to stimulus axon guidance negative regulation of neuron projection development regulation of plasma membrane bounded cell projection organization regulation of anatomical structure size 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 positive regulation of biological process 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 positive regulation of cellular process regulation of signaling positive regulation of intracellular signal transduction regulation of Rho protein signal transduction positive regulation of Rho protein signal transduction regulation of cell communication positive regulation of small GTPase mediated signal transduction positive regulation of signaling regulation of protein modification process regulation of protein phosphorylation negative regulation of nitrogen compound metabolic process negative regulation of phosphate metabolic process peptidyl-tyrosine modification negative regulation of cellular metabolic process regulation of primary metabolic process regulation of nitrogen compound metabolic process organic substance metabolic process regulation of phosphate metabolic process peptidyl-amino acid modification phosphate-containing compound metabolic process negative regulation of protein modification process nitrogen compound metabolic process protein metabolic process protein modification process phosphorus metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process negative regulation of peptidyl-tyrosine phosphorylation organonitrogen compound metabolic process protein phosphorylation phosphorylation cellular metabolic process regulation of protein metabolic process negative regulation of metabolic process regulation of peptidyl-tyrosine phosphorylation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process negative regulation of protein phosphorylation macromolecule modification negative regulation of phosphorus metabolic process metabolic process regulation of phosphorylation regulation of phosphorus metabolic process macromolecule metabolic process negative regulation of phosphorylation peptidyl-tyrosine phosphorylation regulation of metabolic process 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 positive regulation of nervous system development positive regulation of cellular component organization cellular component biogenesis positive regulation of developmental process 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 positive regulation of multicellular organismal process 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 negative chemotaxis positive regulation of locomotion regulation of cell motility positive regulation of cell migration positive regulation of cell motility regulation of cell migration positive regulation of cell projection organization positive regulation of developmental growth positive regulation of collateral sprouting positive regulation of cell development regulation of collateral sprouting positive regulation of cell differentiation positive regulation of neurogenesis positive regulation of axonogenesis collateral sprouting positive regulation of cell growth positive regulation of growth dendrite development regulation of dendrite morphogenesis dendrite morphogenesis regulation of dendrite development positive regulation of phosphorylation positive regulation of protein metabolic process positive regulation of cellular metabolic process positive regulation of phosphate metabolic process positive regulation of metabolic process positive regulation of protein modification process positive regulation of macromolecule metabolic process positive regulation of protein phosphorylation positive regulation of phosphorus metabolic process positive regulation of nitrogen compound metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II heterocycle metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II cellular nitrogen compound metabolic process negative regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process aromatic compound biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process regulation of RNA biosynthetic process regulation of biosynthetic process nucleobase-containing compound biosynthetic process heterocycle biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process cellular aromatic compound metabolic process positive regulation of peptidyl-tyrosine phosphorylation regulation of cell adhesion negative regulation of cell adhesion	cell periphery plasma membrane membrane cellular anatomical entity protein-containing complex semaphorin receptor complex receptor complex extracellular region extracellular space

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	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	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B	IPR013151	Immunoglobulin	Domain
A, B	IPR036352	Sema domain superfamily	Homologous Superfamily
A, B	IPR007110	Immunoglobulin-like domain	Domain
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 National Science Foundation (DBI-1832184), 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.