1LD4 | pdb_00001ld4

Placement of the Structural Proteins in Sindbis Virus

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
O	d1ld4o_	Low resolution protein structures	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Structural proteins	(Sindbis virus ) [TaxId: 11034 ],	SCOPe (2.08)
P	d1ld4p_	Low resolution protein structures	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Structural proteins	(Sindbis virus ) [TaxId: 11034 ],	SCOPe (2.08)
N	d1ld4n_	Low resolution protein structures	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Structural proteins	(Sindbis virus ) [TaxId: 11034 ],	SCOPe (2.08)
M	d1ld4m_	Low resolution protein structures	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Structural proteins	(Sindbis virus ) [TaxId: 11034 ],	SCOPe (2.08)
L	d1ld4l_	Low resolution protein structures	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Structural proteins	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
K	d1ld4k_	Low resolution protein structures	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Structural proteins	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
J	d1ld4j_	Low resolution protein structures	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Structural proteins	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
I	d1ld4i_	Low resolution protein structures	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Structural proteins	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
H	d1ld4h_	Low resolution protein structures	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Structural proteins	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
G	d1ld4g_	Low resolution protein structures	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Structural proteins	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
F	d1ld4f_	Low resolution protein structures	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Structural proteins	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
E	d1ld4e_	Low resolution protein structures	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Structural proteins	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d1ld4b_	Low resolution protein structures	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Structural proteins	(Sindbis virus ) [TaxId: 11034 ],	SCOPe (2.08)
D	d1ld4d_	Low resolution protein structures	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Structural proteins	(Sindbis virus ) [TaxId: 11034 ],	SCOPe (2.08)
C	d1ld4c_	Low resolution protein structures	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Structural proteins	(Sindbis virus ) [TaxId: 11034 ],	SCOPe (2.08)
A	d1ld4a_	Low resolution protein structures	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Structural proteins	(Sindbis virus ) [TaxId: 11034 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Trypsin-like serine proteases	8071561	3000114	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Trypsin-like serine proteases	8071561	3000114	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Trypsin-like serine proteases	8071561	3000114	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Trypsin-like serine proteases	8071561	3000114	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)
O	DUF1684	e1ld4O1	A: beta barrels	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: DUF1684	ECOD (v294.2)
P	DUF1684	e1ld4P1	A: beta barrels	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: DUF1684	ECOD (v294.2)
N	DUF1684	e1ld4N1	A: beta barrels	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: DUF1684	ECOD (v294.2)
M	DUF1684	e1ld4M1	A: beta barrels	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: DUF1684	ECOD (v294.2)
E		e1ld4E01	A: beta barrels	X: RNase A-like	H: RNase A-like	T: RNase A-like	F:	ECOD (v294.2)
B	DUF1684	e1ld4B1	A: beta barrels	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: DUF1684	ECOD (v294.2)
D	DUF1684	e1ld4D1	A: beta barrels	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: DUF1684	ECOD (v294.2)
C	DUF1684	e1ld4C1	A: beta barrels	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: DUF1684	ECOD (v294.2)
A	DUF1684	e1ld4A1	A: beta barrels	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: DUF1684	ECOD (v294.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
M, N, O, P	PF01589	Alphavirus E1 glycoprotein (Alpha_E1_glycop)	Alphavirus E1 glycoprotein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
M, N, O, P	Spike glycoprotein E1	peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity RNA binding binding nucleic acid binding protein binding ubiquitin-like protein ligase binding enzyme binding peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity RNA binding binding nucleic acid binding protein binding ubiquitin-like protein ligase binding enzyme binding passive transmembrane transporter activity channel activity transporter activity transmembrane transporter activity structural molecule activity	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis symbiont-mediated suppression of host signal transduction pathway symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated suppression of host toll-like receptor signaling pathway symbiont-mediated perturbation of host signal transduction pathway viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis symbiont-mediated suppression of host signal transduction pathway symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated suppression of host toll-like receptor signaling pathway symbiont-mediated perturbation of host signal transduction pathway modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction import into cell receptor-mediated endocytosis of virus by host cell transport viral life cycle establishment of localization vesicle-mediated transport localization symbiont entry into host cell clathrin-dependent endocytosis symbiont entry into host clathrin-dependent endocytosis of virus by host cell receptor-mediated endocytosis endocytosis endocytosis involved in viral entry into host cell viral gene expression viral translational frameshifting viral translation transmembrane transport monoatomic ion transmembrane transport monoatomic ion transport virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process receptor-mediated virion attachment to host cell entry receptor-mediated virion attachment to host cell	host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum other organism part host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell cytoplasm host cell part host intracellular region viral capsid icosahedral viral capsid virion component host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum other organism part host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell cytoplasm host cell part host intracellular region viral capsid icosahedral viral capsid virion component icosahedral viral capsid, spike host cell plasma membrane host cell membrane virion membrane T=4 icosahedral viral capsid host cell Golgi apparatus host cell nucleus viral membrane viral envelope
E, F, G, H, I E, F, G, H, I, J, K, L	GENERAL CONTROL PROTEIN GCN4	TFIID-class transcription factor complex binding transcription factor binding RNA polymerase binding protein binding binding RNA polymerase II complex binding general transcription initiation factor binding RNA polymerase core enzyme binding enzyme binding RNA polymerase II general transcription initiation factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding DNA binding sequence-specific DNA binding TFIID-class transcription factor complex binding transcription factor binding RNA polymerase binding protein binding binding RNA polymerase II complex binding general transcription initiation factor binding RNA polymerase core enzyme binding enzyme binding RNA polymerase II general transcription initiation factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding DNA binding sequence-specific DNA binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding chromatin binding transcription regulator activity DNA-binding transcription factor activity protein-containing complex binding mediator complex binding DNA-binding transcription factor activity, RNA polymerase II-specific DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity identical protein binding	response to nutrient levels response to stimulus response to stress response to amino acid starvation response to starvation cellular response to stimulus cellular response to nutrient levels cellular process positive regulation of cellular response to amino acid starvation regulation of response to nutrient levels regulation of cellular process positive regulation of biological process regulation of cellular response to stress cellular response to amino acid starvation response to nutrient levels response to stimulus response to stress response to amino acid starvation response to starvation cellular response to stimulus cellular response to nutrient levels cellular process positive regulation of cellular response to amino acid starvation regulation of response to nutrient levels regulation of cellular process positive regulation of biological process regulation of cellular response to stress cellular response to amino acid starvation positive regulation of response to stimulus cellular response to stress regulation of response to stress positive regulation of cellular process regulation of biological process biological regulation cellular response to starvation regulation of response to stimulus regulation of cellular response to amino acid starvation positive regulation of response to nutrient levels transcription preinitiation complex assembly positive regulation of macromolecule biosynthetic process regulation of primary metabolic process cellular component biogenesis nucleobase-containing compound metabolic process DNA-templated transcription positive regulation of metabolic process regulation of DNA-templated transcription initiation regulation of RNA metabolic process cellular component assembly transcription by RNA polymerase II positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process transcription initiation at RNA polymerase II promoter regulation of transcription by RNA polymerase II primary metabolic process positive regulation of transcription by RNA polymerase II positive regulation of DNA-templated transcription initiation positive regulation of RNA metabolic process regulation of gene expression biosynthetic process RNA polymerase II preinitiation complex assembly metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process regulation of RNA polymerase II transcription preinitiation complex assembly positive regulation of cellular component organization regulation of cellular component organization positive regulation of DNA-templated transcription RNA metabolic process cellular component organization protein-DNA complex organization RNA biosynthetic process nucleic acid biosynthetic process positive regulation of protein-containing complex assembly regulation of protein-containing complex assembly positive regulation of biosynthetic process protein-containing complex assembly cellular component organization or biogenesis regulation of RNA biosynthetic process regulation of biosynthetic process positive regulation of RNA polymerase II transcription preinitiation complex assembly protein-containing complex organization positive regulation of cellular component biogenesis positive regulation of transcription initiation by RNA polymerase II protein-DNA complex assembly regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression regulation of cellular component biogenesis macromolecule biosynthetic process DNA-templated transcription initiation nucleic acid metabolic process positive regulation of RNA biosynthetic process regulation of transcription initiation by RNA polymerase II localization protein localization to organelle macromolecule localization protein localization to nuclear periphery protein localization to nucleus intracellular protein localization amino acid biosynthetic process amino acid metabolic process signaling signal transduction intracellular signal transduction cell communication negative regulation of biological process negative regulation of RNA biosynthetic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process regulation of ribosomal protein gene transcription by RNA polymerase II negative regulation of ribosomal protein gene transcription by RNA polymerase II	RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure organelle
A, B, C, D	Coat protein C	peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity RNA binding binding nucleic acid binding protein binding ubiquitin-like protein ligase binding enzyme binding peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity RNA binding binding nucleic acid binding protein binding ubiquitin-like protein ligase binding enzyme binding passive transmembrane transporter activity channel activity transporter activity transmembrane transporter activity structural molecule activity	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis symbiont-mediated suppression of host signal transduction pathway symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated suppression of host toll-like receptor signaling pathway symbiont-mediated perturbation of host signal transduction pathway viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis symbiont-mediated suppression of host signal transduction pathway symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated suppression of host toll-like receptor signaling pathway symbiont-mediated perturbation of host signal transduction pathway modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction import into cell receptor-mediated endocytosis of virus by host cell transport viral life cycle establishment of localization vesicle-mediated transport localization symbiont entry into host cell clathrin-dependent endocytosis symbiont entry into host clathrin-dependent endocytosis of virus by host cell receptor-mediated endocytosis endocytosis endocytosis involved in viral entry into host cell viral gene expression viral translational frameshifting viral translation transmembrane transport monoatomic ion transmembrane transport monoatomic ion transport virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process receptor-mediated virion attachment to host cell entry receptor-mediated virion attachment to host cell	host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum other organism part host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell cytoplasm host cell part host intracellular region viral capsid icosahedral viral capsid virion component host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum other organism part host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell cytoplasm host cell part host intracellular region viral capsid icosahedral viral capsid virion component icosahedral viral capsid, spike host cell plasma membrane host cell membrane virion membrane T=4 icosahedral viral capsid host cell Golgi apparatus host cell nucleus viral membrane viral envelope

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
M, N, O, P	IPR002533	Alphavirus E3 spike glycoprotein	Domain
M, N, O, P	IPR038055	Flaviviral glycoprotein E, dimerisation domain	Homologous Superfamily
M, N, O, P	IPR014756	Immunoglobulin E-set	Homologous Superfamily
M, N, O, P	IPR042304	Alphavirus E2 glycoprotein, domain A	Homologous Superfamily
M, N, O, P	IPR036253	Flavivirus glycoprotein, central and dimerisation domain superfamily	Homologous Superfamily
M, N, O, P	IPR043504	Peptidase_S1_PA_chymotrypsin	Unknown
M, N, O, P	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
M, N, O, P	IPR042305	Alphavirus E2 glycoprotein, domain B	Homologous Superfamily
M, N, O, P	IPR042306	Alphavirus E2 glycoprotein, domain C	Homologous Superfamily
M, N, O, P	IPR000936	Alphavirus E2 glycoprotein	Family
M, N, O, P	IPR000930	Peptidase S3, togavirin	Domain
M, N, O, P	IPR002548	Alphavirus E1 glycoprotein	Domain
M, N, O, P	IPR000336	Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily	Homologous Superfamily
E, F, G, H, I E, F, G, H, I, J, K, L	IPR004827	Basic-leucine zipper domain	Domain
E, F, G, H, I E, F, G, H, I, J, K, L	IPR050946	AP-1 Transcription Factor bZIP	Family
E, F, G, H, I E, F, G, H, I, J, K, L	IPR046347	Basic-leucine zipper domain superfamily	Homologous Superfamily
A, B, C, D	IPR002533	Alphavirus E3 spike glycoprotein	Domain
A, B, C, D	IPR038055	Flaviviral glycoprotein E, dimerisation domain	Homologous Superfamily
A, B, C, D	IPR014756	Immunoglobulin E-set	Homologous Superfamily
A, B, C, D	IPR042304	Alphavirus E2 glycoprotein, domain A	Homologous Superfamily
A, B, C, D	IPR036253	Flavivirus glycoprotein, central and dimerisation domain superfamily	Homologous Superfamily
A, B, C, D	IPR043504	Peptidase_S1_PA_chymotrypsin	Unknown
A, B, C, D	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A, B, C, D	IPR042305	Alphavirus E2 glycoprotein, domain B	Homologous Superfamily
A, B, C, D	IPR042306	Alphavirus E2 glycoprotein, domain C	Homologous Superfamily
A, B, C, D	IPR000936	Alphavirus E2 glycoprotein	Family
A, B, C, D	IPR000930	Peptidase S3, togavirin	Domain
A, B, C, D	IPR002548	Alphavirus E1 glycoprotein	Domain
A, B, C, D	IPR000336	Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily	Homologous Superfamily

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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.