3L28 | pdb_00003l28

Crystal structure of Zaire Ebola VP35 interferon inhibitory domain K339A mutant

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
A	d3l28a_	Alpha and beta proteins (a+b)	Filoviridae VP35-like	Filoviridae VP35-like	Filoviridae VP35	Filoviridae VP35	ZEBOV (Ebola virus - Mayinga, Zaire, 1976 ) [TaxId: 128952 ],	SCOPe (2.08)
B	d3l28b_	Alpha and beta proteins (a+b)	Filoviridae VP35-like	Filoviridae VP35-like	Filoviridae VP35	Filoviridae VP35	ZEBOV (Ebola virus - Mayinga, Zaire, 1976 ) [TaxId: 128952 ],	SCOPe (2.08)
C	d3l28c_	Alpha and beta proteins (a+b)	Filoviridae VP35-like	Filoviridae VP35-like	Filoviridae VP35	Filoviridae VP35	ZEBOV (Ebola virus - Mayinga, Zaire, 1976 ) [TaxId: 128952 ],	SCOPe (2.08)
D	d3l28d_	Alpha and beta proteins (a+b)	Filoviridae VP35-like	Filoviridae VP35-like	Filoviridae VP35	Filoviridae VP35	ZEBOV (Ebola virus - Mayinga, Zaire, 1976 ) [TaxId: 128952 ],	SCOPe (2.08)
E	d3l28e_	Alpha and beta proteins (a+b)	Filoviridae VP35-like	Filoviridae VP35-like	Filoviridae VP35	Filoviridae VP35	ZEBOV (Ebola virus - Mayinga, Zaire, 1976 ) [TaxId: 128952 ],	SCOPe (2.08)
F	d3l28f_	Alpha and beta proteins (a+b)	Filoviridae VP35-like	Filoviridae VP35-like	Filoviridae VP35	Filoviridae VP35	ZEBOV (Ebola virus - Mayinga, Zaire, 1976 ) [TaxId: 128952 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Ebola VP35 IID-like	8092332	3002590	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ebola VP35 IID-like	8092332	3002590	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ebola VP35 IID-like	8092332	3002590	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ebola VP35 IID-like	8092332	3002590	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ebola VP35 IID-like	8092332	3002590	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ebola VP35 IID-like	8092332	3002590	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	Trypsin	e3l28A1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Trypsin	ECOD (v294.1)
B	Trypsin	e3l28B1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Trypsin	ECOD (v294.1)
C	Trypsin	e3l28C1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Trypsin	ECOD (v294.1)
D	Trypsin	e3l28D1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Trypsin	ECOD (v294.1)
E	Trypsin	e3l28E1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Trypsin	ECOD (v294.1)
F	Trypsin	e3l28F1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Trypsin	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.8.950	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
A	2.10.10.70	Mainly Beta	Ribbon	Seminal Fluid Protein PDC-109 (Domain B)	Filoviridae VP35, C-terminal inhibitory domain, beta-sheet subdomain	CATH (4.3.0)
B	1.10.8.950	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
B	2.10.10.70	Mainly Beta	Ribbon	Seminal Fluid Protein PDC-109 (Domain B)	Filoviridae VP35, C-terminal inhibitory domain, beta-sheet subdomain	CATH (4.3.0)
C	1.10.8.950	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
C	2.10.10.70	Mainly Beta	Ribbon	Seminal Fluid Protein PDC-109 (Domain B)	Filoviridae VP35, C-terminal inhibitory domain, beta-sheet subdomain	CATH (4.3.0)
D	1.10.8.950	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
D	2.10.10.70	Mainly Beta	Ribbon	Seminal Fluid Protein PDC-109 (Domain B)	Filoviridae VP35, C-terminal inhibitory domain, beta-sheet subdomain	CATH (4.3.0)
E	1.10.8.950	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
E	2.10.10.70	Mainly Beta	Ribbon	Seminal Fluid Protein PDC-109 (Domain B)	Filoviridae VP35, C-terminal inhibitory domain, beta-sheet subdomain	CATH (4.3.0)
F	1.10.8.950	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
F	2.10.10.70	Mainly Beta	Ribbon	Seminal Fluid Protein PDC-109 (Domain B)	Filoviridae VP35, C-terminal inhibitory domain, beta-sheet subdomain	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	Polymerase cofactor VP35	molecular sequestering activity RNA binding binding nucleic acid binding	viral gene expression viral process viral transcription regulation of protein sumoylation regulation of cellular process regulation of protein modification process positive regulation of protein metabolic process peptidyl-lysine modification positive regulation of biological process positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process peptidyl-amino acid modification viral gene expression viral process viral transcription regulation of protein sumoylation regulation of cellular process regulation of protein modification process positive regulation of protein metabolic process peptidyl-lysine modification positive regulation of biological process positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process peptidyl-amino acid modification positive regulation of macromolecule metabolic process protein metabolic process regulation of protein modification by small protein conjugation or removal protein modification process positive regulation of cellular process positive regulation of protein modification by small protein conjugation or removal regulation of biological process regulation of post-translational protein modification regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process protein sumoylation macromolecule modification metabolic process cellular process macromolecule metabolic process positive regulation of protein sumoylation post-translational protein modification regulation of metabolic process protein modification by small protein conjugation protein modification by small protein conjugation or removal symbiont-mediated perturbation of host defense response symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated suppression of host pathogen-associated molecular pattern receptor signaling pathway symbiont-mediated perturbation of host immune response biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response symbiont-mediated perturbation of host process symbiont-mediated perturbation of host innate immune response symbiont-mediated perturbation of host signal transduction pathway modulation of process of another organism symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity negative regulation of biological process positive regulation of macromolecule biosynthetic process regulation of miRNA-mediated gene silencing post-transcriptional regulation of gene expression negative regulation of post-transcriptional gene silencing by regulatory ncRNA regulation of gene silencing by regulatory ncRNA positive regulation of biosynthetic process negative regulation of cellular process regulation of post-transcriptional gene silencing by regulatory ncRNA negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of metabolic process negative regulation of gene silencing by regulatory ncRNA gene expression macromolecule biosynthetic process regulatory ncRNA-mediated post-transcriptional gene silencing regulatory ncRNA-mediated gene silencing miRNA-mediated post-transcriptional gene silencing regulation of gene expression negative regulation of gene expression biosynthetic process regulation of post-transcriptional gene silencing negative regulation of biosynthetic process positive regulation of gene expression negative regulation of miRNA-mediated gene silencing negative regulation of macromolecule biosynthetic process post-transcriptional gene silencing regulation of macromolecule biosynthetic process negative regulation of post-transcriptional gene silencing symbiont-mediated suppression of host RNAi-mediated antiviral immune response symbiont-mediated suppression of host toll-like receptor signaling pathway viral genome replication viral life cycle response to stimulus response to other organism symbiont-mediated perturbation of host defenses symbiont-mediated suppression of host PKR/eIFalpha signaling symbiont-mediated response to host defenses response to external stimulus response to biotic stimulus symbiont-mediated suppression of host-directed shutoff of host translation symbiont-mediated suppression of host defenses response to host response to external biotic stimulus symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II symbiont-mediated suppression of host antigen processing and presentation symbiont-mediated suppression of host adaptive immune response symbiont-mediated suppression of host interferon-mediated signaling pathway symbiont-mediated suppression of host type I interferon-mediated signaling pathway symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity	viral nucleocapsid viral capsid virion component host cellular component host intracellular part cellular anatomical structure host cell cytoplasm host cell part host intracellular region other organism part

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR031163	Filoviruses VP35 interferon inhibitory domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR002953	Filoviridae VP35 protein	Family
A, B, C, D, E A, B, C, D, E, F	IPR043061	Filoviruses VP35 interferon inhibitory domain, beta-sheet subdomain	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR043060	Filoviruses VP35 interferon inhibitory domain, helical subdomain	Homologous Superfamily

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.