3CJI | pdb_00003cji

Structure of Seneca Valley Virus-001

PDB DOI: https://doi.org/10.2210/pdb3CJI/pdb

Classification: VIRUS
Organism(s): Senecavirus A
Mutation(s): No

Deposited: 2008-03-13 Released: 2008-12-16
Deposition Author(s): Venkataraman, S., Reddy, V.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.260 (Depositor), 0.255 (DCC)
R-Value Work:
0.258 (Depositor), 0.253 (DCC)
R-Value Observed:
0.258 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structure of Seneca Valley Virus-001: an oncolytic picornavirus representing a new genus

Venkataraman, S., Reddy, S.P., Loo, J., Idamakanti, N., Hallenbeck, P.L., Reddy, V.S.

(2008) Structure 16: 1555-1561

PubMed: 18940610 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.str.2008.07.013
Primary Citation Related Structures:
3CJI

PubMed Abstract:
The crystal structure of Seneca Valley Virus-001 (SVV-001), the representative member of a new genus, Senecavirus, is reported at 2.3A resolution. SVV-001 is the first naturally occurring nonpathogenic picornavirus shown to mediate selective cytotoxicity towards tumor cells with neuroendocrine cancer features. The nonsegmented (+) ssRNA genome of SVV-001 shares closest sequence similarity with the genomes of the members of Cardiovirus. The overall tertiary structure of VP1-VP4 subunits is conserved with the exception of loops, especially those of VP1 that show large deviations relative to the members of the cardioviruses. The surface loops of VP1 and VP2 are predicted to mediate cell tropism of SVV-001. In addition, the organization of the packaged nucleic acid density indicates that certain regions of VP2 and VP4 interact closely with the packaged nucleic acid.

Organizational Affiliation

Department of Molecular Biology, TPC-6, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

Macromolecule Content

Total Structure Weight: 94.75 kDa
Atom Count: 6,521
Modeled Residue Count: 799
Deposited Residue Count: 857
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyprotein	A	263	Senecavirus A	Mutation(s): 0
UniProt
Find proteins for Q155Z9 (Seneca Valley virus (isolate -/United States/SSV-001/2002)) Explore Q155Z9 Go to UniProtKB: Q155Z9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q155Z9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyprotein	B	239	Senecavirus A	Mutation(s): 0
UniProt
Find proteins for Q155Z9 (Seneca Valley virus (isolate -/United States/SSV-001/2002)) Explore Q155Z9 Go to UniProtKB: Q155Z9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q155Z9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyprotein	C	284	Senecavirus A	Mutation(s): 0
UniProt
Find proteins for Q155Z9 (Seneca Valley virus (isolate -/United States/SSV-001/2002)) Explore Q155Z9 Go to UniProtKB: Q155Z9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q155Z9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyprotein	D	71	Senecavirus A	Mutation(s): 0
UniProt
Find proteins for Q155Z9 (Seneca Valley virus (isolate -/United States/SSV-001/2002)) Explore Q155Z9 Go to UniProtKB: Q155Z9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q155Z9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.260 (Depositor), 0.255 (DCC)
R-Value Work: 0.258 (Depositor), 0.253 (DCC)
R-Value Observed: 0.258 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 311.51	α = 90
b = 311.51	β = 90
c = 1526.401	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-12-16

Deposition Author(s):

Venkataraman, S.

Reddy, V.S.

Revision History (Full details and data files)

Version 1.0: 2008-12-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description