8FJK | pdb_00008fjk

Golden Shiner Reovirus Core Polar Vertex

PDB DOI: https://doi.org/10.2210/pdb8FJK/pdb
NAKB: 8FJK
EM Map EMD-29243: EMDB EMDataResource

Classification: VIRUS
Organism(s): Golden shiner reovirus
Mutation(s): No

Deposited: 2022-12-19 Released: 2023-03-22
Deposition Author(s): Stevens, A.S., Zhou, Z.H.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Asymmetric reconstruction of the aquareovirus core at near-atomic resolution and mechanism of transcription initiation.

Stevens, A., Cui, Y., Shivakoti, S., Zhou, Z.H.

(2023) Protein Cell 14: 544-548

PubMed: 36856784 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1093/procel/pwad002
Primary Citation Related Structures:
8FJK, 8FJL

Organizational Affiliation

Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA ), 609 Charles E Young Dr E, Los Angeles, CA 90095, USA.

Macromolecule Content

Total Structure Weight: 2,815.02 kDa
Atom Count: 193,908
Modeled Residue Count: 24,392
Deposited Residue Count: 24,912
Unique protein chains: 6
Unique nucleic acid chains: 6

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-directed RNA polymerase VP2	A	1,273	Golden shiner reovirus	Mutation(s): 0 EC: 2.7.7.48
UniProt
Find proteins for Q8JU61 (Aquareovirus C (isolate Golden shiner/USA/GSRV/1977)) Explore Q8JU61 Go to UniProtKB: Q8JU61
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8JU61
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Microtubule-associated protein VP5	B	718	Golden shiner reovirus	Mutation(s): 0
UniProt
Find proteins for Q8JU58 (Aquareovirus C (isolate Golden shiner/USA/GSRV/1977)) Explore Q8JU58 Go to UniProtKB: Q8JU58
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8JU58
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Major inner capsid protein VP3	C, D, E, F, G C, D, E, F, G, H, I, J, K, L	1,138	Golden shiner reovirus	Mutation(s): 0 EC: 3.6.4.13
UniProt
Find proteins for Q8JU60 (Aquareovirus C (isolate Golden shiner/USA/GSRV/1977)) Explore Q8JU60 Go to UniProtKB: Q8JU60
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8JU60
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Major inner capsid protein VP3	M, N, OA [auth k], PA [auth l], QA [auth m]	94	Golden shiner reovirus	Mutation(s): 0 EC: 3.6.4.13
UniProt
Find proteins for Q8JU60 (Aquareovirus C (isolate Golden shiner/USA/GSRV/1977)) Explore Q8JU60 Go to UniProtKB: Q8JU60
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8JU60
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Clamp protein VP6	AA [auth b] IA [auth d] JA [auth e] LA [auth g] MA [auth h] AA [auth b], IA [auth d], JA [auth e], LA [auth g], MA [auth h], O [auth V], P [auth W], Q [auth X], RA [auth n], T [auth a]	411	Golden shiner reovirus	Mutation(s): 0
UniProt
Find proteins for Q8JU54 (Aquareovirus C (isolate Golden shiner/USA/GSRV/1977)) Explore Q8JU54 Go to UniProtKB: Q8JU54
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8JU54
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer capsid protein VP1	HA [auth c], KA [auth f], NA [auth i], R [auth Y], S [auth Z]	1,297	Golden shiner reovirus	Mutation(s): 0 EC: 2.7.7.50 (PDB Primary Data), 2.1.1.56 (PDB Primary Data)
UniProt
Find proteins for Q8JU62 (Aquareovirus C (isolate Golden shiner/USA/GSRV/1977)) Explore Q8JU62 Go to UniProtKB: Q8JU62
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8JU62
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 7
RNA (52-MER)	BA [auth b1], U [auth a1]	52	Golden shiner reovirus
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 8
RNA (60-MER)	CA [auth b2], V [auth a2]	60	Golden shiner reovirus
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 9
RNA (40-MER)	DA [auth b3], W [auth a3]	40	Golden shiner reovirus
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 10
RNA (18-MER)	EA [auth b4], X [auth a4]	18	Golden shiner reovirus
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 11
RNA (38-MER)	FA [auth b5], Y [auth a5]	38	Golden shiner reovirus
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 12
RNA (30-MER)	GA [auth b6], Z [auth a6]	30	Golden shiner reovirus
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain VA [auth K] SDF format, chain UA [auth I] SDF format, chain TA [auth G] SDF format, chain SA [auth E] MOL2 format, chain VA [auth K] MOL2 format, chain UA [auth I] MOL2 format, chain TA [auth G] MOL2 format, chain SA [auth E] mmCIF format, chain VA [auth K] mmCIF format, chain UA [auth I] mmCIF format, chain TA [auth G] mmCIF format, chain SA [auth E]	SA [auth E], TA [auth G], UA [auth I], VA [auth K]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain SA [auth E] Focus chain TA [auth G] Focus chain UA [auth I] Focus chain VA [auth K] Interactions & Density Focus chain SA [auth E] Focus chain TA [auth G] Focus chain UA [auth I] Focus chain VA [auth K]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-03-22

Deposition Author(s):

Stevens, A.S.

Zhou, Z.H.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U24GM116792
National Science Foundation (NSF, United States)	United States	DBI-1338135
National Science Foundation (NSF, United States)	United States	DMR-1548924
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI007323
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U24GM116792
National Institutes of Health/Office of the Director	United States	1S10OD018111

Revision History (Full details and data files)

Version 1.0: 2023-03-22
Type: Initial release
Version 1.1: 2023-04-05
Changes: Database references
Version 1.2: 2023-07-12
Changes: Database references
Version 1.3: 2024-06-19
Changes: Data collection

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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.

8FJK | pdb_00008fjk

Golden Shiner Reovirus Core Polar Vertex

Literature

Asymmetric reconstruction of the aquareovirus core at near-atomic resolution and mechanism of transcription initiation.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

Sequence Annotations

Entity ID: 8

Sequence Annotations

Entity ID: 9

Sequence Annotations

Entity ID: 10

Sequence Annotations

Entity ID: 11

Sequence Annotations

Entity ID: 12

Sequence Annotations

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)