6O3V | pdb_00006o3v

Crystal structure for RVA-VP3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 
    0.264 (Depositor), 0.264 (DCC) 
  • R-Value Work: 
    0.229 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 
    0.231 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6O3V

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

2.7 angstrom cryo-EM structure of rotavirus core protein VP3, a unique capping machine with a helicase activity.

Kumar, D.Yu, X.Crawford, S.E.Moreno, R.Jakana, J.Sankaran, B.Anish, R.Kaundal, S.Hu, L.Estes, M.K.Wang, Z.Prasad, B.V.V.

(2020) Sci Adv 6: eaay6410-eaay6410

  • DOI: https://doi.org/10.1126/sciadv.aay6410
  • Primary Citation Related Structures: 
    6O3V

  • PubMed Abstract: 

    In many viruses, including rotavirus (RV), the major pathogen of infantile gastroenteritis, capping of viral messenger RNAs is a pivotal step for efficient translation of the viral genome. In RV, VP3 caps the nascent transcripts synthesized from the genomic dsRNA segments by the RV polymerase VP1 within the particle core. Here, from cryo-electron microscopy, x-ray crystallography, and biochemical analyses, we show that VP3 forms a stable tetrameric assembly with each subunit having a modular domain organization, which uniquely integrates five distinct enzymatic steps required for capping the transcripts. In addition to the previously known guanylyl- and methyltransferase activities, we show that VP3 exhibits hitherto unsuspected RNA triphosphatase activity necessary for initiating transcript capping and RNA helicase activity likely required for separating the RNA duplex formed transiently during endogenous transcription. From our studies, we propose a new mechanism for how VP3 inside the virion core caps the nascent transcripts exiting from the polymerase.


  • Organizational Affiliation
    • Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.

Macromolecule Content 

  • Total Structure Weight: 294.68 kDa 
  • Atom Count: 20,730 
  • Modeled Residue Count: 2,489 
  • Deposited Residue Count: 2,505 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein VP3
A, B, C
835Rotavirus AMutation(s): 0 
Gene Names: VP3
EC: 2.7.7.50 (UniProt), 2.1.1.56 (UniProt), 3.1.4 (UniProt)
UniProt
Find proteins for Q1WK45 (Rotavirus A)
Explore Q1WK45 
Go to UniProtKB:  Q1WK45
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1WK45
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5GP

Query on 5GP



Download:Ideal Coordinates CCD File
D [auth A],
G [auth B],
J [auth C]
GUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O8 P
RQFCJASXJCIDSX-UUOKFMHZSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
F [auth A],
I [auth B],
L [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO

Query on EDO



Download:Ideal Coordinates CCD File
E [auth A],
H [auth B],
K [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free:  0.264 (Depositor), 0.264 (DCC) 
  • R-Value Work:  0.229 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 0.231 (Depositor) 
Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 236.706α = 90
b = 236.706β = 90
c = 349.3γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI36040
Welch FoundationUnited StatesQ1279

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-04
    Type: Initial release
  • Version 1.1: 2020-09-16
    Changes: Database references
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references