8BP8

SPA of Trypsin untreated Rotavirus TLP spike


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Characterization of the rotavirus assembly pathway in situ using cryoelectron tomography.

Shah, P.N.M.Gilchrist, J.B.Forsberg, B.O.Burt, A.Howe, A.Mosalaganti, S.Wan, W.Radecke, J.Chaban, Y.Sutton, G.Stuart, D.I.Boyce, M.

(2023) Cell Host Microbe 31: 604-615.e4

  • DOI: https://doi.org/10.1016/j.chom.2023.03.004
  • Primary Citation of Related Structures:  
    8BP8, 8CO6, 8COA

  • PubMed Abstract: 

    Rotavirus assembly is a complex process that involves the stepwise acquisition of protein layers in distinct intracellular locations to form the fully assembled particle. Understanding and visualization of the assembly process has been hampered by the inaccessibility of unstable intermediates. We characterize the assembly pathway of group A rotaviruses observed in situ within cryo-preserved infected cells through the use of cryoelectron tomography of cellular lamellae. Our findings demonstrate that the viral polymerase VP1 recruits viral genomes during particle assembly, as revealed by infecting with a conditionally lethal mutant. Additionally, pharmacological inhibition to arrest the transiently enveloped stage uncovered a unique conformation of the VP4 spike. Subtomogram averaging provided atomic models of four intermediate states, including a pre-packaging single-layered intermediate, the double-layered particle, the transiently enveloped double-layered particle, and the fully assembled triple-layered virus particle. In summary, these complementary approaches enable us to elucidate the discrete steps involved in forming an intracellular rotavirus particle.


  • Organizational Affiliation

    Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK; CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Headington, Oxford, UK. Electronic address: pranav.shah@strubi.ox.ac.uk.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Outer capsid protein VP4
A, B, C
776Rotavirus AMutation(s): 0 
UniProt
Find proteins for A0A1Q2TSK9 (Rotavirus A)
Explore A0A1Q2TSK9 
Go to UniProtKB:  A0A1Q2TSK9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1Q2TSK9
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Outer capsid glycoprotein VP7
D, E, F, G, H
D, E, F, G, H, I, J, K, L, M, N, O, P
326Rotavirus AMutation(s): 0 
UniProt
Find proteins for A0A1Q2TSM6 (Rotavirus A)
Explore A0A1Q2TSM6 
Go to UniProtKB:  A0A1Q2TSM6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1Q2TSM6
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Intermediate capsid protein VP6397Rotavirus AMutation(s): 0 
UniProt
Find proteins for A2T3S6 (Rotavirus A)
Explore A2T3S6 
Go to UniProtKB:  A2T3S6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA2T3S6
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Inner capsid protein VP2DA [auth q],
EA [auth r]
882Rotavirus AMutation(s): 0 
UniProt
Find proteins for A2T3R1 (Rotavirus A)
Explore A2T3R1 
Go to UniProtKB:  A2T3R1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA2T3R1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
SB [auth e],
TB [auth g],
UB [auth j],
VB [auth m],
WB [auth p]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
AB [auth K]
BB [auth K]
CB [auth K]
DB [auth L]
EB [auth L]
AB [auth K],
BB [auth K],
CB [auth K],
DB [auth L],
EB [auth L],
FA [auth D],
FB [auth L],
GA [auth D],
GB [auth M],
HA [auth D],
HB [auth M],
IA [auth E],
IB [auth M],
JA [auth E],
JB [auth N],
KA [auth E],
KB [auth N],
LA [auth F],
LB [auth N],
MA [auth F],
MB [auth O],
NA [auth F],
NB [auth O],
OA [auth G],
OB [auth O],
PA [auth G],
PB [auth P],
QA [auth G],
QB [auth P],
RA [auth H],
RB [auth P],
SA [auth H],
TA [auth H],
UA [auth I],
VA [auth I],
WA [auth I],
XA [auth J],
YA [auth J],
ZA [auth J]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION4.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMR/N00065X/1
CAMS Innovation Fund for Medical Sciences (CIFMS)United Kingdom2018-I2M-2-002
Wellcome TrustUnited Kingdom03141/Z/16/Z
Wellcome TrustUnited Kingdom060208/Z/00/Z
Wellcome TrustUnited Kingdom093305/Z/10/Z

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-05
    Type: Initial release
  • Version 1.1: 2023-04-12
    Changes: Database references
  • Version 1.2: 2023-04-26
    Changes: Database references