6XF7 | pdb_00006xf7

SLP

• PDB DOI: https://doi.org/10.2210/pdb6XF7/pdb
• EM Map EMD-22165: EMDB EMDataResource

• Classification: VIRUS LIKE PARTICLE
• Organism(s): Mammalian orthoreovirus
• Mutation(s): No 


• Deposited: 2020-06-15 Released: 2020-09-23 
• Deposition Author(s): Sutton, G., Sun, D.P., Fu, X.F., Kotecha, A., Hecksel, G.W., Clare, D.K., Zhang, P., Stuart, D., Boyce, M.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom), Wellcome Trust, National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 6.60 Å
• Aggregation State: CELL 
• Reconstruction Method: SUBTOMOGRAM AVERAGING 

Literature

Assembly intermediates of orthoreovirus captured in the cell.

Sutton, G., Sun, D., Fu, X., Kotecha, A., Hecksel, C.W., Clare, D.K., Zhang, P., Stuart, D.I., Boyce, M.

(2020) Nat Commun 11: 4445-4445

• PubMed: 32895380 
• DOI: https://doi.org/10.1038/s41467-020-18243-9
• Primary Citation Related Structures: 
  6XF7, 6XF8, 6ZTS, 6ZTY, 6ZTZ


• PubMed Abstract: 
  

  Traditionally, molecular assembly pathways for viruses are inferred from high resolution structures of purified stable intermediates, low resolution images of cell sections and genetic approaches. Here, we directly visualise an unsuspected 'single shelled' intermediate for a mammalian orthoreovirus in cryo-preserved infected cells, by cryo-electron tomography of cellular lamellae. Particle classification and averaging yields structures to 5.6 Å resolution, sufficient to identify secondary structural elements and produce an atomic model of the intermediate, comprising 120 copies each of protein λ1 and σ2. This λ1 shell is 'collapsed' compared to the mature virions, with molecules pushed inwards at the icosahedral fivefolds by ~100 Å, reminiscent of the first assembly intermediate of certain prokaryotic dsRNA viruses. This supports the supposition that these viruses share a common ancestor, and suggests mechanisms for the assembly of viruses of the Reoviridae. Such methodology holds promise for dissecting the replication cycle of many viruses.

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Organizational Affiliation: 
• Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
Department of Structure Biology, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA.
Thermo Fisher Scientific, Achtseweg Noorg 5, 5651 GG, Eindhoven, The Netherlands.
Diamond Light Source Limited, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.
Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, USA.
Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK. [e-mail].
Department of Structure Biology, University of Pittsburgh, Pittsburgh, PA, 15260, USA. [e-mail].
Diamond Light Source Limited, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK. [e-mail].
Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK. [e-mail].
Diamond Light Source Limited, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK. [e-mail].
Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content 

• Total Structure Weight: 238.04 kDa 
• Atom Count: 16,454 
• Modeled Residue Count: 2,082 
• Deposited Residue Count: 2,118 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lambda 1 protein	A [auth B], B [auth C]	1,059	Mammalian orthoreovirus	Mutation(s): 0  EC: 3.6.4.13
UniProt
Find proteins for Q9WAB2 (Reovirus type 1 (strain Lang)) Explore Q9WAB2  Go to UniProtKB:  Q9WAB2

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 6.60 Å
• Aggregation State: CELL 
• Reconstruction Method: SUBTOMOGRAM AVERAGING 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	emClarity

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-09-23 
Deposition Author(s): Sutton, G., Sun, D.P., Fu, X.F., Kotecha, A., Hecksel, G.W., Clare, D.K., Zhang, P., Stuart, D., Boyce, M.

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Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/N00065X/1
Wellcome Trust	United Kingdom	206422/Z/17/Z
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)	United States	GM082251

Revision History  

• Version 1.0: 2020-09-23
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references