8YB7

SARS-CoV-2 DMV nsp3-4 pore complex (consensus-pore, C3 symmetry)

• PDB DOI: https://doi.org/10.2210/pdb8YB7/pdb
• EM Map EMD-39112: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-02-12 Released: 2024-06-19 
• Deposition Author(s): Huang, Y.X., Zhong, L.J., Zhang, W.X., Ni, T.
• Funding Organization(s): The University Grants Committee, Research Grants Council (RGC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SUBTOMOGRAM AVERAGING 

Literature

Molecular Architecture of Coronavirus Double Membrane Vesicle Pore Complex

Huang, Y.X., Ni, T.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Hetero 24-mer - A12B12 Pseudo Symmetry: Cyclic - C6  (Explore in 3D)
Pseudo Stoichiometry: Hetero 24-mer - A6B6C6D6 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 1,094.8 kDa 
• Atom Count: 24,327 
• Modelled Residue Count: 3,079 
• Deposited Residue Count: 9,780 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Papain-like protease nsp3	A, B, E, F	1,945	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a EC: 3.4.19.12
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 4	C, D, G, H	500	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SUBTOMOGRAM AVERAGING 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	v4
MODEL REFINEMENT	PHENIX	1.21_5207

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-19 
Deposition Author(s): Huang, Y.X., Zhong, L.J., Zhang, W.X., Ni, T.

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Funding Organization	Location	Grant Number
The University Grants Committee, Research Grants Council (RGC)	Hong Kong	--

Revision History  

• Version 1.0: 2024-06-19
  Type: Initial release