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TitleSARS-CoV-2 DMV nsp3-4 pore complex (full-pore)
AuthorsHuang YX, Zhong LJ, Zhang WX, Ni T
MethodSubtomogram Averaging(Reported Resolution 4.9 Å)PDB:8yax
EMDB image
Primary CitationMolecular architecture of coronavirus double-membrane vesicle pore complex. Huang Y, Wang T, Zhong L, Zhang W, Zhang Y, Yu X, Yuan S, Ni T Nature (2024) PubMed DOI show all entries for this citation
Funding SourceThe University Grants Committee, Research Grants Council (RGC)
StatusDepositedReleasedLast Update
REL2024-02-102024-06-192024-11-06

Name: SARS-CoV-2 nsp3-4 pore complexSpecimenType: particle MW: 0.547 MDa pH: 8

Component Typescomplex
Component Names

SARS-CoV-2 nsp3-4 pore complex

Molecular Typesprotein
Molecule Names
  • Non-structural protein 4
  • Papain-like protease nsp3
Sources

Severe acute respiratory syndrome... ncbi:2697049

Specimen Preparation Details: 150mM NaCl, 10mM Tris-HCl, 1mM EDTA

Imaging Details: The tilt-series were acquired using Thermofisher Krios equipped with a Falcon 4i camera and Selectris energy filter. A dose-symmetric scheme (group of 2) was used, with a tilt range of -51 degree to 51 degree (or -60 to 60) at 3 degree increments and an exposure dose of 3 e/A2 per image. The total dose was 105 or 123 e/A2.

Specimen Preparationvitrification
VitrificationFEI VITROBOT MARK IV
MicroscopeTFS KRIOS (300 kV)
DetectorTFS FALCON 4i (4k x 4k)
Electron Dose3 (e/sq. Å)
Imposed SymmetryC6
Reconstruction SoftwareRELION
Fitting ProtocolFLEXIBLE FIT
Fitting SoftwareUCSF Chimera
Fitting Source Models6wrh 8f2e

Details: local resolution map, processed by relion_postprocess

Map File Size96 Mbytes
Voxel Dimensions (Å)1.571 x 1.571 x 1.571
Map Dimensions (voxels) 288 x 288 x 288
Map Data Type IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Density StatisticsMin -2.361Max 2.945Avg 0Std 0.088
Recommended Contour Level0.1 (1.1 σ)
Mol*3DViewer Map Visual Analysis @ EMDB
Header Metadataemd-39107.xml emd-39107.cif.gz
Primary Mapemd_39107.map.gz (96 Mbytes)
Masksemd_39107_msk_1.map
Imagesemd_39107.png
FSC Curvesemd_39107_fsc.xml
Additional Maps
local refinement map focused on nsp3NTD domainemd_39107_additional_1.map.gz
Half Maps
emd_39107_half_map_2.map.gz
emd_39107_half_map_1.map.gz
Fitted PDB8yax


Current: files.wwpdb.org (USA)

wwPDB Map Validation Reportemd_39107_full_validation.pdf.gz
wwPDB Model Validation Report8yax_full_validation.pdf.gz
View EMDB map entry EMD-39107: EMDB PDBj 3Dbionotes
View associated model PDB 8yax: RCSB-PDB PDBe PDBj