7MSX | pdb_00007msx

SARS-CoV-2 Nsp2

PDB DOI: https://doi.org/10.2210/pdb7MSX/pdb
EM Map EMD-23971: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-05-12 Released: 2021-05-26
Deposition Author(s): QCRG Structural Biology Consortium
Funding Organization(s): DARPA, FastGrants, Laboratory for Genomics Research, Quantitative Biosciences Institute

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.15 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 7MSX

This is version 1.1 of the entry. See complete history.

Literature

CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes.

QCRG Structural Biology Consortium

To be published.

Macromolecule Content

Total Structure Weight: 70.79 kDa
Atom Count: 3,706
Modeled Residue Count: 473
Deposited Residue Count: 638
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 2	A	638	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: rep, 1a-1b
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1 Go to UniProtKB: P0DTD1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.15 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Rosetta	2020.08.61146
MODEL REFINEMENT	ISOLDE	1.0
RECONSTRUCTION	RELION	3.0.8

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-05-26

Deposition Author(s):

QCRG Structural Biology Consortium

Funding Organization	Location	Grant Number
DARPA	United States	HR0011-19-2-0020
FastGrants	United States	COVID19 grant
Laboratory for Genomics Research	United States	Excellence in Research Award COVID19
Quantitative Biosciences Institute	United States	--

Revision History (Full details and data files)

Version 1.0: 2021-05-26
Type: Initial release
Version 1.1: 2024-05-29
Changes: Data collection, Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.