7BNM

Closed conformation of D614G SARS-CoV-2 spike protein

PDB DOI: https://doi.org/10.2210/pdb7BNM/pdb
EM Map EMD-12229: EMDB EMDataResource

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

Deposited: 2021-01-22 Released: 2021-02-03
Deposition Author(s): Benton, D.J., Wrobel, A.G., Rosenthal, P.B., Gamblin, S.J.
Funding Organization(s): The Francis Crick Institute

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

The effect of the D614G substitution on the structure of the spike glycoprotein of SARS-CoV-2.

Benton, D.J., Wrobel, A.G., Roustan, C., Borg, A., Xu, P., Martin, S.R., Rosenthal, P.B., Skehel, J.J., Gamblin, S.J.

(2021) Proc Natl Acad Sci U S A 118

PubMed: 33579792 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1073/pnas.2022586118
Primary Citation of Related Structures:
7BNM, 7BNN, 7BNO

PubMed Abstract:
The majority of currently circulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viruses have mutant spike glycoproteins that contain the D614G substitution. Several studies have suggested that spikes with this substitution are associated with higher virus infectivity. We use cryo-electron microscopy to compare G614 and D614 spikes and show that the G614 mutant spike adopts a range of more open conformations that may facilitate binding to the SARS-CoV-2 receptor, ACE2, and the subsequent structural rearrangements required for viral membrane fusion.

Organizational Affiliation

Structural Biology of Disease Processes Laboratory, Francis Crick Institute, London NW1 1AT, United Kingdom; Donald.Benton@crick.ac.uk John.Skehel@crick.ac.uk Antoni.Wrobel@crick.ac.uk Steve.Gamblin@crick.ac.uk.

Macromolecule Content

Total Structure Weight: 403.04 kDa
Atom Count: 25,971
Modelled Residue Count: 3,207
Deposited Residue Count: 3,531
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,177	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2 Go to UniProtKB: P0DTC2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTC2
Glycosylation
Glycosylation Sites: 16	Glycosylation Focus chain A Focus chain B Focus chain C	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, E [auth N], F [auth R], G [auth T], H [auth V], D, E [auth N], F [auth R], G [auth T], H [auth V], I [auth Y], J [auth i], K [auth m], L [auth o], M [auth q], N [auth t], O [auth 3], P [auth 7], Q [auth 9], R [auth BA]	2		N-Glycosylation	Interactions Focus chain D Focus chain E [auth N] Focus chain F [auth R] Focus chain G [auth T] Focus chain H [auth V] Focus chain I [auth Y] Focus chain J [auth i] Focus chain K [auth m] Focus chain L [auth o] Focus chain M [auth q] Focus chain N [auth t] Focus chain O [auth 3] Focus chain P [auth 7] Focus chain Q [auth 9] Focus chain R [auth BA] Interactions & Density Focus chain D Focus chain E [auth N] Focus chain F [auth R] Focus chain G [auth T] Focus chain H [auth V] Focus chain I [auth Y] Focus chain J [auth i] Focus chain K [auth m] Focus chain L [auth o] Focus chain M [auth q] Focus chain N [auth t] Focus chain O [auth 3] Focus chain P [auth 7] Focus chain Q [auth 9] Focus chain R [auth BA]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain CA [auth A] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain JA [auth B] SDF format, chain KA [auth B] SDF format, chain LA [auth B] SDF format, chain MA [auth B] SDF format, chain NA [auth B] SDF format, chain OA [auth C] SDF format, chain PA [auth C] SDF format, chain QA [auth C] SDF format, chain RA [auth C] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain TA [auth C] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain VA [auth C] SDF format, chain W [auth A] SDF format, chain WA [auth C] SDF format, chain X [auth A] SDF format, chain XA [auth C] SDF format, chain Y [auth A] SDF format, chain YA [auth C] SDF format, chain Z [auth A] SDF format, chain IA [auth B] SDF format, chain SA [auth C] SDF format, chain UA [auth C] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain OA [auth C] MOL2 format, chain PA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain RA [auth C] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth C] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth C] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth C] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth C] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth C] MOL2 format, chain Z [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain SA [auth C] MOL2 format, chain UA [auth C] mmCIF format, chain AA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain KA [auth B] mmCIF format, chain LA [auth B] mmCIF format, chain MA [auth B] mmCIF format, chain NA [auth B] mmCIF format, chain OA [auth C] mmCIF format, chain PA [auth C] mmCIF format, chain QA [auth C] mmCIF format, chain RA [auth C] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth C] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain VA [auth C] mmCIF format, chain W [auth A] mmCIF format, chain WA [auth C] mmCIF format, chain X [auth A] mmCIF format, chain XA [auth C] mmCIF format, chain Y [auth A] mmCIF format, chain YA [auth C] mmCIF format, chain Z [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain SA [auth C] mmCIF format, chain UA [auth C]	AA [auth A] BA [auth A] CA [auth A] DA [auth B] EA [auth B] AA [auth A], BA [auth A], CA [auth A], DA [auth B], EA [auth B], FA [auth B], GA [auth B], HA [auth B], IA [auth B], JA [auth B], KA [auth B], LA [auth B], MA [auth B], NA [auth B], OA [auth C], PA [auth C], QA [auth C], RA [auth C], S [auth A], SA [auth C], T [auth A], TA [auth C], U [auth A], UA [auth C], V [auth A], VA [auth C], W [auth A], WA [auth C], X [auth A], XA [auth C], Y [auth A], YA [auth C], Z [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain S [auth A] Focus chain SA [auth C] Focus chain T [auth A] Focus chain TA [auth C] Focus chain U [auth A] Focus chain UA [auth C] Focus chain V [auth A] Focus chain VA [auth C] Focus chain W [auth A] Focus chain WA [auth C] Focus chain X [auth A] Focus chain XA [auth C] Focus chain Y [auth A] Focus chain YA [auth C] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain S [auth A] Focus chain SA [auth C] Focus chain T [auth A] Focus chain TA [auth C] Focus chain U [auth A] Focus chain UA [auth C] Focus chain V [auth A] Focus chain VA [auth C] Focus chain W [auth A] Focus chain WA [auth C] Focus chain X [auth A] Focus chain XA [auth C] Focus chain Y [auth A] Focus chain YA [auth C] Focus chain Z [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-02-03

Deposition Author(s):

Funding Organization	Location	Grant Number
The Francis Crick Institute	United Kingdom	FC001078
The Francis Crick Institute	United Kingdom	FC001143

Revision History (Full details and data files)

Version 1.0: 2021-02-03
Type: Initial release
Version 1.1: 2021-02-24
Changes: Database references
Version 1.2: 2021-03-10
Changes: Database references, Source and taxonomy, Structure summary
Version 1.3: 2024-11-06
Changes: Data collection, Database references, Structure summary