7QDH

SARS-CoV-2 S protein S:D614G mutant 1-up

PDB DOI: https://doi.org/10.2210/pdb7QDH/pdb
EM Map EMD-13919: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2, Tequatrovirus T4
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2021-11-27 Released: 2022-05-25
Deposition Author(s): Ginex, T., Marco-Marin, C., Wieczor, M., Mata, C.P., Krieger, J., Lopez-Redondo, M.L., Frances-Gomez, C., Ruiz-Rodriguez, P., Melero, R., Sanchez-Sorzano, C.O., Martinez, M., Gougeard, N., Forcada-Nadal, A., Zamora-Caballero, S., Gozalbo-Rovira, R., Sanz-Frasquet, C., Bravo, J., Rubio, V., Marina, A., Geller, R., Comas, I., Gil, C., Coscolla, M., Orozco, M., LLacer, J.L., Carazo, J.M.
Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities, H2020 Marie Curie Actions of the European Commission, European Research Council (ERC), Spanish National Research Council

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

The structural role of SARS-CoV-2 genetic background in the emergence and success of spike mutations: The case of the spike A222V mutation.

Ginex, T., Marco-Marin, C., Wieczor, M., Mata, C.P., Krieger, J., Ruiz-Rodriguez, P., Lopez-Redondo, M.L., Frances-Gomez, C., Melero, R., Sanchez-Sorzano, C.O., Martinez, M., Gougeard, N., Forcada-Nadal, A., Zamora-Caballero, S., Gozalbo-Rovira, R., Sanz-Frasquet, C., Arranz, R., Bravo, J., Rubio, V., Marina, A., Geller, R., Comas, I., Gil, C., Coscolla, M., Orozco, M., Llacer, J.L., Carazo, J.M.

(2022) PLoS Pathog 18: e1010631-e1010631

PubMed: 35816514 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1371/journal.ppat.1010631
Primary Citation of Related Structures:
7QDG, 7QDH

PubMed Abstract:
The S:A222V point mutation, within the G clade, was characteristic of the 20E (EU1) SARS-CoV-2 variant identified in Spain in early summer 2020. This mutation has since reappeared in the Delta subvariant AY.4.2, raising questions about its specific effect on viral infection. We report combined serological, functional, structural and computational studies characterizing the impact of this mutation. Our results reveal that S:A222V promotes an increased RBD opening and slightly increases ACE2 binding as compared to the parent S:D614G clade. Finally, S:A222V does not reduce sera neutralization capacity, suggesting it does not affect vaccine effectiveness.

Organizational Affiliation

Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), Madrid, Spain.

Macromolecule Content

Total Structure Weight: 426.26 kDa
Atom Count: 25,712
Modelled Residue Count: 3,219
Deposited Residue Count: 3,750
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,Fibritin	A, B, C	1,250	Severe acute respiratory syndrome coronavirus 2, Tequatrovirus T4 This entity is chimeric	Mutation(s): 0 Gene Names: S, 2, wac
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2 Go to UniProtKB: P0DTC2
Find proteins for P10104 (Enterobacteria phage T4) Explore P10104 Go to UniProtKB: P10104
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P0DTC2P10104
Glycosylation
Glycosylation Sites: 11	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 [auth E], E [auth G], F [auth I], G [auth J], H [auth K], D [auth E], E [auth G], F [auth I], G [auth J], H [auth K], I [auth L], J [auth M], K [auth N], L [auth O], M [auth P]	2		N-Glycosylation	Interactions Focus chain D [auth E] Focus chain E [auth G] Focus chain F [auth I] Focus chain G [auth J] Focus chain H [auth K] Focus chain I [auth L] Focus chain J [auth M] Focus chain K [auth N] Focus chain L [auth O] Focus chain M [auth P] Interactions & Density Focus chain D [auth E] Focus chain E [auth G] Focus chain F [auth I] Focus chain G [auth J] Focus chain H [auth K] Focus chain I [auth L] Focus chain J [auth M] Focus chain K [auth N] Focus chain L [auth O] Focus chain M [auth P]
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 B] SDF format, chain BA [auth B] SDF format, chain DA [auth B] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain KA [auth C] SDF format, chain N [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain CA [auth B] SDF format, chain EA [auth B] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain W [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain W [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain FA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain KA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain W [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] EA [auth B] AA [auth B], BA [auth B], CA [auth B], DA [auth B], EA [auth B], FA [auth C], GA [auth C], HA [auth C], IA [auth C], JA [auth C], KA [auth C], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth B], X [auth B], Y [auth B], Z [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	REFMAC

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-05-25

Deposition Author(s):

Sanchez-Sorzano, C.O.

Funding Organization	Location	Grant Number
Spanish Ministry of Science, Innovation, and Universities	Spain	PID2019-104757RB-I00
Spanish Ministry of Science, Innovation, and Universities	Spain	RTI2018-094399-A-I00
Spanish Ministry of Science, Innovation, and Universities	Spain	Grant SEV 2017-0712
H2020 Marie Curie Actions of the European Commission	Spain	MSCA IF 2020, Proposal: 101024130
European Research Council (ERC)	Spain	HighResCells, ERC - 2018 - SyG, Proposal: 810057
Spanish National Research Council	Spain	CSIC PTI Salud Global Proposal: 202080E110
European Research Council (ERC)	Spain	ERC CoG 101001038
Spanish Ministry of Science, Innovation, and Universities	Spain	SEJI/2019/011