6ZP5 | pdb_00006zp5

SARS-CoV-2 spike in prefusion state (flexibility analysis, 1-up closed conformation)

PDB DOI: https://doi.org/10.2210/pdb6ZP5/pdb
EM Map EMD-11336: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2020-07-08 Released: 2020-07-29
Deposition Author(s): Martinez, M., Marabini, R., Carazo, J.M.
Funding Organization(s): Spanish National Research Council, Spanish Ministry of Science, Innovation, and Universities, European Research Council (ERC), National Institutes of Health/National Library of Medicine (NIH/NLM)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Literature

Continuous flexibility analysis of SARS-CoV-2 spike prefusion structures.

Melero, R., Sorzano, C.O.S., Foster, B., Vilas, J.L., Martinez, M., Marabini, R., Ramirez-Aportela, E., Sanchez-Garcia, R., Herreros, D., Del Cano, L., Losana, P., Fonseca-Reyna, Y.C., Conesa, P., Wrapp, D., Chacon, P., McLellan, J.S., Tagare, H.D., Carazo, J.M.

(2020) IUCrJ 7: 1059-1069

PubMed: 33063791 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S2052252520012725
Primary Citation Related Structures:
6ZOW, 6ZP5, 6ZP7

PubMed Abstract:
Using a new consensus-based image-processing approach together with principal component analysis, the flexibility and conformational dynamics of the SARS-CoV-2 spike in the prefusion state have been analysed. These studies revealed concerted motions involving the receptor-binding domain (RBD), N-terminal domain, and subdomains 1 and 2 around the previously characterized 1-RBD-up state, which have been modeled as elastic deformations. It is shown that in this data set there are not well defined, stable spike conformations, but virtually a continuum of states. An ensemble map was obtained with minimum bias, from which the extremes of the change along the direction of maximal variance were modeled by flexible fitting. The results provide a warning of the potential image-processing classification instability of these complicated data sets, which has a direct impact on the interpretability of the results.

Organizational Affiliation

Centro Nacional de Biotecnologia-CSIC, Calle Darwin 3, 28049 Cantoblanco, Madrid, Spain.

Macromolecule Content

Total Structure Weight: 445.67 kDa
Atom Count: 23,615
Modeled Residue Count: 2,861
Deposited Residue Count: 3,864
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,288	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 5 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTC2
Glycosylation
Glycosylation Sites: 3	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	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	CA [auth c], D, DA [auth d], G, H, CA [auth c], D, DA [auth d], G, H, I, J, K, L, M, P, S, T, V, X, Z	2		N-Glycosylation	Interactions Focus chain CA [auth c] Focus chain D Focus chain DA [auth d] Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain P Focus chain S Focus chain T Focus chain V Focus chain X Focus chain Z Interactions & Density Focus chain CA [auth c] Focus chain D Focus chain DA [auth d] Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain P Focus chain S Focus chain T Focus chain V Focus chain X Focus chain Z
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, R, U	4		N-Glycosylation	Interactions Focus chain E Focus chain F Focus chain R Focus chain U Interactions & Density Focus chain E Focus chain F Focus chain R Focus chain U
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], BA [auth b], N, O, W, AA [auth a], BA [auth b], N, O, W, Y	3		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain BA [auth b] Focus chain N Focus chain O Focus chain W Focus chain Y Interactions & Density Focus chain AA [auth a] Focus chain BA [auth b] Focus chain N Focus chain O Focus chain W Focus chain Y
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	Q	3		N/A	Interactions Focus chain Q Interactions & Density Focus chain Q
Glycosylation Resources
GlyTouCan: G62916OK GlyCosmos: G62916OK GlyGen: G62916OK

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain FA [auth A] SDF format, chain GA [auth A] SDF format, chain HA [auth A] SDF format, chain IA [auth A] SDF format, chain JA [auth A] SDF format, chain OA [auth B] SDF format, chain PA [auth B] SDF format, chain QA [auth B] SDF format, chain RA [auth B] SDF format, chain SA [auth B] SDF format, chain UA [auth B] SDF format, chain XA [auth C] SDF format, chain YA [auth C] SDF format, chain WA [auth C] SDF format, chain VA [auth B] SDF format, chain TA [auth B] SDF format, chain EA [auth A] MOL2 format, chain AB [auth C] MOL2 format, chain FA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain PA [auth B] MOL2 format, chain QA [auth B] MOL2 format, chain RA [auth B] MOL2 format, chain SA [auth B] MOL2 format, chain UA [auth B] MOL2 format, chain XA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain WA [auth C] MOL2 format, chain VA [auth B] MOL2 format, chain TA [auth B] MOL2 format, chain EA [auth A] mmCIF format, chain AB [auth C] mmCIF format, chain FA [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain IA [auth A] mmCIF format, chain JA [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain PA [auth B] mmCIF format, chain QA [auth B] mmCIF format, chain RA [auth B] mmCIF format, chain SA [auth B] mmCIF format, chain UA [auth B] mmCIF format, chain XA [auth C] mmCIF format, chain YA [auth C] mmCIF format, chain WA [auth C] mmCIF format, chain VA [auth B] mmCIF format, chain TA [auth B] mmCIF format, chain EA [auth A]	AB [auth C] EA [auth A] FA [auth A] GA [auth A] HA [auth A] AB [auth C], EA [auth A], FA [auth A], GA [auth A], HA [auth A], IA [auth A], JA [auth A], OA [auth B], PA [auth B], QA [auth B], RA [auth B], SA [auth B], TA [auth B], UA [auth B], VA [auth B], WA [auth C], XA [auth C], YA [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth C] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Interactions & Density Focus chain AB [auth C] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C]
MAN Query on MAN Download:Ideal Coordinates CCD File SDF format, chain ZA [auth C] SDF format, chain KA [auth A] MOL2 format, chain ZA [auth C] MOL2 format, chain KA [auth A] mmCIF format, chain ZA [auth C] mmCIF format, chain KA [auth A]	KA [auth A], ZA [auth C]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain KA [auth A] Focus chain ZA [auth C] Interactions & Density Focus chain KA [auth A] Focus chain ZA [auth C]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain LA [auth A] SDF format, chain MA [auth A] SDF format, chain NA [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain NA [auth A] mmCIF format, chain LA [auth A] mmCIF format, chain MA [auth A] mmCIF format, chain NA [auth A]	LA [auth A], MA [auth A], NA [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NA [auth A] Interactions & Density Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NA [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-07-29

Deposition Author(s):

Martinez, M.

Marabini, R.

Carazo, J.M.

Funding Organization	Location	Grant Number
Spanish National Research Council	Spain	PIE/COVID-19 202020E079
Spanish Ministry of Science, Innovation, and Universities	Spain	SEV 2017-0712
European Research Council (ERC)	Spain	ERC - 2018 - SyG, Proposal: 810057
National Institutes of Health/National Library of Medicine (NIH/NLM)	United States	GM125769
National Institutes of Health/National Library of Medicine (NIH/NLM)	United States	R01-AI127521

Revision History (Full details and data files)

Version 1.0: 2020-07-29
Type: Initial release
Version 2.0: 2021-02-03
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
Version 2.1: 2022-12-21
Changes: Database references, Refinement description
Version 2.2: 2024-10-23
Changes: Data collection, Refinement description, Structure summary