6XRA | pdb_00006xra

Distinct conformational states of SARS-CoV-2 spike protein

PDB DOI: https://doi.org/10.2210/pdb6XRA/pdb
EM Map EMD-22293: EMDB EMDataResource

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

Deposited: 2020-07-11 Released: 2020-07-22
Deposition Author(s): Zhang, J., Cai, Y.F., Xiao, T.S., Peng, H.Q., Sterling, S.M., Walsh Jr, R.M., Rawson, S., Rits-Volloch, S., Chen, B.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.3 of the entry. See complete history.

Literature

Distinct conformational states of SARS-CoV-2 spike protein.

Cai, Y., Zhang, J., Xiao, T., Peng, H., Sterling, S.M., Walsh Jr., R.M., Rawson, S., Rits-Volloch, S., Chen, B.

(2020) Science 369: 1586-1592

PubMed: 32694201 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/science.abd4251
Primary Citation Related Structures:
6XR8, 6XRA

PubMed Abstract:
Intervention strategies are urgently needed to control the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. The trimeric viral spike (S) protein catalyzes fusion between viral and target cell membranes to initiate infection. Here, we report two cryo-electron microscopy structures derived from a preparation of the full-length S protein, representing its prefusion (2.9-angstrom resolution) and postfusion (3.0-angstrom resolution) conformations, respectively. The spontaneous transition to the postfusion state is independent of target cells. The prefusion trimer has three receptor-binding domains clamped down by a segment adjacent to the fusion peptide. The postfusion structure is strategically decorated by N-linked glycans, suggesting possible protective roles against host immune responses and harsh external conditions. These findings advance our understanding of SARS-CoV-2 entry and may guide the development of vaccines and therapeutics.

Organizational Affiliation

Division of Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA.

Macromolecule Content

Total Structure Weight: 446.08 kDa
Atom Count: 8,808
Modeled Residue Count: 1,044
Deposited Residue Count: 3,930
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A [auth C], B [auth A], C [auth B]	1,310	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTC2
Glycosylation
Glycosylation Sites: 6	Glycosylation Focus chain A [auth C] Focus chain B [auth A] Focus chain C [auth B]	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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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	D, H, I, M, N D, H, I, M, N, R	2		N-Glycosylation	Interactions Focus chain D Focus chain H Focus chain I Focus chain M Focus chain N Focus chain R Interactions & Density Focus chain D Focus chain H Focus chain I Focus chain M Focus chain N Focus chain R
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, J, K, O E, F, J, K, O, P	4		N-Glycosylation	Interactions Focus chain E Focus chain F Focus chain J Focus chain K Focus chain O Focus chain P Interactions & Density Focus chain E Focus chain F Focus chain J Focus chain K Focus chain O Focus chain P
Glycosylation Resources
GlyTouCan: G48068RF GlyCosmos: G48068RF GlyGen: G48068RF

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, L, Q	3		N-Glycosylation	Interactions Focus chain G Focus chain L Focus chain Q Interactions & Density Focus chain G Focus chain L Focus chain Q
Glycosylation Resources
GlyTouCan: G62182OO GlyCosmos: G62182OO GlyGen: G62182OO

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) 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 S [auth C] SDF format, chain T [auth C] SDF format, chain V [auth C] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Z [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Z [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain V [auth C] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Z [auth A]	AA [auth B] BA [auth B] DA [auth B] S [auth C] T [auth C] AA [auth B], BA [auth B], DA [auth B], S [auth C], T [auth C], V [auth C], W [auth A], X [auth A], Z [auth A]	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 DA [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth C] Focus chain W [auth A] Focus chain X [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain DA [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth C] Focus chain W [auth A] Focus chain X [auth A] Focus chain Z [auth A]
MAN (Subject of Investigation/LOI) Query on MAN Download:Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain U [auth C] SDF format, chain Y [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain U [auth C] MOL2 format, chain Y [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain U [auth C] mmCIF format, chain Y [auth A]	CA [auth B], U [auth C], Y [auth A]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain CA [auth B] Focus chain U [auth C] Focus chain Y [auth A] Interactions & Density Focus chain CA [auth B] Focus chain U [auth C] Focus chain Y [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION
MODEL REFINEMENT	PHENIX

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-07-22

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI147884
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI147884 01A1S1

Revision History (Full details and data files)

Version 1.0: 2020-07-22
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2020-08-05
Changes: Database references
Version 2.2: 2020-10-07
Changes: Database references, Structure summary
Version 2.3: 2024-10-30
Changes: Data collection, Database references, Refinement description, Structure summary