6XR8 | pdb_00006xr8

Distinct conformational states of SARS-CoV-2 spike protein

PDB DOI: https://doi.org/10.2210/pdb6XR8/pdb
EM Map EMD-22292: 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., Volloch, S.R., 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: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 3.2 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: 459.49 kDa
Atom Count: 27,627
Modeled Residue Count: 3,321
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, B, C	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: 19	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
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	BA [auth cA], D [auth I], EA [auth kA], G [auth Q], HA [auth sA], BA [auth cA], D [auth I], EA [auth kA], G [auth Q], HA [auth sA], IA [auth vA], J [auth Y], JA [auth yA], K [auth b], KA [auth 1A], L [auth e], LA [auth 4A], M [auth h], N [auth k], P [auth x], S [auth 5], V [auth DA], W [auth GA], X [auth JA], Y [auth MA], Z [auth PA]	3		N-Glycosylation	Interactions Focus chain BA [auth cA] Focus chain D [auth I] Focus chain EA [auth kA] Focus chain G [auth Q] Focus chain HA [auth sA] Focus chain IA [auth vA] Focus chain J [auth Y] Focus chain JA [auth yA] Focus chain K [auth b] Focus chain KA [auth 1A] Focus chain L [auth e] Focus chain LA [auth 4A] Focus chain M [auth h] Focus chain N [auth k] Focus chain P [auth x] Focus chain S [auth 5] Focus chain V [auth DA] Focus chain W [auth GA] Focus chain X [auth JA] Focus chain Y [auth MA] Focus chain Z [auth PA] Interactions & Density Focus chain BA [auth cA] Focus chain D [auth I] Focus chain EA [auth kA] Focus chain G [auth Q] Focus chain HA [auth sA] Focus chain IA [auth vA] Focus chain J [auth Y] Focus chain JA [auth yA] Focus chain K [auth b] Focus chain KA [auth 1A] Focus chain L [auth e] Focus chain LA [auth 4A] Focus chain M [auth h] Focus chain N [auth k] Focus chain P [auth x] Focus chain S [auth 5] Focus chain V [auth DA] Focus chain W [auth GA] Focus chain X [auth JA] Focus chain Y [auth MA] Focus chain Z [auth PA]
Glycosylation Resources
GlyTouCan: G62182OO GlyCosmos: G62182OO GlyGen: G62182OO

Entity ID: 3
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 fA], E [auth L], FA [auth oA], GA [auth qA], H [auth U], CA [auth fA], E [auth L], FA [auth oA], GA [auth qA], H [auth U], I [auth W], Q [auth 0], T [auth 9], U [auth BA]	2		N-Glycosylation	Interactions Focus chain CA [auth fA] Focus chain E [auth L] Focus chain FA [auth oA] Focus chain GA [auth qA] Focus chain H [auth U] Focus chain I [auth W] Focus chain Q [auth 0] Focus chain T [auth 9] Focus chain U [auth BA] Interactions & Density Focus chain CA [auth fA] Focus chain E [auth L] Focus chain FA [auth oA] Focus chain GA [auth qA] Focus chain H [auth U] Focus chain I [auth W] Focus chain Q [auth 0] Focus chain T [auth 9] Focus chain U [auth BA]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	DA [auth hA], F [auth N], R [auth 2]	3		N-Glycosylation	Interactions Focus chain DA [auth hA] Focus chain F [auth N] Focus chain R [auth 2] Interactions & Density Focus chain DA [auth hA] Focus chain F [auth N] Focus chain R [auth 2]
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Entity ID: 5
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	AA [auth SA], MA [auth 7A], O [auth n]	4		N-Glycosylation	Interactions Focus chain AA [auth SA] Focus chain MA [auth 7A] Focus chain O [auth n] Interactions & Density Focus chain AA [auth SA] Focus chain MA [auth 7A] Focus chain O [auth n]
Glycosylation Resources
GlyTouCan: G48068RF GlyCosmos: G48068RF GlyGen: G48068RF

Small Molecules

Ligands 1 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 DB [auth C] SDF format, chain EB [auth C] SDF format, chain FB [auth C] SDF format, chain HB [auth C] SDF format, chain OA [auth A] SDF format, chain PA [auth A] SDF format, chain QA [auth A] SDF format, chain RA [auth A] SDF format, chain UA [auth B] SDF format, chain XA [auth B] SDF format, chain ZA [auth B] SDF format, chain YA [auth B] SDF format, chain WA [auth B] SDF format, chain VA [auth B] SDF format, chain TA [auth A] SDF format, chain SA [auth A] SDF format, chain NA [auth A] SDF format, chain GB [auth C] SDF format, chain CB [auth C] SDF format, chain BB [auth C] SDF format, chain AB [auth B] MOL2 format, chain DB [auth C] MOL2 format, chain EB [auth C] MOL2 format, chain FB [auth C] MOL2 format, chain HB [auth C] MOL2 format, chain OA [auth A] MOL2 format, chain PA [auth A] MOL2 format, chain QA [auth A] MOL2 format, chain RA [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain XA [auth B] MOL2 format, chain ZA [auth B] MOL2 format, chain YA [auth B] MOL2 format, chain WA [auth B] MOL2 format, chain VA [auth B] MOL2 format, chain TA [auth A] MOL2 format, chain SA [auth A] MOL2 format, chain NA [auth A] MOL2 format, chain GB [auth C] MOL2 format, chain CB [auth C] MOL2 format, chain BB [auth C] MOL2 format, chain AB [auth B] mmCIF format, chain DB [auth C] mmCIF format, chain EB [auth C] mmCIF format, chain FB [auth C] mmCIF format, chain HB [auth C] mmCIF format, chain OA [auth A] mmCIF format, chain PA [auth A] mmCIF format, chain QA [auth A] mmCIF format, chain RA [auth A] mmCIF format, chain UA [auth B] mmCIF format, chain XA [auth B] mmCIF format, chain ZA [auth B] mmCIF format, chain YA [auth B] mmCIF format, chain WA [auth B] mmCIF format, chain VA [auth B] mmCIF format, chain TA [auth A] mmCIF format, chain SA [auth A] mmCIF format, chain NA [auth A] mmCIF format, chain GB [auth C] mmCIF format, chain CB [auth C] mmCIF format, chain BB [auth C] mmCIF format, chain AB [auth B]	AB [auth B] BB [auth C] CB [auth C] DB [auth C] EB [auth C] AB [auth B], BB [auth C], CB [auth C], DB [auth C], EB [auth C], FB [auth C], GB [auth C], HB [auth C], NA [auth A], OA [auth A], PA [auth A], QA [auth A], RA [auth A], SA [auth A], TA [auth A], UA [auth B], VA [auth B], WA [auth B], XA [auth B], YA [auth B], ZA [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth B] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GB [auth C] Focus chain HB [auth C] Focus chain NA [auth A] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain QA [auth A] Focus chain RA [auth A] Focus chain SA [auth A] Focus chain TA [auth A] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain YA [auth B] Focus chain ZA [auth B] Interactions & Density Focus chain AB [auth B] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GB [auth C] Focus chain HB [auth C] Focus chain NA [auth A] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain QA [auth A] Focus chain RA [auth A] Focus chain SA [auth A] Focus chain TA [auth A] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain YA [auth B] Focus chain ZA [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION

Structure Validation

View Full Validation Report

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 3.0: 2020-11-18
Type: Coordinate replacement
Reason: Sequence discrepancy
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Refinement description, Structure summary
Version 3.1: 2020-11-25
Changes: Database references
Version 3.2: 2024-11-13
Changes: Data collection, Database references, Refinement description, Structure summary

6XR8 | pdb_00006xr8

Distinct conformational states of SARS-CoV-2 spike protein

Literature

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

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Glycosylation

Sequence Annotations

Expand

Oligosaccharides

Entity ID: 2

Glycosylation Resources

Entity ID: 3

Glycosylation Resources

Entity ID: 4

Glycosylation Resources

Entity ID: 5

Glycosylation Resources

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)