7JJI | pdb_00007jji

Structure of SARS-CoV-2 3Q-2P full-length prefusion spike trimer (C3 symmetry)

PDB DOI: https://doi.org/10.2210/pdb7JJI/pdb
EM Map EMD-22352: EMDB EMDataResource

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

Deposited: 2020-07-26 Released: 2020-08-26
Deposition Author(s): Bangaru, S., Turner, H.L., Ozorowski, G., Antanasijevic, A., Ward, A.B.
Funding Organization(s): Bill & Melinda Gates Foundation, National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

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

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Structural analysis of full-length SARS-CoV-2 spike protein from an advanced vaccine candidate.

Bangaru, S., Ozorowski, G., Turner, H.L., Antanasijevic, A., Huang, D., Wang, X., Torres, J.L., Diedrich, J.K., Tian, J.H., Portnoff, A.D., Patel, N., Massare, M.J., Yates 3rd, J.R., Nemazee, D., Paulson, J.C., Glenn, G., Smith, G., Ward, A.B.

(2020) Science 370: 1089-1094

PubMed: 33082295 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/science.abe1502
Primary Citation Related Structures:
7JJI, 7JJJ

PubMed Abstract:
Vaccine efforts to combat the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is responsible for the current coronavirus disease 2019 (COVID-19) pandemic, are focused on SARS-CoV-2 spike glycoprotein, the primary target for neutralizing antibodies. We performed cryo-election microscopy and site-specific glycan analysis of one of the leading subunit vaccine candidates from Novavax, which is based on a full-length spike protein formulated in polysorbate 80 detergent. Our studies reveal a stable prefusion conformation of the spike immunogen with slight differences in the S1 subunit compared with published spike ectodomain structures. We also observed interactions between the spike trimers, allowing formation of higher-order spike complexes. This study confirms the structural integrity of the full-length spike protein immunogen and provides a basis for interpreting immune responses to this multivalent nanoparticle immunogen.

Organizational Affiliation

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

Macromolecule Content

Total Structure Weight: 445.95 kDa
Atom Count: 27,459
Modeled Residue Count: 3,327
Deposited Residue Count: 3,819
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	1,273	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: 16	Glycosylation Focus chain A Focus chain B Focus chain C	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	AA [auth a], BA [auth b], CA [auth c], D, DA [auth d], AA [auth a], BA [auth b], CA [auth c], D, DA [auth d], E, EA [auth e], F, FA [auth f], G, GA [auth g], H, HA [auth h], I, IA [auth i], J, JA [auth j], K, KA [auth k], L, LA [auth l], M, MA [auth m], N, NA [auth n], O, OA [auth o], P, PA [auth p], Q, QA [auth q], R, RA [auth r], S, SA [auth s], T, TA [auth t], U, UA [auth u], V, VA [auth v], W, X, Y, Z	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain D Focus chain DA [auth d] Focus chain E Focus chain EA [auth e] Focus chain F Focus chain FA [auth f] Focus chain G Focus chain GA [auth g] Focus chain H Focus chain HA [auth h] Focus chain I Focus chain IA [auth i] Focus chain J Focus chain JA [auth j] Focus chain K Focus chain KA [auth k] Focus chain L Focus chain LA [auth l] Focus chain M Focus chain MA [auth m] Focus chain N Focus chain NA [auth n] Focus chain O Focus chain OA [auth o] Focus chain P Focus chain PA [auth p] Focus chain Q Focus chain QA [auth q] Focus chain R Focus chain RA [auth r] Focus chain S Focus chain SA [auth s] Focus chain T Focus chain TA [auth t] Focus chain U Focus chain UA [auth u] Focus chain V Focus chain VA [auth v] Focus chain W Focus chain X Focus chain Y Focus chain Z Interactions & Density Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain D Focus chain DA [auth d] Focus chain E Focus chain EA [auth e] Focus chain F Focus chain FA [auth f] Focus chain G Focus chain GA [auth g] Focus chain H Focus chain HA [auth h] Focus chain I Focus chain IA [auth i] Focus chain J Focus chain JA [auth j] Focus chain K Focus chain KA [auth k] Focus chain L Focus chain LA [auth l] Focus chain M Focus chain MA [auth m] Focus chain N Focus chain NA [auth n] Focus chain O Focus chain OA [auth o] Focus chain P Focus chain PA [auth p] Focus chain Q Focus chain QA [auth q] Focus chain R Focus chain RA [auth r] Focus chain S Focus chain SA [auth s] Focus chain T Focus chain TA [auth t] Focus chain U Focus chain UA [auth u] Focus chain V Focus chain VA [auth v] Focus chain W Focus chain X Focus chain Y Focus chain Z
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VCG (Subject of Investigation/LOI) Query on VCG Download:Ideal Coordinates CCD File SDF format, chain BB [auth B] SDF format, chain EB [auth C] SDF format, chain XA [auth A] MOL2 format, chain BB [auth B] MOL2 format, chain EB [auth C] MOL2 format, chain XA [auth A] mmCIF format, chain BB [auth B] mmCIF format, chain EB [auth C] mmCIF format, chain XA [auth A]	BB [auth B], EB [auth C], XA [auth A]	2-hydroxyethyl 2-deoxy-3,5-bis-O-(2-hydroxyethyl)-6-O-(2-{[(9E)-octadec-9-enoyl]oxy}ethyl)-alpha-L-xylo-hexofuranoside C₃₂ H₆₀ O₁₀ RGPBUVUVZKQNHD-YPJAPDKZSA-N		Interactions Focus chain BB [auth B] Focus chain EB [auth C] Focus chain XA [auth A] Interactions & Density Focus chain BB [auth B] Focus chain EB [auth C] Focus chain XA [auth A]
EIC (Subject of Investigation/LOI) Query on EIC Download:Ideal Coordinates CCD File SDF format, chain CB [auth C] SDF format, chain ZA [auth B] SDF format, chain YA [auth A] MOL2 format, chain CB [auth C] MOL2 format, chain ZA [auth B] MOL2 format, chain YA [auth A] mmCIF format, chain CB [auth C] mmCIF format, chain ZA [auth B] mmCIF format, chain YA [auth A]	CB [auth C], YA [auth A], ZA [auth B]	LINOLEIC ACID C₁₈ H₃₂ O₂ OYHQOLUKZRVURQ-HZJYTTRNSA-N		Interactions Focus chain CB [auth C] Focus chain YA [auth A] Focus chain ZA [auth B] Interactions & Density Focus chain CB [auth C] Focus chain YA [auth A] Focus chain ZA [auth B]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain AB [auth B] SDF format, chain DB [auth C] SDF format, chain WA [auth A] MOL2 format, chain AB [auth B] MOL2 format, chain DB [auth C] MOL2 format, chain WA [auth A] mmCIF format, chain AB [auth B] mmCIF format, chain DB [auth C] mmCIF format, chain WA [auth A]	AB [auth B], DB [auth C], WA [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth B] Focus chain DB [auth C] Focus chain WA [auth A] Interactions & Density Focus chain AB [auth B] Focus chain DB [auth C] Focus chain WA [auth A]

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	2
MODEL REFINEMENT	Rosetta	2020.03.61102

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-08-26

Deposition Author(s):

Funding Organization	Location	Grant Number
Bill & Melinda Gates Foundation	United States	OPP1170236
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	UM1 AI144462

Revision History (Full details and data files)

Version 1.0: 2020-08-26
Type: Initial release
Version 1.1: 2020-12-23
Changes: Database references
Version 1.2: 2024-11-13
Changes: Data collection, Database references, Refinement description, Structure summary