7E9T | pdb_00007e9t

Nanometer resolution in situ structure of SARS-CoV-2 post-fusion spike

PDB DOI: https://doi.org/10.2210/pdb7E9T/pdb
EM Map EMD-31037: EMDB EMDataResource

Classification: VIRUS
Organism(s): Severe acute respiratory syndrome coronavirus 2
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD

Deposited: 2021-03-05 Released: 2021-11-17
Deposition Author(s): Zhu, Y., Tai, L., Zhu, G., Yin, G., Sun, F.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 10.9 Å
Aggregation State: PARTICLE
Reconstruction Method: SUBTOMOGRAM AVERAGING

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Nanometer-resolution in situ structure of the SARS-CoV-2 postfusion spike protein.

Tai, L., Zhu, G., Yang, M., Cao, L., Xing, X., Yin, G., Chan, C., Qin, C., Rao, Z., Wang, X., Sun, F., Zhu, Y.

(2021) Proc Natl Acad Sci U S A 118

PubMed: 34782481 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.2112703118
Primary Citation Related Structures:
7E9T

PubMed Abstract:
The spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mediates membrane fusion to allow entry of the viral genome into host cells. To understand its detailed entry mechanism and develop a specific entry inhibitor, in situ structural information on the SARS-CoV-2 spike protein in different states is urgent. Here, by using cryo-electron tomography, we observed both prefusion and postfusion spikes in β-propiolactone-inactivated SARS-CoV-2 virions and solved the in situ structure of the postfusion spike at nanometer resolution. Compared to previous reports, the six-helix bundle fusion core, the glycosylation sites, and the location of the transmembrane domain were clearly resolved. We observed oligomerization patterns of the spikes on the viral membrane, likely suggesting a mechanism of fusion pore formation.

Organizational Affiliation

National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.

Macromolecule Content

Total Structure Weight: 184.56 kDa
Atom Count: 9,198
Modeled Residue Count: 1,113
Deposited Residue Count: 1,596
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S2	A, B, C	532	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Membrane Entity: Yes
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 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	D, G [auth H], J [auth L]	2		N-Glycosylation	Interactions Focus chain D Focus chain G [auth H] Focus chain J [auth L] Interactions & Density Focus chain D Focus chain G [auth H] Focus chain J [auth L]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
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	E, F, H [auth I], I [auth J], K [auth M], E, F, H [auth I], I [auth J], K [auth M], L [auth N], M [auth K], N [auth O], O [auth G]	3		N-Glycosylation	Interactions Focus chain E Focus chain F Focus chain H [auth I] Focus chain I [auth J] Focus chain K [auth M] Focus chain L [auth N] Focus chain M [auth K] Focus chain N [auth O] Focus chain O [auth G] Interactions & Density Focus chain E Focus chain F Focus chain H [auth I] Focus chain I [auth J] Focus chain K [auth M] Focus chain L [auth N] Focus chain M [auth K] Focus chain N [auth O] Focus chain O [auth G]
Glycosylation Resources
GlyTouCan: G62182OO GlyCosmos: G62182OO GlyGen: G62182OO

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 P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C]	P [auth A] Q [auth A] R [auth A] S [auth B] T [auth B] P [auth A], Q [auth A], R [auth A], S [auth B], T [auth B], U [auth B], V [auth C], W [auth C], X [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C]