8VCR

SARS-CoV-2 Spike S2 bound to Fab 54043-5

PDB DOI: https://doi.org/10.2210/pdb8VCR/pdb
EM Map EMD-43139: EMDB EMDataResource

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

Deposited: 2023-12-14 Released: 2024-07-31
Deposition Author(s): Johnson, N.V., McLellan, J.S.
Funding Organization(s): Not funded

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Discovery and Characterization of a Pan-betacoronavirus S2-binding antibody

Johnson, N.V., Wall, S.C., Kramer, K.J., Holt, C.M., Periasamy, S., Richardson, S., Suryadevara, N., Andreano, E., Paciello, I., Pierleoni, G., Piccini, G., Huang, Y., Ge, P., Allen, J.D., Uno, N., Shiakolas, A.R., Pilewski, K.A., Nargi, R.S., Sutton, R.E., Abu-Shmais, A.A., Parks, R., Haynes, B.F., Carnahan, R.H., Crowe Jr., J.E., Rappuoli, R., Bukreyev, A., Ross, T.M., Sautto, G.A., McLellan, J.S., Georgiev, I.S.

To be published.

Macromolecule Content

Total Structure Weight: 347.71 kDa
Atom Count: 15,987
Modelled Residue Count: 2,040
Deposited Residue Count: 3,132
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S2	A, H [auth B], I [auth C]	597	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 9 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTC2
Glycosylation
Glycosylation Sites: 5	Glycosylation Focus chain A Focus chain H [auth B] Focus chain I [auth C]	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
54043-5 Fab Heavy Chain	B [auth D], C [auth E], F [auth H]	233	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B [auth D] Focus chain C [auth E] Focus chain F [auth H]
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
54043-5 Fab Light Chain	D [auth F], E [auth G], G [auth L]	214	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J [auth I], K [auth J], L [auth K]	2		N-Glycosylation	Interactions Focus chain J [auth I] Focus chain K [auth J] Focus chain L [auth K] Interactions & Density Focus chain J [auth I] Focus chain K [auth J] Focus chain L [auth K]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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