8G77

SARS-CoV-2 spike/Nb6 complex

PDB DOI: https://doi.org/10.2210/pdb8G77/pdb
EM Map EMD-29799: EMDB EMDataResource

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Severe acute respiratory syndrome coronavirus 2, Vicugna pacos
Expression System: Homo sapiens, Escherichia coli
Mutation(s): No

Deposited: 2023-02-16 Released: 2024-02-21
Deposition Author(s): Ye, G., Bu, F., Liu, B., Li, F.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.80 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

SARS-CoV-2 spike/Nb6 complex

Ye, G., Bu, F., Pan, R., Wen, W., Mendoza, A., Spiller, B., Du, L., Perlman, S., Liu, B., Li, F.

To be published.

Macromolecule Content

Total Structure Weight: 469.82 kDa
Atom Count: 28,942
Modelled Residue Count: 3,608
Deposited Residue Count: 4,125
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C [auth D]	1,234	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTC2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanosota-6	D [auth G], E [auth F], F [auth K]	141	Vicugna pacos	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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

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 AA [auth A] SDF format, chain AB [auth D] SDF format, chain BA [auth A] SDF format, chain BB [auth D] SDF format, chain CA [auth A] SDF format, chain CB [auth D] SDF format, chain DA [auth A] SDF format, chain DB [auth D] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain IA [auth B] SDF format, chain JA [auth B] SDF format, chain KA [auth B] SDF format, chain LA [auth B] SDF format, chain MA [auth B] SDF format, chain NA [auth B] SDF format, chain OA [auth B] SDF format, chain PA [auth B] SDF format, chain QA [auth B] SDF format, chain R [auth A] SDF format, chain RA [auth B] SDF format, chain S [auth A] SDF format, chain SA [auth D] SDF format, chain T [auth A] SDF format, chain TA [auth D] SDF format, chain U [auth A] SDF format, chain UA [auth D] SDF format, chain V [auth A] SDF format, chain VA [auth D] SDF format, chain W [auth A] SDF format, chain WA [auth D] SDF format, chain X [auth A] SDF format, chain XA [auth D] SDF format, chain Y [auth A] SDF format, chain YA [auth D] SDF format, chain Z [auth A] SDF format, chain ZA [auth D] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth D] MOL2 format, chain BA [auth A] MOL2 format, chain BB [auth D] MOL2 format, chain CA [auth A] MOL2 format, chain CB [auth D] MOL2 format, chain DA [auth A] MOL2 format, chain DB [auth D] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain OA [auth B] MOL2 format, chain PA [auth B] MOL2 format, chain QA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth D] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth D] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth D] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth D] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth D] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth D] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth D] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth D]	AA [auth A] AB [auth D] BA [auth A] BB [auth D] CA [auth A] AA [auth A], AB [auth D], BA [auth A], BB [auth D], CA [auth A], CB [auth D], DA [auth A], DB [auth D], EA [auth B], FA [auth B], GA [auth B], HA [auth B], IA [auth B], JA [auth B], KA [auth B], LA [auth B], MA [auth B], NA [auth B], OA [auth B], PA [auth B], QA [auth B], R [auth A], RA [auth B], S [auth A], SA [auth D], T [auth A], TA [auth D], U [auth A], UA [auth D], V [auth A], VA [auth D], W [auth A], WA [auth D], X [auth A], XA [auth D], Y [auth A], YA [auth D], Z [auth A], ZA [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth D] Focus chain BA [auth A] Focus chain BB [auth D] Focus chain CA [auth A] Focus chain CB [auth D] Focus chain DA [auth A] Focus chain DB [auth D] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth D] Focus chain T [auth A] Focus chain TA [auth D] Focus chain U [auth A] Focus chain UA [auth D] Focus chain V [auth A] Focus chain VA [auth D] Focus chain W [auth A] Focus chain WA [auth D] Focus chain X [auth A] Focus chain XA [auth D] Focus chain Y [auth A] Focus chain YA [auth D] Focus chain Z [auth A] Focus chain ZA [auth D] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth D] Focus chain BA [auth A] Focus chain BB [auth D] Focus chain CA [auth A] Focus chain CB [auth D] Focus chain DA [auth A] Focus chain DB [auth D] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth D] Focus chain T [auth A] Focus chain TA [auth D] Focus chain U [auth A] Focus chain UA [auth D] Focus chain V [auth A] Focus chain VA [auth D] Focus chain W [auth A] Focus chain WA [auth D] Focus chain X [auth A] Focus chain XA [auth D] Focus chain Y [auth A] Focus chain YA [auth D] Focus chain Z [auth A] Focus chain ZA [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-02-21

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI089728
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI110700