9BBK | pdb_00009bbk

SARS-CoV-2 full-length spike protein with His1271Lys substitution in the coatomer binding motif, 2RBD-up conformation (SPIKE-KxK)

PDB DOI: https://doi.org/10.2210/pdb9BBK/pdb
EM Map EMD-44420: EMDB EMDataResource

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

Deposited: 2024-04-06 Released: 2025-04-16
Deposition Author(s): Singh, S., Hasan, S.S.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.95 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structure of SARS CoV-2 full-length spike protein with His1271Lys substitution in the coatomer binding motif, 2RBD-up conformation

Singh, S., Hasan, S.S.

To be published.

Macromolecule Content

Total Structure Weight: 455.96 kDa
Atom Count: 25,915
Modeled Residue Count: 3,144
Deposited Residue Count: 3,936
Unique protein chains: 1

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	1,312	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 7 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: 15	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	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, EA [auth f], FA [auth g], L, M, D, EA [auth f], FA [auth g], L, M, N, U [auth V], X [auth Y], Y [auth Z]	2		N-Glycosylation	Interactions Focus chain D Focus chain EA [auth f] Focus chain FA [auth g] Focus chain L Focus chain M Focus chain N Focus chain U [auth V] Focus chain X [auth Y] Focus chain Y [auth Z] Interactions & Density Focus chain D Focus chain EA [auth f] Focus chain FA [auth g] Focus chain L Focus chain M Focus chain N Focus chain U [auth V] Focus chain X [auth Y] Focus chain Y [auth Z]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	DA [auth e], E, F, G, I, DA [auth e], E, F, G, I, J, K, S [auth T], T [auth U], V [auth W], W [auth X]	3		N-Glycosylation	Interactions Focus chain DA [auth e] Focus chain E Focus chain F Focus chain G Focus chain I Focus chain J Focus chain K Focus chain S [auth T] Focus chain T [auth U] Focus chain V [auth W] Focus chain W [auth X] Interactions & Density Focus chain DA [auth e] Focus chain E Focus chain F Focus chain G Focus chain I Focus chain J Focus chain K Focus chain S [auth T] Focus chain T [auth U] Focus chain V [auth W] Focus chain W [auth X]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

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

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	O [auth P], P [auth Q]	4		N-Glycosylation	Interactions Focus chain O [auth P] Focus chain P [auth Q] Interactions & Density Focus chain O [auth P] Focus chain P [auth Q]
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	Q [auth R]	4		N-Glycosylation	Interactions Focus chain Q [auth R] Interactions & Density Focus chain Q [auth R]
Glycosylation Resources
GlyTouCan: G32152BH GlyCosmos: G32152BH GlyGen: G32152BH

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth b], R [auth S], Z [auth a]	4		N-Glycosylation	Interactions Focus chain AA [auth b] Focus chain R [auth S] Focus chain Z [auth a] Interactions & Density Focus chain AA [auth b] Focus chain R [auth S] Focus chain Z [auth a]
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	CA [auth d]	5		N-Glycosylation	Interactions Focus chain CA [auth d] Interactions & Density Focus chain CA [auth d]
Glycosylation Resources
GlyTouCan: G42466VF GlyCosmos: G42466VF GlyGen: G42466VF

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 HA [auth A] SDF format, chain IA [auth A] SDF format, chain JA [auth A] SDF format, chain NA [auth A] SDF format, chain QA [auth B] SDF format, chain RA [auth B] SDF format, chain TA [auth B] SDF format, chain UA [auth B] SDF format, chain WA [auth C] SDF format, chain ZA [auth C] SDF format, chain YA [auth C] SDF format, chain XA [auth C] SDF format, chain VA [auth B] SDF format, chain SA [auth B] SDF format, chain PA [auth B] SDF format, chain OA [auth B] SDF format, chain MA [auth A] SDF format, chain LA [auth A] SDF format, chain KA [auth A] SDF format, chain GA [auth A] SDF format, chain AB [auth C] MOL2 format, chain HA [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain NA [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain RA [auth B] MOL2 format, chain TA [auth B] MOL2 format, chain UA [auth B] MOL2 format, chain WA [auth C] MOL2 format, chain ZA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain VA [auth B] MOL2 format, chain SA [auth B] MOL2 format, chain PA [auth B] MOL2 format, chain OA [auth B] MOL2 format, chain MA [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain AB [auth C] mmCIF format, chain HA [auth A] mmCIF format, chain IA [auth A] mmCIF format, chain JA [auth A] mmCIF format, chain NA [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain RA [auth B] mmCIF format, chain TA [auth B] mmCIF format, chain UA [auth B] mmCIF format, chain WA [auth C] mmCIF format, chain ZA [auth C] mmCIF format, chain YA [auth C] mmCIF format, chain XA [auth C] mmCIF format, chain VA [auth B] mmCIF format, chain SA [auth B] mmCIF format, chain PA [auth B] mmCIF format, chain OA [auth B] mmCIF format, chain MA [auth A] mmCIF format, chain LA [auth A] mmCIF format, chain KA [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain AB [auth C]	AB [auth C] GA [auth A] HA [auth A] IA [auth A] JA [auth A] AB [auth C], GA [auth A], HA [auth A], IA [auth A], JA [auth A], KA [auth A], LA [auth A], MA [auth A], NA [auth A], OA [auth B], PA [auth B], QA [auth B], RA [auth B], SA [auth B], TA [auth B], UA [auth B], VA [auth B], WA [auth C], XA [auth C], YA [auth C], ZA [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth C] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C] Interactions & Density Focus chain AB [auth C] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C]