7ND9

EM structure of SARS-CoV-2 Spike glycoprotein (one RBD up) in complex with COVOX-253H55L Fab

PDB DOI: https://doi.org/10.2210/pdb7ND9/pdb
EM Map EMD-12280: EMDB EMDataResource

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

Deposited: 2021-01-30 Released: 2021-03-03
Deposition Author(s): Duyvesteyn, H.M.E., Zhao, Y., Ren, J., Stuart, D.
Funding Organization(s): Medical Research Council (MRC, United Kingdom), CAMS Innovation Fund for Medical Sciences (CIFMS)

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 1.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 488.45 kDa
Atom Count: 27,336
Modelled Residue Count: 3,482
Deposited Residue Count: 4,333
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,288	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTC2
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
COVOX-253H55L Fab heavy chain	D [auth H]	241	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
COVOX-253H55L Fab light chain	E [auth L]	228	Homo sapiens	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: 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	F [auth D], G [auth E], H [auth F], I [auth G], J [auth I], F [auth D], G [auth E], H [auth F], I [auth G], J [auth I], K [auth J], L [auth K], M, N, O	2		N-Glycosylation	Interactions Focus chain F [auth D] Focus chain G [auth E] Focus chain H [auth F] Focus chain I [auth G] Focus chain J [auth I] Focus chain K [auth J] Focus chain L [auth K] Focus chain M Focus chain N Focus chain O Interactions & Density Focus chain F [auth D] Focus chain G [auth E] Focus chain H [auth F] Focus chain I [auth G] Focus chain J [auth I] Focus chain K [auth J] Focus chain L [auth K] Focus chain M Focus chain N Focus chain O
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
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	P	3		N-Glycosylation	Interactions Focus chain P Interactions & Density Focus chain P
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

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 B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] 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 C] SDF format, chain KA [auth C] SDF format, chain MA [auth C] SDF format, chain NA [auth C] SDF format, chain OA [auth C] SDF format, chain Q [auth A] SDF format, chain QA [auth C] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth B] SDF format, chain LA [auth C] SDF format, chain PA [auth C] SDF format, chain U [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] 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 C] MOL2 format, chain KA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain NA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth C] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain LA [auth C] MOL2 format, chain PA [auth C] MOL2 format, chain U [auth A]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] EA [auth B] AA [auth B], BA [auth B], CA [auth B], DA [auth B], EA [auth B], FA [auth B], GA [auth B], HA [auth B], IA [auth B], JA [auth C], KA [auth C], LA [auth C], MA [auth C], NA [auth C], OA [auth C], PA [auth C], Q [auth A], QA [auth C], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] 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 C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] 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 C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth B]