7K8W

Structure of the SARS-CoV-2 S 2P trimer in complex with the human neutralizing antibody Fab fragment, C119

PDB DOI: https://doi.org/10.2210/pdb7K8W/pdb
EM Map EMD-22733: EMDB EMDataResource

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

Deposited: 2020-09-27 Released: 2020-10-21
Deposition Author(s): Sharaf, N.G., Barnes, C.O., Bjorkman, P.J.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 529.97 kDa
Atom Count: 26,499
Modelled Residue Count: 3,403
Deposited Residue Count: 4,689
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 glycoprotein	A, B, C [auth G]	1,259	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

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
C119 Fab Heavy Chain	D [auth H], F [auth N]	239	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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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
C119 Fab Light Chain	E [auth L], G [auth S]	217	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	H [auth C], I [auth D], J [auth E], K [auth F], L [auth I], H [auth C], I [auth D], J [auth E], K [auth F], L [auth I], M [auth J], N [auth K], O [auth M], P [auth O], Q [auth P], R [auth Q], S [auth R], T	2		N-Glycosylation	Interactions Focus chain H [auth C] Focus chain I [auth D] Focus chain J [auth E] Focus chain K [auth F] Focus chain L [auth I] Focus chain M [auth J] Focus chain N [auth K] Focus chain O [auth M] Focus chain P [auth O] Focus chain Q [auth P] Focus chain R [auth Q] Focus chain S [auth R] Focus chain T Interactions & Density Focus chain H [auth C] Focus chain I [auth D] Focus chain J [auth E] Focus chain K [auth F] Focus chain L [auth I] Focus chain M [auth J] Focus chain N [auth K] Focus chain O [auth M] Focus chain P [auth O] Focus chain Q [auth P] Focus chain R [auth Q] Focus chain S [auth R] Focus chain T
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 A] SDF format, chain AB [auth G] SDF format, chain BA [auth A] SDF format, chain CA [auth A] SDF format, chain DA [auth A] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain GA [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 SA [auth G] SDF format, chain TA [auth G] SDF format, chain U [auth A] SDF format, chain UA [auth G] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain WA [auth G] SDF format, chain X [auth A] SDF format, chain XA [auth G] SDF format, chain Y [auth A] SDF format, chain YA [auth G] SDF format, chain Z [auth A] SDF format, chain ZA [auth G] SDF format, chain BB [auth G] SDF format, chain HA [auth B] SDF format, chain OA [auth B] SDF format, chain PA [auth B] SDF format, chain QA [auth B] SDF format, chain RA [auth G] SDF format, chain VA [auth G] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth G] MOL2 format, chain BA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain GA [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 SA [auth G] MOL2 format, chain TA [auth G] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth G] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth G] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth G] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth G] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth G] MOL2 format, chain BB [auth G] MOL2 format, chain HA [auth B] MOL2 format, chain OA [auth B] MOL2 format, chain PA [auth B] MOL2 format, chain QA [auth B] MOL2 format, chain RA [auth G] MOL2 format, chain VA [auth G]	AA [auth A] AB [auth G] BA [auth A] BB [auth G] CA [auth A] AA [auth A], AB [auth G], BA [auth A], BB [auth G], CA [auth A], DA [auth A], 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], RA [auth G], SA [auth G], TA [auth G], U [auth A], UA [auth G], V [auth A], VA [auth G], W [auth A], WA [auth G], X [auth A], XA [auth G], Y [auth A], YA [auth G], Z [auth A], ZA [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth G] Focus chain BA [auth A] Focus chain BB [auth G] Focus chain CA [auth A] Focus chain DA [auth A] 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 RA [auth G] Focus chain SA [auth G] Focus chain TA [auth G] Focus chain U [auth A] Focus chain UA [auth G] Focus chain V [auth A] Focus chain VA [auth G] Focus chain W [auth A] Focus chain WA [auth G] Focus chain X [auth A] Focus chain XA [auth G] Focus chain Y [auth A] Focus chain YA [auth G] Focus chain Z [auth A] Focus chain ZA [auth G] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth G] Focus chain BA [auth A] Focus chain BB [auth G] Focus chain CA [auth A] Focus chain DA [auth A] 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 RA [auth G] Focus chain SA [auth G] Focus chain TA [auth G] Focus chain U [auth A] Focus chain UA [auth G] Focus chain V [auth A] Focus chain VA [auth G] Focus chain W [auth A] Focus chain WA [auth G] Focus chain X [auth A] Focus chain XA [auth G] Focus chain Y [auth A] Focus chain YA [auth G] Focus chain Z [auth A] Focus chain ZA [auth G]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.17
RECONSTRUCTION	cryoSPARC	2.15

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-10-21

Deposition Author(s):

Sharaf, N.G.

Barnes, C.O.

Bjorkman, P.J.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	P01-AI138938-S1
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	P50-AI150464-13