6ZDH

SARS-CoV-2 Spike glycoprotein in complex with a neutralizing antibody EY6A Fab

PDB DOI: https://doi.org/10.2210/pdb6ZDH/pdb
EM Map EMD-11174: EMDB EMDataResource

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

Deposited: 2020-06-14 Released: 2020-07-01
Deposition Author(s): Duyvesteyn, H.M.E., Zhou, D., Zhao, Y., Fry, E.E., Ren, J., Stuart, D.I.
Funding Organization(s): Medical Research Council (MRC, United Kingdom), Wellcome Trust, CAMS Innovation Fund for Medical Sciences (CIFMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.4 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 580.79 kDa
Atom Count: 34,058
Modelled Residue Count: 4,308
Deposited Residue Count: 5,187
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	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
EY6A heavy chain	D [auth H], F [auth D], H [auth G]	226	Homo sapiens	Mutation(s): 0
Entity Groups
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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
EY6A light chain	E [auth L], G [auth F], I	215	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	J [auth E], K [auth J], L [auth K], M, N, J [auth E], K [auth J], L [auth K], M, N, O, P, Q, R, S, T, U, V	2		N-Glycosylation	Interactions Focus chain J [auth E] Focus chain K [auth J] Focus chain L [auth K] Focus chain M Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Interactions & Density Focus chain J [auth E] Focus chain K [auth J] Focus chain L [auth K] Focus chain M Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V
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 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 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 C] SDF format, chain NA [auth C] SDF format, chain OA [auth C] SDF format, chain PA [auth C] SDF format, chain QA [auth C] SDF format, chain RA [auth C] SDF format, chain SA [auth C] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth A] MOL2 format, chain AA [auth A] 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 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 C] MOL2 format, chain NA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain PA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain RA [auth C] MOL2 format, chain SA [auth C] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A]	AA [auth A] BA [auth A] CA [auth A] DA [auth A] EA [auth B] AA [auth A], BA [auth A], 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 C], NA [auth C], OA [auth C], PA [auth C], QA [auth C], RA [auth C], SA [auth C], W [auth A], X [auth A], Y [auth A], Z [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] 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 C] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] 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 C] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-07-01

Deposition Author(s):

Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/N00065X/1
Wellcome Trust	United Kingdom	101122/Z/13/Z
CAMS Innovation Fund for Medical Sciences (CIFMS)	China	2018-I2M-2-002

Revision History (Full details and data files)

Version 1.0: 2020-07-01
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2020-08-12
Changes: Database references, Structure summary
Version 2.2: 2020-10-21
Changes: Database references
Version 2.3: 2021-02-10
Changes: Database references
Version 2.4: 2021-12-22
Changes: Database references