6Z43

Cryo-EM Structure of SARS-CoV-2 Spike : H11-D4 Nanobody Complex

PDB DOI: https://doi.org/10.2210/pdb6Z43/pdb
EM Map EMD-11068: EMDB EMDataResource

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

Deposited: 2020-05-22 Released: 2020-06-03
Deposition Author(s): Ruza, R.R., Duyvesteyn, H.M.E., Shah, P., Carrique, L., Ren, J., Malinauskas, T., Zhou, D., Stuart, D.I., Naismith, J.H.
Funding Organization(s): Engineering and Physical Sciences Research Council, Wellcome Trust, Cancer Research UK, Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Structural basis for a potent neutralising single-domain antibody that blocks SARS-CoV-2 binding to its receptor ACE2

Huo, J., Le Bas, A., Ruza, R.R., Duyvesteyn, H.M.E., Mikolajek, H., Malinauskas, T., Tan, T., Rijal, P., Dumoux, M., Ward, P.N., Ren, J., Zhou, D., Harrison, P.J., Radecke, J., Zhao, Y., Jaramillo, J.G., Knight, M., Carrique, L., Shah, P., James, W., Townsend, A., Stuart, D.I., Owens, R.J., Naismith, J.H.

To be published.

Macromolecule Content

Total Structure Weight: 491.48 kDa
Atom Count: 26,725
Modelled Residue Count: 3,351
Deposited Residue Count: 4,317
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	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
Glycosylation
Glycosylation Sites: 16	Glycosylation Focus chain A Focus chain B Focus chain C	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody	D [auth X], E [auth Y], F [auth Z]	151	Lama glama	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 D], H [auth E], I [auth F], J [auth G], K [auth H], G [auth D], H [auth E], I [auth F], J [auth G], K [auth H], L [auth I], M [auth J], N [auth K], O [auth L], P [auth M], Q [auth N], R [auth O], S [auth P], T [auth Q], U [auth R], V [auth S], W [auth T], X [auth U], Y [auth V], Z [auth W]	2		N-Glycosylation	Interactions Focus chain G [auth D] Focus chain H [auth E] Focus chain I [auth F] Focus chain J [auth G] Focus chain K [auth H] Focus chain L [auth I] Focus chain M [auth J] Focus chain N [auth K] Focus chain O [auth L] Focus chain P [auth M] Focus chain Q [auth N] Focus chain R [auth O] Focus chain S [auth P] Focus chain T [auth Q] Focus chain U [auth R] Focus chain V [auth S] Focus chain W [auth T] Focus chain X [auth U] Focus chain Y [auth V] Focus chain Z [auth W] Interactions & Density Focus chain G [auth D] Focus chain H [auth E] Focus chain I [auth F] Focus chain J [auth G] Focus chain K [auth H] Focus chain L [auth I] Focus chain M [auth J] Focus chain N [auth K] Focus chain O [auth L] Focus chain P [auth M] Focus chain Q [auth N] Focus chain R [auth O] Focus chain S [auth P] Focus chain T [auth Q] Focus chain U [auth R] Focus chain V [auth S] Focus chain W [auth T] Focus chain X [auth U] Focus chain Y [auth V] Focus chain Z [auth W]
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 CA [auth A] SDF format, chain DA [auth A] SDF format, chain EA [auth A] SDF format, chain FA [auth A] SDF format, chain HA [auth A] SDF format, chain JA [auth B] SDF format, chain MA [auth B] SDF format, chain NA [auth B] SDF format, chain PA [auth B] SDF format, chain RA [auth B] SDF format, chain UA [auth C] SDF format, chain VA [auth C] SDF format, chain XA [auth C] SDF format, chain YA [auth C] SDF format, chain ZA [auth C] SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain GA [auth A] SDF format, chain IA [auth B] SDF format, chain KA [auth B] SDF format, chain LA [auth B] SDF format, chain OA [auth B] SDF format, chain QA [auth B] SDF format, chain SA [auth C] SDF format, chain TA [auth C] SDF format, chain WA [auth C] MOL2 format, chain CA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain PA [auth B] MOL2 format, chain RA [auth B] MOL2 format, chain UA [auth C] MOL2 format, chain VA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain ZA [auth C] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain OA [auth B] MOL2 format, chain QA [auth B] MOL2 format, chain SA [auth C] MOL2 format, chain TA [auth C] MOL2 format, chain WA [auth C] mmCIF format, chain CA [auth A] mmCIF format, chain DA [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain MA [auth B] mmCIF format, chain NA [auth B] mmCIF format, chain PA [auth B] mmCIF format, chain RA [auth B] mmCIF format, chain UA [auth C] mmCIF format, chain VA [auth C] mmCIF format, chain XA [auth C] mmCIF format, chain YA [auth C] mmCIF format, chain ZA [auth C] mmCIF format, chain AA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain KA [auth B] mmCIF format, chain LA [auth B] mmCIF format, chain OA [auth B] mmCIF format, chain QA [auth B] mmCIF format, chain SA [auth C] mmCIF format, chain TA [auth C] mmCIF format, chain WA [auth C]	AA [auth A] BA [auth A] CA [auth A] DA [auth A] EA [auth A] AA [auth A], BA [auth A], CA [auth A], DA [auth A], EA [auth A], FA [auth A], GA [auth A], HA [auth A], 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 B], SA [auth C], TA [auth C], UA [auth C], VA [auth C], 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 AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] 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 B] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C] 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 A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] 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 B] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.1
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-06-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Engineering and Physical Sciences Research Council	United Kingdom	EP/S025243/1
Wellcome Trust	United Kingdom	100209/Z/12/Z
Cancer Research UK	United Kingdom	C20724/A14414
Cancer Research UK	United Kingdom	C20724/A26752
Wellcome Trust	United Kingdom	101122/Z/13/Z
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/N00065X/1

Revision History (Full details and data files)

Version 1.0: 2020-06-03
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: 2024-10-16
Changes: Data collection, Database references, Refinement description, Structure summary