7UKM

Cryo-EM structure of Antibody 12-19 in complex with prefusion SARS-CoV-2 Spike glycoprotein

PDB DOI: https://doi.org/10.2210/pdb7UKM/pdb
EM Map EMD-26584: 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: 2022-04-01 Released: 2023-10-04
Deposition Author(s): Casner, R.G., Shapiro, L.
Funding Organization(s): Jack Ma Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.03 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.

Literature

Structure and Neutralization of two quaternary SARS-CoV-2 omicron antibodies

Casner, R.G.

To be published.

Macromolecule Content

Total Structure Weight: 516.08 kDa
Atom Count: 30,145
Modelled Residue Count: 3,771
Deposited Residue Count: 4,554
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 [auth B], D [auth A], G [auth C]	1,273	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1 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 [auth B] Focus chain D [auth A] Focus chain G [auth C]	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
12-19 Fab Heavy Chain	B [auth X], E [auth H], H [auth M]	133	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
12-19 Fab Light Chain	C [auth Y], F [auth L], I [auth N]	112	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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 C] SDF format, chain BA [auth A] SDF format, chain BB [auth C] SDF format, chain CA [auth A] SDF format, chain CB [auth C] SDF format, chain DA [auth A] SDF format, chain DB [auth C] SDF format, chain EA [auth A] SDF format, chain FA [auth A] SDF format, chain GA [auth A] SDF format, chain HA [auth A] SDF format, chain IA [auth A] SDF format, chain J [auth B] SDF format, chain JA [auth A] SDF format, chain K [auth B] SDF format, chain KA [auth A] SDF format, chain L [auth B] SDF format, chain LA [auth A] SDF format, chain M [auth B] SDF format, chain MA [auth A] SDF format, chain N [auth B] SDF format, chain NA [auth A] SDF format, chain O [auth B] SDF format, chain OA [auth A] SDF format, chain P [auth B] SDF format, chain PA [auth C] SDF format, chain Q [auth B] SDF format, chain QA [auth C] SDF format, chain R [auth B] SDF format, chain RA [auth C] SDF format, chain S [auth B] SDF format, chain SA [auth C] SDF format, chain T [auth B] SDF format, chain TA [auth C] SDF format, chain U [auth B] SDF format, chain UA [auth C] SDF format, chain V [auth B] SDF format, chain VA [auth C] SDF format, chain W [auth B] SDF format, chain WA [auth C] SDF format, chain X [auth B] SDF format, chain XA [auth C] SDF format, chain Y [auth B] SDF format, chain YA [auth C] SDF format, chain Z [auth A] SDF format, chain ZA [auth C] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth C] MOL2 format, chain BA [auth A] MOL2 format, chain BB [auth C] MOL2 format, chain CA [auth A] MOL2 format, chain CB [auth C] MOL2 format, chain DA [auth A] MOL2 format, chain DB [auth C] MOL2 format, chain EA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain J [auth B] MOL2 format, chain JA [auth A] MOL2 format, chain K [auth B] MOL2 format, chain KA [auth A] MOL2 format, chain L [auth B] MOL2 format, chain LA [auth A] MOL2 format, chain M [auth B] MOL2 format, chain MA [auth A] MOL2 format, chain N [auth B] MOL2 format, chain NA [auth A] MOL2 format, chain O [auth B] MOL2 format, chain OA [auth A] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth C] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth C] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth C] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth C] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth C] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth C] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth C] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth C] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth C] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth C] mmCIF format, chain AA [auth A] mmCIF format, chain AB [auth C] mmCIF format, chain BA [auth A] mmCIF format, chain BB [auth C] mmCIF format, chain CA [auth A] mmCIF format, chain CB [auth C] mmCIF format, chain DA [auth A] mmCIF format, chain DB [auth C] mmCIF format, chain EA [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain IA [auth A] mmCIF format, chain J [auth B] mmCIF format, chain JA [auth A] mmCIF format, chain K [auth B] mmCIF format, chain KA [auth A] mmCIF format, chain L [auth B] mmCIF format, chain LA [auth A] mmCIF format, chain M [auth B] mmCIF format, chain MA [auth A] mmCIF format, chain N [auth B] mmCIF format, chain NA [auth A] mmCIF format, chain O [auth B] mmCIF format, chain OA [auth A] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth C] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth C] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth C] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth C] mmCIF format, chain U [auth B] mmCIF format, chain UA [auth C] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth C] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth C] mmCIF format, chain X [auth B] mmCIF format, chain XA [auth C] mmCIF format, chain Y [auth B] mmCIF format, chain YA [auth C] mmCIF format, chain Z [auth A] mmCIF format, chain ZA [auth C]	AA [auth A] AB [auth C] BA [auth A] BB [auth C] CA [auth A] AA [auth A], AB [auth C], BA [auth A], BB [auth C], CA [auth A], CB [auth C], DA [auth A], DB [auth C], EA [auth A], FA [auth A], GA [auth A], HA [auth A], IA [auth A], J [auth B], JA [auth A], K [auth B], KA [auth A], L [auth B], LA [auth A], M [auth B], MA [auth A], N [auth B], NA [auth A], O [auth B], OA [auth A], P [auth B], PA [auth C], Q [auth B], QA [auth C], R [auth B], RA [auth C], S [auth B], SA [auth C], T [auth B], TA [auth C], U [auth B], UA [auth C], V [auth B], VA [auth C], W [auth B], WA [auth C], X [auth B], XA [auth C], Y [auth B], YA [auth C], Z [auth A], 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 AB [auth C] Focus chain BA [auth A] Focus chain BB [auth C] Focus chain CA [auth A] Focus chain CB [auth C] Focus chain DA [auth A] Focus chain DB [auth C] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain IA [auth A] Focus chain J [auth B] Focus chain JA [auth A] Focus chain K [auth B] Focus chain KA [auth A] Focus chain L [auth B] Focus chain LA [auth A] Focus chain M [auth B] Focus chain MA [auth A] Focus chain N [auth B] Focus chain NA [auth A] Focus chain O [auth B] Focus chain OA [auth A] Focus chain P [auth B] Focus chain PA [auth C] Focus chain Q [auth B] Focus chain QA [auth C] Focus chain R [auth B] Focus chain RA [auth C] Focus chain S [auth B] Focus chain SA [auth C] Focus chain T [auth B] Focus chain TA [auth C] Focus chain U [auth B] Focus chain UA [auth C] Focus chain V [auth B] Focus chain VA [auth C] Focus chain W [auth B] Focus chain WA [auth C] Focus chain X [auth B] Focus chain XA [auth C] Focus chain Y [auth B] Focus chain YA [auth C] Focus chain Z [auth A] Focus chain ZA [auth C] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth C] Focus chain BA [auth A] Focus chain BB [auth C] Focus chain CA [auth A] Focus chain CB [auth C] Focus chain DA [auth A] Focus chain DB [auth C] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain IA [auth A] Focus chain J [auth B] Focus chain JA [auth A] Focus chain K [auth B] Focus chain KA [auth A] Focus chain L [auth B] Focus chain LA [auth A] Focus chain M [auth B] Focus chain MA [auth A] Focus chain N [auth B] Focus chain NA [auth A] Focus chain O [auth B] Focus chain OA [auth A] Focus chain P [auth B] Focus chain PA [auth C] Focus chain Q [auth B] Focus chain QA [auth C] Focus chain R [auth B] Focus chain RA [auth C] Focus chain S [auth B] Focus chain SA [auth C] Focus chain T [auth B] Focus chain TA [auth C] Focus chain U [auth B] Focus chain UA [auth C] Focus chain V [auth B] Focus chain VA [auth C] Focus chain W [auth B] Focus chain WA [auth C] Focus chain X [auth B] Focus chain XA [auth C] Focus chain Y [auth B] Focus chain YA [auth C] Focus chain Z [auth A] Focus chain ZA [auth C]