8DZI

Structure of SARS-CoV-2 Omicron BA.1.1.529 Spike trimer with one RBD down in complex with the Fab fragment of human neutralizing antibody MB.02

PDB DOI: https://doi.org/10.2210/pdb8DZI/pdb
EM Map EMD-27799: 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: 2022-08-07 Released: 2022-08-31
Deposition Author(s): Hu, Y., Xiong, Y.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Function and Cryo-EM structures of broadly potent bispecific antibodies against multiple SARS-CoV-2 Omicron sublineages.

Ren, P., Hu, Y., Peng, L., Yang, L., Suzuki, K., Fang, Z., Bai, M., Zhou, L., Feng, Y., Zou, Y., Xiong, Y., Chen, S.

(2023) Signal Transduct Target Ther 8: 281-281

PubMed: 37518189 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41392-023-01509-1
Primary Citation of Related Structures:
8DZH, 8DZI

Organizational Affiliation

Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.

Macromolecule Content

Total Structure Weight: 515.3 kDa
Atom Count: 31,470
Modelled Residue Count: 3,918
Deposited Residue Count: 4,536
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 C], D [auth A], G [auth E]	1,285	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 10 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: 11	Glycosylation Focus chain A [auth C] Focus chain D [auth A] Focus chain G [auth E]	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
antibody MB.02 heavy chain	B [auth H], E [auth B], I [auth G]	118	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
antibody MB.02 light chain	C [auth L], F [auth D], H [auth F]	109	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	AA [auth a], BA [auth b], CA [auth c], J [auth I], K [auth J], AA [auth a], BA [auth b], CA [auth c], J [auth I], K [auth J], L [auth K], M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain J [auth I] 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 Focus chain W Focus chain X Focus chain Y Focus chain Z Interactions & Density Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain J [auth I] 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 Focus chain W Focus chain X Focus chain Y Focus chain Z
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain JA [auth A] SDF format, chain KA [auth A] SDF format, chain LA [auth A] SDF format, chain MA [auth A] SDF format, chain NA [auth A] SDF format, chain PA [auth A] SDF format, chain QA [auth A] SDF format, chain RA [auth E] SDF format, chain TA [auth E] SDF format, chain UA [auth E] SDF format, chain VA [auth E] SDF format, chain WA [auth E] SDF format, chain XA [auth E] SDF format, chain YA [auth E] SDF format, chain ZA [auth E] SDF format, chain IA [auth A] SDF format, chain OA [auth A] SDF format, chain SA [auth E] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain JA [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain NA [auth A] MOL2 format, chain PA [auth A] MOL2 format, chain QA [auth A] MOL2 format, chain RA [auth E] MOL2 format, chain TA [auth E] MOL2 format, chain UA [auth E] MOL2 format, chain VA [auth E] MOL2 format, chain WA [auth E] MOL2 format, chain XA [auth E] MOL2 format, chain YA [auth E] MOL2 format, chain ZA [auth E] MOL2 format, chain IA [auth A] MOL2 format, chain OA [auth A] MOL2 format, chain SA [auth E] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain JA [auth A] mmCIF format, chain KA [auth A] mmCIF format, chain LA [auth A] mmCIF format, chain MA [auth A] mmCIF format, chain NA [auth A] mmCIF format, chain PA [auth A] mmCIF format, chain QA [auth A] mmCIF format, chain RA [auth E] mmCIF format, chain TA [auth E] mmCIF format, chain UA [auth E] mmCIF format, chain VA [auth E] mmCIF format, chain WA [auth E] mmCIF format, chain XA [auth E] mmCIF format, chain YA [auth E] mmCIF format, chain ZA [auth E] mmCIF format, chain IA [auth A] mmCIF format, chain OA [auth A] mmCIF format, chain SA [auth E]	DA [auth C] EA [auth C] FA [auth C] GA [auth C] HA [auth C] DA [auth C], EA [auth C], FA [auth C], GA [auth C], HA [auth C], IA [auth A], JA [auth A], KA [auth A], LA [auth A], MA [auth A], NA [auth A], OA [auth A], PA [auth A], QA [auth A], RA [auth E], SA [auth E], TA [auth E], UA [auth E], VA [auth E], WA [auth E], XA [auth E], YA [auth E], ZA [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain QA [auth A] Focus chain RA [auth E] Focus chain SA [auth E] Focus chain TA [auth E] Focus chain UA [auth E] Focus chain VA [auth E] Focus chain WA [auth E] Focus chain XA [auth E] Focus chain YA [auth E] Focus chain ZA [auth E] Interactions & Density Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain QA [auth A] Focus chain RA [auth E] Focus chain SA [auth E] Focus chain TA [auth E] Focus chain UA [auth E] Focus chain VA [auth E] Focus chain WA [auth E] Focus chain XA [auth E] Focus chain YA [auth E] Focus chain ZA [auth E]