8BE1

SARS-CoV-2 RBD in complex with a Fab fragment of a neutralising antibody mRBD2

PDB DOI: https://doi.org/10.2210/pdb8BE1/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus, Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-10-21 Released: 2023-01-25
Deposition Author(s): Lulla, A., Brear, P., Fischer, K., Hollfelder, F., Hyvonen, M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free: 0.284
R-Value Work: 0.247
R-Value Observed: 0.249

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Microfluidics-enabled fluorescence-activated cell sorting of single pathogen-specific antibody secreting cells for the rapid discovery of monoclonal antibodies

Fischer, K., Lulla, A., So, T.Y., Pereyra-Gerber, P., Raybould, M.I.J., Kohler, T.N., Kaminski, T.S., Yam-Puc, J.C., Hughes, R., Leiss-Maier, F., Brear, P., Matheson, N.J., Deane, C.M., Hyvonen, M., Thaventhiran, J.E.D., Hollfelder, F.

(2023) bioRxiv

DOI: https://doi.org/10.1101/2023.01.10.523494

Macromolecule Content

Total Structure Weight: 143.3 kDa
Atom Count: 9,866
Modelled Residue Count: 1,221
Deposited Residue Count: 1,286
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody heavy chain	A, D	230	Mus musculus	Mutation(s): 0
Entity Groups
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody light chain	B, E	215	Mus musculus	Mutation(s): 0
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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
Spike protein S1	C, F	198	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain M [auth D] SDF format, chain N [auth D] SDF format, chain O [auth D] SDF format, chain P [auth D] SDF format, chain Q [auth D] SDF format, chain R [auth E] SDF format, chain S [auth E] SDF format, chain T [auth E] SDF format, chain U [auth F] SDF format, chain V [auth F] SDF format, chain W [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth E] MOL2 format, chain S [auth E] MOL2 format, chain T [auth E] MOL2 format, chain U [auth F] MOL2 format, chain V [auth F] MOL2 format, chain W [auth F] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth E] mmCIF format, chain S [auth E] mmCIF format, chain T [auth E] mmCIF format, chain U [auth F] mmCIF format, chain V [auth F] mmCIF format, chain W [auth F]	G [auth A] H [auth A] I [auth B] J [auth B] K [auth C] G [auth A], H [auth A], I [auth B], J [auth B], K [auth C], L [auth C], M [auth D], N [auth D], O [auth D], P [auth D], Q [auth D], R [auth E], S [auth E], T [auth E], U [auth F], V [auth F], W [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth F] Focus chain V [auth F] Focus chain W [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth F] Focus chain V [auth F] Focus chain W [auth F]