8BH5 | pdb_00008bh5

SARS-CoV-2 BA.2.12.1 RBD in complex with Beta-27 Fab and C1 nanobody

PDB DOI: https://doi.org/10.2210/pdb8BH5/pdb

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

Deposited: 2022-10-29 Released: 2022-11-23
Deposition Author(s): Huo, J., Zhou, D., Ren, J., Stuart, D.I.
Funding Organization(s): CAMS Innovation Fund for Medical Sciences (CIFMS), Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free:
0.233 (Depositor), 0.230 (DCC)
R-Value Work:
0.186 (Depositor), 0.190 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Humoral responses against SARS-CoV-2 Omicron BA.2.11, BA.2.12.1 and BA.2.13 from vaccine and BA.1 serum.

Huo, J., Dijokaite-Guraliuc, A., Nutalai, R., Das, R., Zhou, D., Mentzer, A.J., Fry, E.E., Mongkolsapaya, J., Ren, J., Stuart, D.I., Screaton, G.R.

(2022) Cell Discov 8: 119-119

PubMed: 36319620 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41421-022-00482-3
Primary Citation of Related Structures:
8BH5

Organizational Affiliation

Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK. huojiandong@gird.cn.

Macromolecule Content

Total Structure Weight: 85.93 kDa
Atom Count: 5,982
Modeled Residue Count: 742
Deposited Residue Count: 769
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-27 heavy chain	A [auth H]	222	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-27 light chain	B [auth L]	214	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	C [auth E]	202	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 18 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: 1	Glycosylation Focus chain C [auth E]	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody C1	D [auth C]	131	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: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth A]	2		N-Glycosylation	Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain J [auth H] MOL2 format, chain J [auth H] mmCIF format, chain J [auth H]	J [auth H]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain J [auth H] Interactions & Density Focus chain J [auth H]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth H] SDF format, chain G [auth H] SDF format, chain H SDF format, chain I [auth H] SDF format, chain K [auth L] SDF format, chain L SDF format, chain M [auth L] SDF format, chain N [auth E] SDF format, chain O [auth E] SDF format, chain P [auth E] SDF format, chain Q [auth E] SDF format, chain R [auth C] MOL2 format, chain F [auth H] MOL2 format, chain G [auth H] MOL2 format, chain H MOL2 format, chain I [auth H] MOL2 format, chain K [auth L] MOL2 format, chain L MOL2 format, chain M [auth L] MOL2 format, chain N [auth E] MOL2 format, chain O [auth E] MOL2 format, chain P [auth E] MOL2 format, chain Q [auth E] MOL2 format, chain R [auth C] mmCIF format, chain F [auth H] mmCIF format, chain G [auth H] mmCIF format, chain H mmCIF format, chain I [auth H] mmCIF format, chain K [auth L] mmCIF format, chain L mmCIF format, chain M [auth L] mmCIF format, chain N [auth E] mmCIF format, chain O [auth E] mmCIF format, chain P [auth E] mmCIF format, chain Q [auth E] mmCIF format, chain R [auth C]	F [auth H] G [auth H] H I [auth H] K [auth L] F [auth H], G [auth H], H, I [auth H], K [auth L], L, M [auth L], N [auth E], O [auth E], P [auth E], Q [auth E], R [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth H] Focus chain G [auth H] Focus chain H Focus chain I [auth H] Focus chain K [auth L] Focus chain L Focus chain M [auth L] Focus chain N [auth E] Focus chain O [auth E] Focus chain P [auth E] Focus chain Q [auth E] Focus chain R [auth C] Interactions & Density Focus chain F [auth H] Focus chain G [auth H] Focus chain H Focus chain I [auth H] Focus chain K [auth L] Focus chain L Focus chain M [auth L] Focus chain N [auth E] Focus chain O [auth E] Focus chain P [auth E] Focus chain Q [auth E] Focus chain R [auth C]