8BH5
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 
- 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 
- R-Value Work: 0.186 
- R-Value Observed: 0.188 
wwPDB Validation   3D Report Full Report
This is version 1.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Beta-27 heavy chain | A [auth H] | 222 | Homo sapiens | Mutation(s): 0  | |
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Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Beta-27 light chain | B [auth L] | 214 | Homo sapiens | Mutation(s): 0  | |
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Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
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(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
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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 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 4 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Nanobody C1 | D [auth C] | 131 | Lama glama | Mutation(s): 0  | |
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Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
PO4 Query on PO4 | J [auth H] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K | |||
GOL Query on GOL | F [auth H] G [auth H] H I [auth H] K [auth L] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.38 Å
- R-Value Free: 0.233 
- R-Value Work: 0.186 
- R-Value Observed: 0.188 
- Space Group: C 1 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 186.846 | α = 90 |
b = 99.987 | β = 104.105 |
c = 56.486 | γ = 90 |
Software Name | Purpose |
---|---|
GDA | data collection |
PHENIX | refinement |
xia2 | data reduction |
xia2 | data scaling |
PHENIX | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2022-11-23  Deposition Author(s): Huo, J., Zhou, D., Ren, J., Stuart, D.I.
Funding Organization | Location | Grant Number |
---|---|---|
CAMS Innovation Fund for Medical Sciences (CIFMS) | United Kingdom | 2018-I2M-2-002 |
Medical Research Council (MRC, United Kingdom) | United Kingdom | MR/N00065X/1 |
Revision History (Full details and data files)
- Version 1.0: 2022-11-23
Type: Initial release - Version 1.1: 2024-01-31
Changes: Data collection, Refinement description