8WFH | pdb_00008wfh

Crystal structure of Omicron BA.4/5 in complex with a neutralizing antibody scFv D1

PDB DOI: https://doi.org/10.2210/pdb8WFH/pdb

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
Expression System: Trichoplusia
Mutation(s): Yes

Deposited: 2023-09-19 Released: 2024-09-25
Deposition Author(s): Terekhov, S.S., Mokrushina, Y.A., Zhang, M., Zhang, N., Gabibov, A., Guo, Y.
Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.72 Å
R-Value Free:
0.250 (Depositor), 0.251 (DCC)
R-Value Work:
0.211 (Depositor), 0.213 (DCC)
R-Value Observed:
0.215 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of Omicron BA.4/5 in complex with a neutralizing antibody scFv D1

Terekhov, S.S., Mokrushina, Y.A., Zhang, M., Zhang, N., Gabibov, A., Guo, Y.

To be published.

Macromolecule Content

Total Structure Weight: 47.5 kDa
Atom Count: 3,284
Modeled Residue Count: 422
Deposited Residue Count: 430
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A	198	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 17 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTC2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
D1 scFv	B [auth E]	232	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.72 Å
R-Value Free: 0.250 (Depositor), 0.251 (DCC)
R-Value Work: 0.211 (Depositor), 0.213 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.57	α = 90
b = 95.5	β = 109.41
c = 53.07	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-09-25

Deposition Author(s):

Mokrushina, Y.A.

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2018YFE0200400

Revision History (Full details and data files)

Version 1.0: 2024-09-25
Type: Initial release
Version 1.1: 2024-11-20
Changes: Structure summary
Version 1.2: 2024-11-27
Changes: Database references, Structure summary
Version 1.3: 2026-02-04
Changes: Data collection

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.