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), 0.248 (DCC)
R-Value Work:
0.211 (Depositor), 0.209 (DCC)
R-Value Observed:
0.215 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 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

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(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTC2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
D1 scFv	B [auth E]	232	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.72 Å
R-Value Free: 0.250 (Depositor), 0.248 (DCC)
R-Value Work: 0.211 (Depositor), 0.209 (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

View Full Validation Report

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

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.