7XIK | pdb_00007xik

SARS-CoV-2-Omicron-RBD and B38-GWP/P-VK antibody complex

PDB DOI: https://doi.org/10.2210/pdb7XIK/pdb

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

Deposited: 2022-04-13 Released: 2023-04-26
Deposition Author(s): Shi, R., Wang, Y., Wu, Z., Han, X., Yan, J.
Funding Organization(s): Ministry of Science and Technology (MoST, China), Chinese Academy of Sciences, National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.89 Å
R-Value Free:
0.263 (Depositor), 0.263 (DCC)
R-Value Work:
0.211 (Depositor), 0.208 (DCC)
R-Value Observed:
0.216 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

SARS-CoV-2-Omicron-RBD and B38-GWP/P-VK antibody complex

Shi, R., Wang, Y., Wu, Z., Han, X., Yan, J.

To be published.

Macromolecule Content

Total Structure Weight: 73.15 kDa
Atom Count: 4,851
Modeled Residue Count: 629
Deposited Residue Count: 666
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A	225	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 15 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

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
B38 Fab heavy chain	B [auth H]	222	Homo sapiens	Mutation(s): 0

Find similar proteins by:

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
B38 Fab light chain	C [auth L]	219	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.89 Å
R-Value Free: 0.263 (Depositor), 0.263 (DCC)
R-Value Work: 0.211 (Depositor), 0.208 (DCC)
R-Value Observed: 0.216 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.959	α = 90
b = 145.859	β = 90
c = 144.152	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
Coot	model building

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-04-26

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	--
Chinese Academy of Sciences	China	--
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2023-04-26
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary

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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.