8F2J | pdb_00008f2j

Crystal structure of antibody WRAIR-2134 in complex with SARS-CoV-2 receptor binding domain

PDB DOI: https://doi.org/10.2210/pdb8F2J/pdb

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2022-11-08 Released: 2023-12-13
Deposition Author(s): Sankhala, R.S., Joyce, M.G.
Funding Organization(s): Department of Defense (DOD, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.16 Å
R-Value Free:
0.245 (Depositor), 0.250 (DCC)
R-Value Work:
0.209 (Depositor), 0.217 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Models: experimental
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Ligand Structure Quality Assessment

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

Literature

Antibody Targeting of Conserved Sites of Vulnerability on the SARS-CoV-2 Spike Receptor-Binding Domain.

Sankhala, R.S., Dussupt, V., Jensen, J., Modjarrad, K., Joyce, M.G.

To be published.

Macromolecule Content

Total Structure Weight: 285.57 kDa
Atom Count: 19,674
Modeled Residue Count: 2,556
Deposited Residue Count: 2,608
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WRAIR-2134 Fab Heavy Chain	A, C [auth D], E [auth H], F [auth I]	233	Homo sapiens	Mutation(s): 0

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
WRAIR-2134 Fab Light Chain	B, D [auth F], G [auth J], H [auth L]	214	Homo sapiens	Mutation(s): 0

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	I [auth C], J [auth E], K [auth G], L [auth K]	205	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 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
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain I [auth C] Focus chain J [auth E] Focus chain K [auth G] Focus chain L [auth K]	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M, N	2		N-Glycosylation	Interactions Focus chain M Focus chain N Interactions & Density Focus chain M Focus chain N
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain P [auth E] SDF format, chain O [auth C] MOL2 format, chain P [auth E] MOL2 format, chain O [auth C] mmCIF format, chain P [auth E] mmCIF format, chain O [auth C]	O [auth C], P [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain O [auth C] Focus chain P [auth E] Interactions & Density Focus chain O [auth C] Focus chain P [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.16 Å
R-Value Free: 0.245 (Depositor), 0.250 (DCC)
R-Value Work: 0.209 (Depositor), 0.217 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.19	α = 90
b = 154.43	β = 90
c = 165.25	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-12-13

Deposition Author(s):

Funding Organization	Location	Grant Number
Department of Defense (DOD, United States)	United States	W81XWH-18-2-0040

Revision History (Full details and data files)

Version 1.0: 2023-12-13
Type: Initial release
Version 1.1: 2024-10-30
Changes: Structure summary
Version 1.2: 2026-03-04
Changes: Refinement description

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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.