8SDF | pdb_00008sdf

Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody CC25.4

PDB DOI: https://doi.org/10.2210/pdb8SDF/pdb

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

Deposited: 2023-04-06 Released: 2024-03-13
Deposition Author(s): Yuan, M., Wilson, I.A.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Bill & Melinda Gates Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free:
0.218 (Depositor), 0.217 (DCC)
R-Value Work:
0.185 (Depositor), 0.186 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Broadly neutralizing antibodies targeting a conserved silent face of spike RBD resist extreme SARS-CoV-2 antigenic drift

Song, G., Yuan, M., Liu, H., Capozzola, T., Lin, R.N., Torres, J.L., He, W.T., Musharrafieh, R., Dueker, K., Zhou, P., Callaghan, S., Mishra, N., Yong, P., Anzanello, F., Avillion, G., Vo, A.L., Li, X., Zhang, Y., Makhdoomi, M., Feng, Z., Zhu, X., Peng, L., Nemazee, D., Safonova, Y., Briney, B., Ward, A.B., Burton, D.R., Wilson, I.A., Andrabi, R.

(2025) Cell Rep 44: 115948

DOI: https://doi.org/10.1016/j.celrep.2025.115948

Macromolecule Content

Total Structure Weight: 143.81 kDa
Atom Count: 10,506
Modeled Residue Count: 1,261
Deposited Residue Count: 1,302
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A [auth Z], D [auth A]	205	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
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 A [auth Z] Focus chain D [auth A]	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Neutralizing antibody CC25.4 heavy chain	B [auth H], E [auth B]	229	Homo sapiens	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Neutralizing antibody CC25.4 light chain	C [auth L], F [auth C]	217	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth D]	3		N-Glycosylation	Interactions Focus chain G [auth D] Interactions & Density Focus chain G [auth D]
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain H [auth Z] SDF format, chain I [auth Z] SDF format, chain J [auth H] SDF format, chain K [auth L] SDF format, chain N [auth A] SDF format, chain P [auth C] SDF format, chain O [auth B] SDF format, chain L MOL2 format, chain H [auth Z] MOL2 format, chain I [auth Z] MOL2 format, chain J [auth H] MOL2 format, chain K [auth L] MOL2 format, chain N [auth A] MOL2 format, chain P [auth C] MOL2 format, chain O [auth B] MOL2 format, chain L mmCIF format, chain H [auth Z] mmCIF format, chain I [auth Z] mmCIF format, chain J [auth H] mmCIF format, chain K [auth L] mmCIF format, chain N [auth A] mmCIF format, chain P [auth C] mmCIF format, chain O [auth B] mmCIF format, chain L	H [auth Z] I [auth Z] J [auth H] K [auth L] L H [auth Z], I [auth Z], J [auth H], K [auth L], L, N [auth A], O [auth B], P [auth C]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain H [auth Z] Focus chain I [auth Z] Focus chain J [auth H] Focus chain K [auth L] Focus chain L Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth C] Interactions & Density Focus chain H [auth Z] Focus chain I [auth Z] Focus chain J [auth H] Focus chain K [auth L] Focus chain L Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free: 0.218 (Depositor), 0.217 (DCC)
R-Value Work: 0.185 (Depositor), 0.186 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.204	α = 90
b = 142.996	β = 94.13
c = 82.928	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
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: 2024-03-13

Deposition Author(s):

Yuan, M.

Wilson, I.A.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI170928
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	CHAVD UM1 AI44462
Bill & Melinda Gates Foundation	United States	INV-004923

Revision History (Full details and data files)

Version 1.0: 2024-03-13
Type: Initial release
Version 1.1: 2024-03-20
Changes: Database references
Version 1.2: 2024-12-25
Changes: Advisory, Derived calculations, Structure summary
Version 1.3: 2025-07-16
Changes: Database references