9SSM | pdb_00009ssm

Crystal structure of 084-7D Fab bound to SARS-CoV-2 Beta RBD

PDB DOI: https://doi.org/10.2210/pdb9SSM/pdb

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

Deposited: 2025-09-26 Released: 2026-02-18
Deposition Author(s): Ayres, F., Moyo-Gwete, T., Wibmer, C.K.
Funding Organization(s): Wellcome Trust, European Union (EU), South African Medical Research Council self-initiated research grant (SAMRC SIR Grant)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.269 (Depositor), 0.267 (DCC)
R-Value Work:
0.223 (Depositor), 0.222 (DCC)
R-Value Observed:
0.225 (Depositor)

Starting Model: in silico
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This is version 1.1 of the entry. See complete history.

Literature

Defining the mechanism of cross-reactivity for a SARS-CoV-2 Beta-elicited antibody toward omicron sub-lineages.

Ayres, F., Lambson, B., Mkhize, N.N., Makhado, Z., Mhlanga, D., Serage, R., Moore, P.L., Wibmer, C.K., Moyo-Gwete, T.

(2026) Structure 34: 552

PubMed: 41643669 Search on PubMed
DOI: https://doi.org/10.1016/j.str.2026.01.006
Primary Citation Related Structures:
9SSM

PubMed Abstract:
Despite the continual emergence of SARS-CoV-2 variants and increasing diversity within the receptor binding domain (RBD), some antibody responses that are directed to conserved regions can display cross-reactivity against variants. We previously isolated an RBD-directed monoclonal antibody (084-7D) from a Beta-infected donor that neutralized Beta and emerging Omicron variants. Here, we solved a high-resolution crystal structure of the 084-7D Fab in complex with the Beta RBD. These data revealed an epitope overlapping both the ACE2 binding site and those of other class 1 antibodies. Furthermore, the epitope includes highly conserved residues, Q409, D420, and Y489, that are present in recent Omicron variants. The N417 residue that emerged with Beta and has since persisted is tolerated within the epitope of 084-7D, explaining the preferential neutralization of contemporaneous N417-containing variants. These structural data defined the mechanism for cross-reactivity of a Beta-elicited neutralizing antibody, potentially informing the design of future broadly reactive SARS-CoV-2 therapeutics.

Organizational Affiliation

SA MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Wits Health Consortium, University of the Witwatersrand, Johannesburg, South Africa; Venom & Vaccine Immunotherapeutic & Immunogen Protein Engineering Research (VïPER), Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.

Macromolecule Content

Total Structure Weight: 76.16 kDa
Atom Count: 4,717
Modeled Residue Count: 626
Deposited Residue Count: 693
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
084-7D Fab Heavy Chain	A [auth H]	230	Homo sapiens	Mutation(s): 0 Gene Names: IgHV

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
084-7D Fab Light Chain	B [auth K]	214	Homo sapiens	Mutation(s): 0 Gene Names: IgKV

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	C [auth R]	249	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
UniProt
Find proteins for A0A8A5XRG7 (Severe acute respiratory syndrome coronavirus 2) Explore A0A8A5XRG7 Go to UniProtKB: A0A8A5XRG7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8A5XRG7
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain C [auth R]
Sequence Annotations Expand
Reference Sequence

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 D [auth R] MOL2 format, chain D [auth R] mmCIF format, chain D [auth R]	D [auth R]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth R] Interactions & Density Focus chain D [auth R]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.269 (Depositor), 0.267 (DCC)
R-Value Work: 0.223 (Depositor), 0.222 (DCC)
R-Value Observed: 0.225 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.45	α = 90
b = 84.368	β = 90
c = 126.239	γ = 90

Software Package:

Software Name	Purpose
PHENIX	model building
PHENIX	refinement
xia2	data scaling
xia2	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-02-18

Deposition Author(s):

Ayres, F.

Moyo-Gwete, T.

Wibmer, C.K.

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	226137/Z/22/Z
European Union (EU)	European Union	101046041
South African Medical Research Council self-initiated research grant (SAMRC SIR Grant)	South Africa	--