9IB1 | pdb_00009ib1

Cryo-EM focus map of prefusion SARS-CoV-2 spike (RBDs: 1 up & 2 down) bound to RBD-targeting MO176-117 antibody

PDB DOI: https://doi.org/10.2210/pdb9IB1/pdb
EM Map EMD-52789: EMDB EMDataResource

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

Deposited: 2025-02-11 Released: 2026-03-04
Deposition Author(s): Schulte, T., Wallden, W., Andrell, J., Ohlin, M.
Funding Organization(s): Knut and Alice Wallenberg Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental, in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

A stochastic codon deletion generates a SARS-CoV-2-neutralizing antibody

Blascitz, K., Schulte, T., Nyesiga, B., Samojlovic, M., Godzwon, M., Walle, M., Israelsson, L., Wallden, K., Roos, A., Esbjornsson, J., von Schantz, L., Andrell, J., Woestenenk, E., Ohlin, M.

To be published.

Macromolecule Content

Total Structure Weight: 215.6 kDa
Atom Count: 3,297
Modeled Residue Count: 421
Deposited Residue Count: 1,950
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A	1,288	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 6 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: 2	Glycosylation Focus chain A	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of antibody MO176-117	B [auth L]	214	Homo sapiens	Mutation(s): 0

Find similar proteins by:

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of antibody MO176-117	C [auth H]	448	Homo sapiens	Mutation(s): 0

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

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3.3.1
MODEL REFINEMENT	PHENIX	1.21rc1_5109

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-03-04

Deposition Author(s):

Funding Organization	Location	Grant Number
Knut and Alice Wallenberg Foundation	Sweden	VC-2020-0015(8)

Revision History (Full details and data files)

Version 1.0: 2026-03-04
Type: Initial release

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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.