8K9J | pdb_00008k9j

SARS-CoV-2 spike protein in complex with two S2H5 Fabs on NTD-1 and NTD-2

PDB DOI: https://doi.org/10.2210/pdb8K9J/pdb
EM Map EMD-36988: EMDB EMDataResource

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

Deposited: 2023-08-01 Released: 2024-07-31
Deposition Author(s): Hong, Q., Cong, Y.
Funding Organization(s): Chinese Academy of Sciences

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 6.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8K9J

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

Literature

Molecular basis of SARS-CoV-2 immune evasion of NTD neutralizing antibodies.

Hong, Q., Xu, S.Q., Huang, Z., Cong, Y.

(2024) Dian Zi Xian Wei Xue Bao

DOI: https://doi.org/10.3969/j.issn.1000-6281.2024.03.009

Macromolecule Content

Total Structure Weight: 515.15 kDa
Atom Count: 31,772
Modeled Residue Count: 4,078
Deposited Residue Count: 4,653
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A [auth E], D [auth C], E [auth D]	1,261	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 5 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 A [auth E]	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of S2H5 Fab	B [auth A], F [auth G]	216	Mus musculus	Mutation(s): 0

Find similar proteins by:

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of S2H5 Fab	C [auth B], G [auth F]	219	Mus musculus	Mutation(s): 0

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 6.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-07-31

Deposition Author(s):

Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	--

Revision History (Full details and data files)

Version 1.0: 2024-07-31
Type: Initial release
Version 1.1: 2024-10-16
Changes: Data collection, Structure summary
Version 1.2: 2025-07-02
Changes: Data collection

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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.