9KT3 | pdb_00009kt3

Structure of EG.5.1 S trimer with 2 down-RBDs complex with antibody CYFN1006-2.

PDB DOI: https://doi.org/10.2210/pdb9KT3/pdb
EM Map EMD-62556: EMDB EMDataResource

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Severe acute respiratory syndrome coronavirus 2, Tequatrovirus T4, synthetic construct
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2024-12-01 Released: 2025-01-29
Deposition Author(s): Wang, Y.J., Sun, L.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.63 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9KT3

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

Literature

Structure of EG.5.1 S trimer with 2 down-RBDs complex with antibody CYFN1006-2.

Wang, Y.J., Sun, L.

To be published.

Macromolecule Content

Total Structure Weight: 567.63 kDa
Atom Count: 34,950
Modeled Residue Count: 4,524
Deposited Residue Count: 5,184
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein,Fibritin,Expression Tag	A, D [auth B], I [auth C]	1,295	Severe acute respiratory syndrome coronavirus 2, Tequatrovirus T4, synthetic construct This entity is chimeric	Mutation(s): 42 Gene Names: S, 2, wac
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2 Go to UniProtKB: P0DTC2
Find proteins for P10104 (Enterobacteria phage T4) Explore P10104 Go to UniProtKB: P10104
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	P0DTC2 P10104
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CYFN1006-2 light chain	B [auth K], E [auth J], G [auth L]	215	Tequatrovirus T4	Mutation(s): 0 Gene Names: wac

Find similar proteins by:

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CYFN1006-2 heavy chain	C [auth H], F [auth G], H [auth I]	218	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.63 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.17.1_3660

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-01-29

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-01-29
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.