9U35 | pdb_00009u35

Helical Reconstruction of DENV2 THSTI/TRC/01 tubular particles bound with D14.F25.S02 fab

PDB DOI: https://doi.org/10.2210/pdb9U35/pdb
EM Map EMD-63810: EMDB EMDataResource

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): dengue virus type 2, Homo sapiens
Expression System: Cricetulus griseus
Mutation(s): No

Deposited: 2025-03-18 Released: 2026-04-08
Deposition Author(s): Chatterjee, A., Prasad, V.M.
Funding Organization(s): Science and Engineering Research Board (SERB), Department of Biotechnology (DBT, India)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 17.3 Å
Aggregation State: PARTICLE
Reconstruction Method: HELICAL

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

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

Literature

Structural determinants of broadly neutralizing human antibodies binding to morphological dengue virus variants.

Chatterjee, A., Roy, A., Srinivasan, S., Charles, S., Lubow, J., Goo, L., Prasad, V.M.

To be published.

Macromolecule Content

Total Structure Weight: 134.19 kDa
Atom Count: 7,906
Modeled Residue Count: 1,027
Deposited Residue Count: 1,229
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope Glycoprotein	A, B	495	dengue virus type 2	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
D14.F25.S02 light chain	C [auth M]	111	Homo sapiens	Mutation(s): 0 Gene Names: D14.F25.S02 light chain
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
D14.F25.S02 heavy chain	D [auth K]	128	Homo sapiens	Mutation(s): 0 Gene Names: D14.F25.S02 heavy chain
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 17.3 Å
Aggregation State: PARTICLE
Reconstruction Method: HELICAL

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.6.0

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2026-04-08

Deposition Author(s):

Funding Organization	Location	Grant Number
Science and Engineering Research Board (SERB)	India	SPG/2021/002433
Department of Biotechnology (DBT, India)	India	IA/I/22/1/506233

Revision History (Full details and data files)

Version 1.0: 2026-04-08
Type: Initial release

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.