9MB0 | pdb_00009mb0

Cryo-EM structure of Dengue virus serotype2 THSTI/TRC/01 strain bound with J9 fab

• PDB DOI: https://doi.org/10.2210/pdb9MB0/pdb
• EM Map EMD-63763: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): dengue virus type 2, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2025-03-14 Released: 2026-04-01 
• Deposition Author(s): Roy, A., Prasad, V.M.
• Funding Organization(s): Science and Engineering Research Board (SERB), Department of Biotechnology (DBT, India)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 7.21 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: in silico

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.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Hetero 600-mer - A180B180C120D120 Pseudo Symmetry: Icosahedral - I  (Explore in 3D)
Pseudo Stoichiometry: Hetero 600-mer - A240B180C180 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 236.16 kDa 
• Atom Count: 16,547 
• Modeled Residue Count: 2,152 
• Deposited Residue Count: 2,152 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Membrane glycoprotein	A [auth B], C [auth D], E [auth F]	75	dengue virus type 2	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope Glycoprotein	B [auth A], D [auth C], F [auth E]	495	dengue virus type 2	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
J9 heavy chain variable region	G [auth H], I [auth K]	116	Homo sapiens	Mutation(s): 0  Gene Names: J9 heavy chain variable

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
J9 Light chain variable region	H [auth L], J [auth M]	105	Homo sapiens	Mutation(s): 0  Gene Names: J9 light chain variable

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 7.21 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.6.0

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-04-01 
Deposition Author(s): Roy, A., Prasad, V.M.

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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  

• Version 1.0: 2026-04-01
  Type: Initial release