9MAV | pdb_00009mav

Cryo-EM structure of Dengue virus serotype2 US/BID-V594/2006 strain bound with J9 fab.

• PDB DOI: https://doi.org/10.2210/pdb9MAV/pdb
• EM Map EMD-63759: 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: 3.85 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: 239.53 kDa 
• Atom Count: 16,772 
• 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
Envelope Glycoprotein E	A, C, E	495	dengue virus type 2	Mutation(s): 0
UniProt
Find proteins for B1PP76 (Dengue virus type 2) Explore B1PP76  Go to UniProtKB:  B1PP76
Glycosylation
Glycosylation Sites: 2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Membrane Glycoprotein	B, D, F	75	dengue virus type 2	Mutation(s): 0
UniProt
Find proteins for B1PP76 (Dengue virus type 2) Explore B1PP76  Go to UniProtKB:  B1PP76

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

Oligosaccharides

Help  

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	K [auth G]	4		N-Glycosylation
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	L [auth I], M [auth J], O	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	N	4		N-Glycosylation
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	P [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.85 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.6.0
MODEL REFINEMENT	PHENIX	1.21.2_5419

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