9C29 | pdb_00009c29

Hexadecamer of NL4-3 WT HIV-1 intasome

• PDB DOI: https://doi.org/10.2210/pdb9C29/pdb
• EM Map EMD-45151: EMDB EMDataResource
• NAKB: 9C29

• Classification: VIRAL PROTEIN/DNA
• Organism(s): HIV-1 06TG.HT008
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2024-05-30 Released: 2025-06-25 
• Deposition Author(s): Lyumkis, D., Jing, T., Zhang, Z.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 8.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental

Literature

Oligomeric HIV-1 Integrase Structures Reveal Functional Plasticity for Intasome Assembly and RNA Binding

Jing, T., Shan, Z., Dinh, T., Biswas, A., Jang, S., Greenwood, J., Li, M., Zhang, Z., Gray, G., Shin, H.J., Zhou, B., Passos, D., Strutzenberg, T.S., Aiyer, S., Andrade, L., Zhang, Y., Li, Z., Craigie, R., Engelman, A.N., Kvaratskhelia, M., Lyumkis, D.

(2025) bioRxiv 

• DOI: https://doi.org/10.1101/2024.01.26.577436

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 16-mer - A16 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 538.05 kDa 
• Atom Count: 21,300 
• Modeled Residue Count: 4,102 
• Deposited Residue Count: 4,680 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrase	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	288	HIV-1 06TG.HT008	Mutation(s): 0  Gene Names: gag-pol EC: 2.7.7 (PDB Primary Data), 3.1 (PDB Primary Data)
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5)) Explore P12497  Go to UniProtKB:  P12497

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*CP*TP*GP*CP*TP*AP*GP*AP*GP*AP*TP*TP*TP*TP*CP*CP*CP*G)-3')	Q, S	19	HIV-1 06TG.HT008

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*GP*GP*GP*AP*AP*AP*AP*TP*CP*TP*CP*TP*AP*GP*CP*A)-3')	R, T	17	HIV-1 06TG.HT008

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	U [auth A], V [auth A], W [auth I], X [auth I]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 8.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.2

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-25 
Deposition Author(s): Lyumkis, D., Jing, T., Zhang, Z.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI136680
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI146017
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI170855
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI039394
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI170791

Revision History  

• Version 1.0: 2025-06-25
  Type: Initial release