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- PDB-9c29: Hexadecamer of NL4-3 WT HIV-1 intasome -

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Basic information

Entry
Database: PDB / ID: 9c29
TitleHexadecamer of NL4-3 WT HIV-1 intasome
Components
  • DNA (5'-D(*AP*CP*TP*GP*CP*TP*AP*GP*AP*GP*AP*TP*TP*TP*TP*CP*CP*CP*G)-3')
  • DNA (5'-D(P*CP*GP*GP*GP*AP*AP*AP*AP*TP*CP*TP*CP*TP*AP*GP*CP*A)-3')
  • Integrase
KeywordsVIRAL PROTEIN/DNA / Viral protein / protein complex / VIRAL PROTEIN-DNA complex
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / viral penetration into host nucleus / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / viral translational frameshifting / lipid binding / symbiont entry into host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain ...Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHIV-1 06TG.HT008 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8 Å
AuthorsLyumkis, D. / Jing, T. / Zhang, Z.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI136680 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI146017 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI170855 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI039394 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI170791 United States
Citation
Journal: Nat Commun / Year: 2025
Title: Oligomeric HIV-1 integrase structures reveal functional plasticity for intasome assembly and RNA binding.
Authors: Tao Jing / Zelin Shan / Tung Dinh / Avik Biswas / Sooin Jang / Juliet Greenwood / Min Li / Zeyuan Zhang / Gennavieve Gray / Hye Jeong Shin / Bo Zhou / Dario Passos / Timothy S Strutzenberg / ...Authors: Tao Jing / Zelin Shan / Tung Dinh / Avik Biswas / Sooin Jang / Juliet Greenwood / Min Li / Zeyuan Zhang / Gennavieve Gray / Hye Jeong Shin / Bo Zhou / Dario Passos / Timothy S Strutzenberg / Sriram Aiyer / Leonardo Andrade / Yuxuan Zhang / Zhen Li / Robert Craigie / Alan N Engelman / Mamuka Kvaratskhelia / Dmitry Lyumkis /
Abstract: Integrase (IN) performs dual essential roles during HIV-1 replication. During ingress, IN functions within an oligomeric "intasome" assembly to catalyze viral DNA integration into host chromatin. ...Integrase (IN) performs dual essential roles during HIV-1 replication. During ingress, IN functions within an oligomeric "intasome" assembly to catalyze viral DNA integration into host chromatin. During late stages of infection, tetrameric IN binds viral RNA and orchestrates the condensation of ribonucleoprotein complexes into the capsid core. The molecular architectures of HIV-1 IN assemblies that mediate these distinct events remain unknown. Furthermore, the IN tetramer is an important antiviral target for investigational allosteric IN inhibitors. Here, we determined cryo-EM structures of wildtype HIV-1 IN tetramers and intasome hexadecamers. Our structures unveil a remarkable plasticity that leverages IN C-terminal domains and abutting linkers to assemble functionally distinct oligomeric forms. Alteration of a newly recognized conserved interface revealed that both IN functions track with tetramerization in vitro and during HIV-1 infection. Collectively, our findings reveal how IN plasticity orchestrates its diverse molecular functions and suggest a working model for IN-viral RNA binding. Moreover, our structure of the IN tetramer provides atomic blueprints for the rational development of improved allosteric inhibitors.
#1: Journal: Biorxiv / Year: 2025
Title: Oligomeric HIV-1 Integrase Structures Reveal Functional Plasticity for Intasome Assembly and RNA Binding
Authors: 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. / ...Authors: 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.
History
DepositionMay 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrase
B: Integrase
C: Integrase
D: Integrase
E: Integrase
F: Integrase
G: Integrase
H: Integrase
I: Integrase
J: Integrase
K: Integrase
L: Integrase
M: Integrase
N: Integrase
O: Integrase
P: Integrase
Q: DNA (5'-D(*AP*CP*TP*GP*CP*TP*AP*GP*AP*GP*AP*TP*TP*TP*TP*CP*CP*CP*G)-3')
R: DNA (5'-D(P*CP*GP*GP*GP*AP*AP*AP*AP*TP*CP*TP*CP*TP*AP*GP*CP*A)-3')
S: DNA (5'-D(*AP*CP*TP*GP*CP*TP*AP*GP*AP*GP*AP*TP*TP*TP*TP*CP*CP*CP*G)-3')
T: DNA (5'-D(P*CP*GP*GP*GP*AP*AP*AP*AP*TP*CP*TP*CP*TP*AP*GP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)538,04624
Polymers537,94920
Non-polymers974
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Integrase / IN


Mass: 32244.787 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 06TG.HT008 (virus) / Gene: gag-pol
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P12497, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds
#2: DNA chain DNA (5'-D(*AP*CP*TP*GP*CP*TP*AP*GP*AP*GP*AP*TP*TP*TP*TP*CP*CP*CP*G)-3')


Mass: 5795.758 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HIV-1 06TG.HT008 (virus)
#3: DNA chain DNA (5'-D(P*CP*GP*GP*GP*AP*AP*AP*AP*TP*CP*TP*CP*TP*AP*GP*CP*A)-3')


Mass: 5220.413 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HIV-1 06TG.HT008 (virus)
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: crosslinked wild-type NL4-3 HIV-1 Intasome / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.6 MDa / Experimental value: YES
Source (natural)Organism: HIV type 1 (virus)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 6.2
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris-HCl1
21000 mMsodium chlorideNaCl1
30.5 mMTCEP1
410 %glycerolC3H5(OH)31
55 mMMagnesium chlorideMgCl21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE
Details: Cryo-EM grids were prepared by freezing using a manual plunger in cold room at 4C

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 29000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 12 sec. / Electron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 775
Image scansWidth: 3710 / Height: 3838 / Movie frames/image: 50 / Used frames/image: 1-50

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Processing

EM software
IDNameVersionCategory
2Leginonimage acquisition
4cryoSPARC4.2CTF correction
7UCSF Chimeramodel fitting
10cryoSPARC4.2initial Euler assignment
11cryoSPARC4.2final Euler assignment
13cryoSPARC4.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 8 Å / Resolution method: OTHER / Num. of particles: 22780
Details: 3D FSC server is used to compute map-model resolution at the threshold of 0.5. This reported resolution is not the map resolution because it is a composite map that does not have two half maps.
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation coefficient
Details: Domains of HIV-1 IN were rigid-body docked into cryo-EM density without any further refinement or adjustment of the coordinates. This rigid-body docked model was then truncated to poly- ...Details: Domains of HIV-1 IN were rigid-body docked into cryo-EM density without any further refinement or adjustment of the coordinates. This rigid-body docked model was then truncated to poly-Alanine and deposited here.
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeSource nameTypeInitial refinement model-ID
16PUT

6put

16PUTPDBexperimental model
21IHV

1ihv

11IHVPDBexperimental model2
31K6Y

1k6y

11K6YPDBexperimental model
47Z1Z

7z1z

17Z1ZPDBexperimental model
51EX4

1ex4

11EX4PDBexperimental model

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