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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 / host multivesicular body / DNA integration / 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 / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / telomerase activity / viral penetration into host nucleus / RNA stem-loop binding / 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 / symbiont entry into host cell / viral translational frameshifting / lipid binding / 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 / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retrovirus capsid, C-terminal / 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
CitationJournal: 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

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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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