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- EMDB-44962: Tetrameric Complex of full-length HIV-1 integrase protein bound t... -

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Basic information

Entry
Database: EMDB / ID: EMD-44962
TitleTetrameric Complex of full-length HIV-1 integrase protein bound to the integrase binding domain of LEDGF/p75
Map data
Sample
  • Complex: Full-length tetrameric HIV-1 integrase bound to LEDGF IBD
    • Protein or peptide: PC4 and SFRS1-interacting protein
    • Protein or peptide: Integrase
KeywordsVIral protein / protein complex / hydrolase
Function / homology
Function and homology information


supercoiled DNA binding / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / 2-LTR circle formation / Formation of WDR5-containing histone-modifying complexes / Vpr-mediated nuclear import of PICs / mRNA 5'-splice site recognition / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / heterochromatin ...supercoiled DNA binding / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / 2-LTR circle formation / Formation of WDR5-containing histone-modifying complexes / Vpr-mediated nuclear import of PICs / mRNA 5'-splice site recognition / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / heterochromatin / nuclear periphery / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / euchromatin / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / response to heat / viral nucleocapsid / response to oxidative stress / DNA recombination / DNA-binding transcription factor binding / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / transcription coactivator activity / chromatin remodeling / symbiont-mediated suppression of host gene expression / viral translational frameshifting / lipid binding / chromatin binding / symbiont entry into host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / positive regulation of transcription by RNA polymerase II / proteolysis / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / membrane / cytosol
Similarity search - Function
Lens epithelium-derived growth factor, integrase-binding domain / HIV integrase-binding domain superfamily / Lens epithelium-derived growth factor (LEDGF) / TFIIS/LEDGF domain superfamily / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Reverse transcriptase connection / Reverse transcriptase connection domain ...Lens epithelium-derived growth factor, integrase-binding domain / HIV integrase-binding domain superfamily / Lens epithelium-derived growth factor (LEDGF) / TFIIS/LEDGF domain superfamily / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP 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
PC4 and SFRS1-interacting protein / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHIV type 1 (virus) / Homo sapiens (human) / HIV-1 06TG.HT008 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsJing T / Shan Z / Lyumkis D / Biswas A
Funding support United States, 5 items
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 HJ / Zhou B / Passos D / Strutzenberg TS / Aiyer S / Andrade L / Zhang Y / Li Z / Craigie R / ...Authors: Jing T / Shan Z / Dinh T / Biswas A / Jang S / Greenwood J / Li M / Zhang Z / Gray G / Shin HJ / Zhou B / Passos D / Strutzenberg TS / Aiyer S / Andrade L / Zhang Y / Li Z / Craigie R / Engelman AN / Kvaratskhelia M / Lyumkis D
History
DepositionMay 21, 2024-
Header (metadata) releaseJun 25, 2025-
Map releaseJun 25, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44962.png

Downloads & links

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Map

FileDownload / File: emd_44962.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
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AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 300 pix.
= 276. Å		0.92 Å/pix.
x 300 pix.
= 276. Å		0.92 Å/pix.
x 300 pix.
= 276. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.031
Minimum - Maximum-0.30283797 - 0.4017269
Average (Standard dev.)0.000113928705 (±0.0066194437)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 276.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_44962_msk_1.map
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Additional map: #1

Fileemd_44962_additional_1.map
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Half map: #2

Fileemd_44962_half_map_1.map
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Half map: #1

Fileemd_44962_half_map_2.map
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Sample components

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Entire : Full-length tetrameric HIV-1 integrase bound to LEDGF IBD

EntireName: Full-length tetrameric HIV-1 integrase bound to LEDGF IBD
Components
  • Complex: Full-length tetrameric HIV-1 integrase bound to LEDGF IBD
    • Protein or peptide: PC4 and SFRS1-interacting protein
    • Protein or peptide: Integrase

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Supramolecule #1: Full-length tetrameric HIV-1 integrase bound to LEDGF IBD

SupramoleculeName: Full-length tetrameric HIV-1 integrase bound to LEDGF IBD
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: HIV type 1 (virus)
Molecular weightTheoretical: 160 KDa

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Macromolecule #1: PC4 and SFRS1-interacting protein

MacromoleculeName: PC4 and SFRS1-interacting protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.460211 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
GGSMDSRLQR IHAEIKNSLK IDNLDVNRCI EALDELASLQ VTMQQAQKHT EMITTLKKIR RFKVSQVIME KSTMLYNKFK NMFLVGEGD SV

UniProtKB: PC4 and SFRS1-interacting protein

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Macromolecule #2: Integrase

MacromoleculeName: Integrase / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
EC number: Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
Source (natural)Organism: HIV-1 06TG.HT008 (virus)
Molecular weightTheoretical: 35.444297 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH SLEVLFQGPG FLDGIDKAQE EHEKYHSNWR AMASDFNLPP VVAKEIVASC DKCQLKGEAM HGQVDCSPG IWQLDCTHLE GKVILVAVHV ASGYIEAEVI PAETGQETAY FLLKLAGRWP VKTVHTDNGS NFTSTTVKAA C WWAGIKQE ...String:
MGSSHHHHHH SSGLVPRGSH SLEVLFQGPG FLDGIDKAQE EHEKYHSNWR AMASDFNLPP VVAKEIVASC DKCQLKGEAM HGQVDCSPG IWQLDCTHLE GKVILVAVHV ASGYIEAEVI PAETGQETAY FLLKLAGRWP VKTVHTDNGS NFTSTTVKAA C WWAGIKQE FGIPYNPQSQ GVIESMNKEL KKIIGQVRDQ AEHLKTAVQM AVFIHNFKRK GGIGGYSAGE RIVDIIATDI QT KELQKQI TKIQNFRVYY RDSRDPVWKG PAKLLWKGEG AVVIQDNSDI KVVPRRKAKI IRDYGKQMAG DDCVASRQDE D

UniProtKB: Gag-Pol polyprotein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.6
Component:
ConcentrationNameFormula
50.0 mMTris-HCl
750.0 mMsodium chlorideNaCl
5.0 mMDTT
10.0 %glycerolC3H5(OH)3
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
Details: Cryo-EM grids were prepared by freezing using a manual plunger in cold room at 4C.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 1-50 / Number real images: 2649 / Average electron dose: 26.5 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 45000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.7) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7) / Number images used: 102050
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 4.7)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 4.7)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

1itg

source_name: PDB, initial_model_type: experimental model

1ihv

source_name: PDB, initial_model_type: experimental model

1wja

source_name: PDB, initial_model_type: experimental model

3hph

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Correlation coefficient
Output model

PDB-9bw9:
Tetrameric Complex of full-length HIV-1 integrase protein bound to the integrase binding domain of LEDGF/p75

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