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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 / Integration of provirus / mRNA 5'-splice site recognition / 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 / Integration of provirus / mRNA 5'-splice site recognition / 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 / telomerase activity / viral penetration into host nucleus / RNA stem-loop binding / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / response to heat / viral nucleocapsid / DNA-binding transcription factor binding / DNA recombination / response to oxidative stress / 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 / symbiont entry into host cell / viral translational frameshifting / lipid binding / chromatin binding / 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
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 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-
UpdateJun 25, 2025-
Current statusJun 25, 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
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

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
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_44962_additional_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_44962_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_44962_half_map_2.map
Projections & Slices
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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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