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- EMDB-45104: Top half of NL4-3 WT HIV-1 intasome -

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Basic information

Entry
Database: EMDB / ID: EMD-45104
TitleTop half of NL4-3 WT HIV-1 intasome
Map data
Sample
  • Complex: crosslinked wild-type NL4-3 HIV-1 Intasome
KeywordsViral protein / protein complex
Biological speciesHIV type 1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.0 Å
AuthorsLyumkis D / Jing T / Zhang Z
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 28, 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_45104.png

Downloads & links

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Map

FileDownload / File: emd_45104.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 320 pix.
= 324.8 Å		1.02 Å/pix.
x 320 pix.
= 324.8 Å		1.02 Å/pix.
x 320 pix.
= 324.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.015 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.5177839 - 1.4013926
Average (Standard dev.)0.000833154 (±0.053286336)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 324.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45104_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: this is the unsharpened map

Fileemd_45104_additional_1.map
Annotationthis is the unsharpened map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_45104_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_45104_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : crosslinked wild-type NL4-3 HIV-1 Intasome

EntireName: crosslinked wild-type NL4-3 HIV-1 Intasome
Components
  • Complex: crosslinked wild-type NL4-3 HIV-1 Intasome

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Supramolecule #1: crosslinked wild-type NL4-3 HIV-1 Intasome

SupramoleculeName: crosslinked wild-type NL4-3 HIV-1 Intasome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: HIV type 1 (virus)
Molecular weightTheoretical: 600 KDa

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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: 6.2
Component:
ConcentrationNameFormula
20.0 mMTris-HCl
1000.0 mMsodium chlorideNaCl
0.5 mMTCEP
10.0 %glycerolC3H5(OH)3
5.0 mMMagnesium chlorideMgCl2
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY
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

MicroscopeTFS KRIOS
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: 775 / Average exposure time: 12.0 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 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: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 29000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 5.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2) / Number images used: 11658
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 4.2)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 4.2)
FSC plot (resolution estimation)

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