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- EMDB-25075: PR-RT portion of HIV-1 Pol -

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Basic information

Entry
Database: EMDB / ID: EMD-25075
TitlePR-RT portion of HIV-1 Pol
Map dataFull-map generated by Focussed Classification
Sample
  • Complex: PR-RT portion of HIV-1 Pol
    • Protein or peptide: PR-RT portion of HIV-1 Pol
Biological speciesHuman immunodeficiency virus type 1 BH10
Methodsingle particle reconstruction / cryo EM / Resolution: 3.74 Å
AuthorsLyumkis D / Passos D / Arnold E / Harrison J
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI136680 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI27690 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54AI150472 United States
CitationJournal: Sci Adv / Year: 2022
Title: Cryo-EM structure of the HIV-1 Pol polyprotein provides insights into virion maturation.
Authors: Jerry Joe E K Harrison / Dario Oliveira Passos / Jessica F Bruhn / Joseph D Bauman / Lynda Tuberty / Jeffrey J DeStefano / Francesc Xavier Ruiz / Dmitry Lyumkis / Eddy Arnold /
Abstract: Key proteins of retroviruses and other RNA viruses are translated and subsequently processed from polyprotein precursors by the viral protease (PR). Processing of the HIV Gag-Pol polyprotein yields ...Key proteins of retroviruses and other RNA viruses are translated and subsequently processed from polyprotein precursors by the viral protease (PR). Processing of the HIV Gag-Pol polyprotein yields the HIV structural proteins and enzymes. Structures of the mature enzymes PR, reverse transcriptase (RT), and integrase (IN) aided understanding of catalysis and design of antiretrovirals, but knowledge of the Pol precursor architecture and function before PR cleavage is limited. We developed a system to produce stable HIV-1 Pol and determined its cryo-electron microscopy structure. RT in Pol has a similar arrangement to the mature RT heterodimer, and its dimerization may draw together two PR monomers to activate proteolytic processing. HIV-1 thus may leverage the dimerization interfaces in Pol to regulate assembly and maturation of polyprotein precursors.
History
DepositionOct 2, 2021-
Header (metadata) releaseAug 10, 2022-
Map releaseAug 10, 2022-
UpdateAug 10, 2022-
Current statusAug 10, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25075.png

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Map

FileDownload / File: emd_25075.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull-map generated by Focussed Classification
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 256 pix.
= 259.84 Å		1.02 Å/pix.
x 256 pix.
= 259.84 Å		1.02 Å/pix.
x 256 pix.
= 259.84 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.015 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 5.0
Minimum - Maximum-8.842363 - 17.400097
Average (Standard dev.)0.0062616 (±0.5817917)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 259.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Full-map generated by Focussed Classification filtered by 2

Fileemd_25075_additional_1.map
AnnotationFull-map generated by Focussed Classification filtered by 2
Projections & Slices
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Additional map: Half-map 1

Fileemd_25075_additional_2.map
AnnotationHalf-map 1
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Additional map: Half-map 2

Fileemd_25075_additional_3.map
AnnotationHalf-map 2
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Sample components

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Entire : PR-RT portion of HIV-1 Pol

EntireName: PR-RT portion of HIV-1 Pol
Components
  • Complex: PR-RT portion of HIV-1 Pol
    • Protein or peptide: PR-RT portion of HIV-1 Pol

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Supramolecule #1: PR-RT portion of HIV-1 Pol

SupramoleculeName: PR-RT portion of HIV-1 Pol / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: 3D reconstruction of the HIV-1 Pol polyprotein comprising the PR-RT portion
Source (natural)Organism: Human immunodeficiency virus type 1 BH10
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
Molecular weightExperimental: 119 KDa

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Macromolecule #1: PR-RT portion of HIV-1 Pol

MacromoleculeName: PR-RT portion of HIV-1 Pol / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus type 1 BH10
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGRDNNSPSE AGADRQGTVS FNFPQITLWQ RPLVTIKIGG QLKEALLATG ADDTVLEEMS LPGRWKPKMI GGIGGFIKVR QYDQILIEIC GHKAIGTVLV GPTPVNIIGR NLLTQIGCTL NFPISPIETV PVKLKPGMDG PKVKQWPLTE EKIKALVEIC TEMEKEGKIS ...String:
MGRDNNSPSE AGADRQGTVS FNFPQITLWQ RPLVTIKIGG QLKEALLATG ADDTVLEEMS LPGRWKPKMI GGIGGFIKVR QYDQILIEIC GHKAIGTVLV GPTPVNIIGR NLLTQIGCTL NFPISPIETV PVKLKPGMDG PKVKQWPLTE EKIKALVEIC TEMEKEGKIS KIGPENPYNT PVFAIKKKDS TKWRKLVDFR ELNKRTQDFW EVQLGIPHPA GLKKKKSVTV LDVGDAYFSV PLDEDFRKYT AFTIPSINNE TPGIRYQYNV LPQGWKGSPA IFQSSMTKIL EPFKKQNPDI VIYQYMDDLY VGSDLEIGQH RTKIEELRQH LLRWGLTTPD KKHQKEPPFL WMGYELHPDK WTVQPIVLPE KDSWTVNDIQ KLVGKLNWAS QIYPGIKVRQ LCKLLRGTKA LTEVIPLTEE AELELAENRE ILKEPVHGVY YDPSKDLIAE IQKQGQGQWT YQIYQEPFKN LKTGKYARMR GAHTNDVKQL TEAVQKITTE SIVIWGKTPK FKLPIQKETW ETWWTEYWQA TWIPEWEFVN TPPLVKLWYQ LEKEPIVGAE TFYVDGAANR ETKLGKAGYV TNKGRQKVVP LTNTTNQKTE LQAIYLALQD SGLEVNIVTD SQYALGIIQA QPDKSESELV NQIIEQLIKK EKVYLAWVPA HKGIGGNEQV DKLVSAGIRK ID

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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

Concentration0.3 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 2710 pixel / Average electron dose: 0.95 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 27555
CTF correctionSoftware - Name: Warp
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.74 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM (ver. 1.0) / Number images used: 11025
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 2 / Software - Name: cisTEM

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Atomic model buiding 1

Initial model(PDB ID:

1dlo

,

3bgr

,

2hb4

)
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coeficient

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