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- EMDB-27625: Helical reconstruction of A92E HIV capsid in presence of FG mutan... -

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Basic information

Entry
Database: EMDB / ID: EMD-27625
TitleHelical reconstruction of A92E HIV capsid in presence of FG mutant CPSF6 construct (filtered by local resolution)
Map dataHelical reconstruction of A92E HIV capsid in presence of FG mutant CPSF6 construct (filtered by local resolution)
Sample
  • Complex: HIV Capsid Protein Hexamer
    • Protein or peptide: HIV Capsid
Biological speciesHuman immunodeficiency virus 1
Methodhelical reconstruction / cryo EM / Resolution: 7.0 Å
AuthorsIqbal N / Asturias F / Kvaratskhelia M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nat Commun / Year: 2022
Title: Prion-like low complexity regions enable avid virus-host interactions during HIV-1 infection.
Authors: Guochao Wei / Naseer Iqbal / Valentine V Courouble / Ashwanth C Francis / Parmit K Singh / Arpa Hudait / Arun S Annamalai / Stephanie Bester / Szu-Wei Huang / Nikoloz Shkriabai / Lorenzo ...Authors: Guochao Wei / Naseer Iqbal / Valentine V Courouble / Ashwanth C Francis / Parmit K Singh / Arpa Hudait / Arun S Annamalai / Stephanie Bester / Szu-Wei Huang / Nikoloz Shkriabai / Lorenzo Briganti / Reed Haney / Vineet N KewalRamani / Gregory A Voth / Alan N Engelman / Gregory B Melikyan / Patrick R Griffin / Francisco Asturias / Mamuka Kvaratskhelia /
Abstract: Cellular proteins CPSF6, NUP153 and SEC24C play crucial roles in HIV-1 infection. While weak interactions of short phenylalanine-glycine (FG) containing peptides with isolated capsid hexamers have ...Cellular proteins CPSF6, NUP153 and SEC24C play crucial roles in HIV-1 infection. While weak interactions of short phenylalanine-glycine (FG) containing peptides with isolated capsid hexamers have been characterized, how these cellular factors functionally engage with biologically relevant mature HIV-1 capsid lattices is unknown. Here we show that prion-like low complexity regions (LCRs) enable avid CPSF6, NUP153 and SEC24C binding to capsid lattices. Structural studies revealed that multivalent CPSF6 assembly is mediated by LCR-LCR interactions, which are templated by binding of CPSF6 FG peptides to a subset of hydrophobic capsid pockets positioned along adjoining hexamers. In infected cells, avid CPSF6 LCR-mediated binding to HIV-1 cores is essential for functional virus-host interactions. The investigational drug lenacapavir accesses unoccupied hydrophobic pockets in the complex to potently impair HIV-1 inside the nucleus without displacing the tightly bound cellular cofactor from virus cores. These results establish previously undescribed mechanisms of virus-host interactions and antiviral action.
History
DepositionJul 14, 2022-
Header (metadata) releaseSep 7, 2022-
Map releaseSep 7, 2022-
UpdateJan 11, 2023-
Current statusJan 11, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27625.png

Downloads & links

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Map

FileDownload / File: emd_27625.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHelical reconstruction of A92E HIV capsid in presence of FG mutant CPSF6 construct (filtered by local resolution)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.8 Å/pix.
x 300 pix.
= 840. Å		2.8 Å/pix.
x 300 pix.
= 840. Å		2.8 Å/pix.
x 300 pix.
= 840. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.059
Minimum - Maximum-0.04103221 - 0.19300179
Average (Standard dev.)0.0013016879 (±0.01798274)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 840.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map 1

Fileemd_27625_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 2

Fileemd_27625_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HIV Capsid Protein Hexamer

EntireName: HIV Capsid Protein Hexamer
Components
  • Complex: HIV Capsid Protein Hexamer
    • Protein or peptide: HIV Capsid

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Supramolecule #1: HIV Capsid Protein Hexamer

SupramoleculeName: HIV Capsid Protein Hexamer / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: HIV Capsid

MacromoleculeName: HIV Capsid / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: PIVQNLQGQM VHQCISPRTL NAWVKVVEEK AFSPEVIPMF SALSCGATPQ DLNTMLNTVG GHQAAMQMLK ETINEEAAEW DRLHPVHAGP IAPGQMREPR GSDIAGTTST LQEQIGWMTH NPPIPVGEIY KRWIILGLNK IVRMYSPTSI LDIRQGPKEP FRDYVDRFYK ...String:
PIVQNLQGQM VHQCISPRTL NAWVKVVEEK AFSPEVIPMF SALSCGATPQ DLNTMLNTVG GHQAAMQMLK ETINEEAAEW DRLHPVHAGP IAPGQMREPR GSDIAGTTST LQEQIGWMTH NPPIPVGEIY KRWIILGLNK IVRMYSPTSI LDIRQGPKEP FRDYVDRFYK TLRAEQASQE VKNAATETLL VQNANPDCKT ILKALGPGAT LEEMMTACQG VGGPGHKARV L

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation state3D array

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Sample preparation

Concentration3 mg/mL
BufferpH: 8 / Details: 1M NaCl, 50mM Tris pH 8, 0.2mM IP6
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 2 / Number real images: 2157 / Average electron dose: 45.65 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 28000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 28000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 6.95455 Å
Applied symmetry - Helical parameters - Δ&Phi: 82.5822 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 7.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 3023
Segment selectionNumber selected: 109696 / Software - Name: RELION
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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