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- EMDB-27599: Helical reconstruction of A92E HIV capsid in complex with CPSF6 c... -

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Basic information

Entry
Database: EMDB / ID: EMD-27599
TitleHelical reconstruction of A92E HIV capsid in complex with CPSF6 construct
Map dataHelical reconstruction of A92E HIV capsid in complex with CPSF6 construct
Sample
  • Complex: HIV Capsid Protein Hexamer
    • Protein or peptide: HIV Capsid
KeywordsComplex / VIRAL PROTEIN
Biological speciesHuman immunodeficiency virus 1
Methodhelical reconstruction / cryo EM / Resolution: 7.85 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: To Be Published
Title: Helical reconstruction of A92E HIV capsid in complex with CPSF6 construct
Authors: Iqbal N / Asturias F / Kvaratskhelia M
History
DepositionJul 13, 2022-
Header (metadata) releaseJul 19, 2023-
Map releaseJul 19, 2023-
UpdateJul 19, 2023-
Current statusJul 19, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27599.png

Downloads & links

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Map

FileDownload / File: emd_27599.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHelical reconstruction of A92E HIV capsid in complex with CPSF6 construct
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: 0.02
Minimum - Maximum-0.014869178 - 0.053707205
Average (Standard dev.)0.0008264776 (±0.006333649)
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_27599_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_27599_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 / 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: 4090 pixel / Number grids imaged: 2 / Number real images: 4706 / 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: 7.12159 Å
Applied symmetry - Helical parameters - Δ&Phi: -55.2834 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 7.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 5894
Segment selectionNumber selected: 236974 / Software - Name: RELION
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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