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- EMDB-8582: Structure of the HIV-1 Capsid Protein and spacer peptide 1 by Cryo-EM -

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Basic information

Entry
Database: EMDB / ID: 8582
TitleStructure of the HIV-1 Capsid Protein and spacer peptide 1 by Cryo-EM
Map dataCryoEM structure of HIV-1 capsid protein and spacer peptide-1 (CA-SP1)
SampleHIV-1 CA-SP1
  • HIV-1 Capsid Protein and spacer peptide 1
Function / homologyRetrovirus capsid, C-terminal / Zinc finger, CCHC-type / Zinc knuckle / Zinc finger, CCHC-type superfamily / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / Retroviral nucleocapsid protein Gag / gag gene protein p24 (core nucleocapsid protein) / Immunodeficiency lentiviral matrix, N-terminal ...Retrovirus capsid, C-terminal / Zinc finger, CCHC-type / Zinc knuckle / Zinc finger, CCHC-type superfamily / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / Retroviral nucleocapsid protein Gag / gag gene protein p24 (core nucleocapsid protein) / Immunodeficiency lentiviral matrix, N-terminal / Zinc finger CCHC-type profile. / gag gene protein p17 (matrix protein) / viral nucleocapsid / host cell cytoplasm / host cell nucleus / viral process / structural molecule activity / RNA binding / zinc ion binding / Gag polyprotein
Function and homology information
SourceHuman immunodeficiency virus 1
Methodhelical reconstruction / cryo EM / 9 Å resolution
AuthorsZhang P / Randall S
CitationJournal: Nat Commun / Year: 2017
Title: Quenching protein dynamics interferes with HIV capsid maturation.
Authors: Mingzhang Wang / Caitlin M Quinn / Juan R Perilla / Huilan Zhang / Randall Shirra / Guangjin Hou / In-Ja Byeon / Christopher L Suiter / Sherimay Ablan / Emiko Urano / Theodore J Nitz / Christopher Aiken / Eric O Freed / Peijun Zhang / Klaus Schulten / Angela M Gronenborn / Tatyana Polenova
Validation ReportPDB-ID: 5up4

SummaryFull reportAbout validation report
DateDeposition: Feb 1, 2017 / Header (metadata) release: Jul 12, 2017 / Map release: Dec 6, 2017 / Last update: Dec 13, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.027
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.027
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5up4
  • Surface level: 0.027
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5up4
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8582.map.gz (map file in CCP4 format, 488096 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
496 pix
1.1 Å/pix.
= 545.6 Å
496 pix
1.1 Å/pix.
= 545.6 Å
496 pix
1.1 Å/pix.
= 545.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density
Contour Level:0.027 (by emdb), 0.027 (movie #1):
Minimum - Maximum-0.005759892 - 0.046030093
Average (Standard dev.)0.0023228726 (0.006946994)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions496496496
Origin000
Limit495495495
Spacing496496496
CellA=B=C: 545.60004 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z496496496
origin x/y/z0.0000.0000.000
length x/y/z545.600545.600545.600
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS496496496
D min/max/mean-0.0060.0460.002

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Supplemental data

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Sample components

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Entire HIV-1 CA-SP1

EntireName: HIV-1 CA-SP1 / Number of components: 2

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Component #1: protein, HIV-1 CA-SP1

ProteinName: HIV-1 CA-SP1 / Recombinant expression: No
SourceSpecies: Human immunodeficiency virus 1
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, HIV-1 Capsid Protein and spacer peptide 1

ProteinName: HIV-1 Capsid Protein and spacer peptide 1 / Recombinant expression: No
MassTheoretical: 24.654268 kDa
Source (engineered)Expression System: Human immunodeficiency virus 1

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Experimental details

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Sample preparation

SpecimenSpecimen state: helical array / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 13.46 Å / Delta phi: 128.88 deg.
Sample solutionSpecimen conc.: 2.2 mg/ml / pH: 8
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 90 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 23 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 59000 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 3500 nm
Specimen HolderModel: OTHER
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 200

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionSoftware: FREALIGN / Resolution: 9 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Input PDB model: 3J34, 2KOD, 3J34, 3J34, 3J34, 3J34, 3J34
Chain ID: 3J34_A, 2KOD_A, 3J34_B, 3J34_C, 3J34_D, 3J34_E, 3J34_F
Output model

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