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- EMDB-4015: A 3.9 Angstrom structure of HIV-1 CA-SP1 assembled in presence of... -

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Basic information

Entry
Database: EMDB / ID: 4015
TitleA 3.9 Angstrom structure of HIV-1 CA-SP1 assembled in presence of Bevirimat
Map data
SampleHuman immunodeficiency virus 1Subtypes of HIV:
virus / Capsid protein p24
Function / homologyRetrovirus capsid, C-terminal / Zinc finger CCHC-type profile. / gag gene protein p24 (core nucleocapsid protein) / gag gene protein p17 (matrix protein) / Zinc knuckle / Zinc finger, CCHC-type superfamily / Gag protein p6 / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal ...Retrovirus capsid, C-terminal / Zinc finger CCHC-type profile. / gag gene protein p24 (core nucleocapsid protein) / gag gene protein p17 (matrix protein) / Zinc knuckle / Zinc finger, CCHC-type superfamily / Gag protein p6 / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / Zinc finger, CCHC-type / Retroviral nucleocapsid protein Gag / Immunodeficiency lentiviral matrix, N-terminal / ISG15 antiviral mechanism / Gag protein p6 / viral budding via host ESCRT complex / host multivesicular body / viral nucleocapsid / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / zinc ion binding / Gag polyprotein
Function and homology information
SourceHuman immunodeficiency virus 1 / Human immunodeficiency virus type 1 group M subtype B (isolate NY5)
Methodsubtomogram averaging / cryo EM / 3.9 Å resolution
AuthorsSchur FKM / Obr M / Hagen WJH / Wan W / Arjen JJ / Kirkpatrick JM / Sachse C / Kraeusslich H-G / Briggs JAG
CitationJournal: Science / Year: 2016
Title: An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation.
Authors: Florian K M Schur / Martin Obr / Wim J H Hagen / William Wan / Arjen J Jakobi / Joanna M Kirkpatrick / Carsten Sachse / Hans-Georg Kräusslich / John A G Briggs
Abstract: Immature HIV-1 assembles at and buds from the plasma membrane before proteolytic cleavage of the viral Gag polyprotein induces structural maturation. Maturation can be blocked by maturation ...Immature HIV-1 assembles at and buds from the plasma membrane before proteolytic cleavage of the viral Gag polyprotein induces structural maturation. Maturation can be blocked by maturation inhibitors (MIs), thereby abolishing infectivity. The CA (capsid) and SP1 (spacer peptide 1) region of Gag is the key regulator of assembly and maturation and is the target of MIs. We applied optimized cryo-electron tomography and subtomogram averaging to resolve this region within assembled immature HIV-1 particles at 3.9 angstrom resolution and built an atomic model. The structure reveals a network of intra- and intermolecular interactions mediating immature HIV-1 assembly. The proteolytic cleavage site between CA and SP1 is inaccessible to protease. We suggest that MIs prevent CA-SP1 cleavage by stabilizing the structure, and MI resistance develops by destabilizing CA-SP1.
Validation ReportPDB-ID: 5l93

SummaryFull reportAbout validation report
DateDeposition: Jun 9, 2016 / Header (metadata) release: Jun 29, 2016 / Map release: Jul 13, 2016 / Last update: Oct 17, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.112
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.112
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5l93
  • Surface level: 0.112
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5l93
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_4015.map.gz (map file in CCP4 format, 28312 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
192 pix
1.35 Å/pix.
= 259.2 Å
192 pix
1.35 Å/pix.
= 259.2 Å
192 pix
1.35 Å/pix.
= 259.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density
Contour Level:0.112 (by author), 0.112 (movie #1):
Minimum - Maximum-0.29335153 - 0.5368952
Average (Standard dev.)0.0006436251 (0.04243836)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions192192192
Origin0.00.00.0
Limit191.0191.0191.0
Spacing192192192
CellA=B=C: 259.2 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z259.200259.200259.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.2930.5370.001

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Supplemental data

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Sample components

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Entire Human immunodeficiency virus 1

EntireName: Human immunodeficiency virus 1
Details: Virus-like particles were obtained by in vitro assembly of a truncated Gag construct (deltaMACANCSP2) in presence of the maturation inhibitor Bevirimat
Number of components: 2

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Component #1: virus, Human immunodeficiency virus 1

VirusName: Human immunodeficiency virus 1Subtypes of HIV / Class: VIRUS-LIKE PARTICLE
Details: Virus-like particles were obtained by in vitro assembly of a truncated Gag construct (deltaMACANCSP2) in presence of the maturation inhibitor Bevirimat
Empty: Yes / Enveloped: No / Isolate: OTHER
SpeciesSpecies: Human immunodeficiency virus 1
Source (engineered)Expression System: Escherichia coli (E. coli) / Vector: pET11C
Source (natural)Host Species: Homo sapiens (human)

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Component #2: protein, Capsid protein p24

ProteinName: Capsid protein p24 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 24.789396 kDa
SourceSpecies: Human immunodeficiency virus type 1 group M subtype B (isolate NY5)
Strain: isolate NY5
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 5 mg/ml
Buffer solution: Virus-like particles were assembled in the presence of nucleic acid (73mer oligonucleotide, 1:10 molar ratio oligonucleotide:protein).
pH: 8
Support filmat 20 mA
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Temperature: 15 K / Humidity: 95 %
Details: 10nM colloidal gold was added to the sample prior to plunge freezing..

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Details: Nanoprobe
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 3.4 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 105000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500.0 - 5000.0 nm / Energy filter: GIF Quantum LS / Energy window: 0-20 eV
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image acquisition

Image acquisitionDetails: Number of frames ranged from 8-10 Exposure time per tilt ranged from 0.8 to 1.0 seconds
Raw dataEMPIAR-10164 (Title: Cryo-electron tomography of immature HIV-1 dMACANC VLPs
Data size: 865.0
Data #1: Compressed, unaligned, multi-frame micrographs of tilt series containing HIV-1 dMACANC virus like particles assembled in the presence of BVM. [micrographs - multiframe])

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Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C6 (6 fold cyclic) / Number of subtomograms: 128733
Details: Frames were aligned using MotionCorr. Tilts in a tilt series were exposure filtered for cumulative electron dose. Tomograms were reconstructed using IMOD.
3D reconstructionSoftware: AV3, TOM Toolbox
CTF correction: CTF correction was performed using the ctfphaseflip program in IMOD prior to backprojection.
Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Euler angles: Cross-correlation based template matching

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Atomic model buiding

Modeling #1Input PDB model: 1L6N, 3DS2, 1U57
Chain ID: 1, 1, 2
Output model

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