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- PDB-5md8: The structure of the mature HIV-1 CA hexameric lattice with curva... -

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Entry
Database: PDB / ID: 5md8
TitleThe structure of the mature HIV-1 CA hexameric lattice with curvature parameters: tilt=17, twist=12
DescriptorGag protein
KeywordsVIRAL PROTEIN / retrovirus / HIV-1 / capsid / lattice curvature / Viral protein
Specimen sourceHuman immunodeficiency virus 1 / virus / ヒト免疫不全ウイルス 1
MethodElectron microscopy (8.6 Å resolution / Particle / Subtomogram averaging)
AuthorsMattei, S. / Glass, B. / Hagen, W.J.H. / Kraeusslich, H.-G. / Briggs, J.A.G.
CitationScience, 2016, 354, 1434-1437

Science, 2016, 354, 1434-1437 Yorodumi Papers
The structure and flexibility of conical HIV-1 capsids determined within intact virions.
Simone Mattei / Bärbel Glass / Wim J H Hagen / Hans-Georg Kräusslich / John A G Briggs

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 10, 2016 / Release: Dec 28, 2016
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 28, 2016Structure modelrepositoryInitial release
1.1Aug 30, 2017Structure modelAuthor supporting evidence / Data collection / Experimental preparation / Refinement descriptionem_3d_fitting / em_imaging_optics / em_sample_support / em_software / pdbx_audit_support_em_3d_fitting.target_criteria / _em_imaging_optics.energyfilter_name / _em_sample_support.grid_type / _em_software.name / _pdbx_audit_support.funding_organization

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Assembly

Deposited unit
A: Gag protein
B: Gag protein
F: Gag protein
W: Gag protein
a: Gag protein
b: Gag protein
f: Gag protein
C: Gag protein
D: Gag protein
E: Gag protein
G: Gag protein
H: Gag protein
I: Gag protein
J: Gag protein


Theoretical massNumber of molelcules
Total (without water)164,77514
Polyers164,77514
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Polypeptide(L)
Gag protein / Capsid protein p24 C-terminal domain


Mass: 8370.568 Da / Num. of mol.: 8
Source: (natural) Human immunodeficiency virus 1 / virus / ヒト免疫不全ウイルス 1
References: UniProt: A0A0K0V8J8

Cellular component

Molecular function

Biological process

#2: Polypeptide(L)
Gag protein / Capsid protein p24 N-terminal domain


Mass: 16301.689 Da / Num. of mol.: 6
Source: (natural) Human immunodeficiency virus 1 / virus / ヒト免疫不全ウイルス 1
References: UniProt: E9MJT0

Cellular component

Molecular function

Biological process

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SUBTOMOGRAM AVERAGING

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Sample preparation

ComponentName: Human immunodeficiency virus 1 / Type: VIRUS
Details: HIV-1 particles were produced by infection of MT-4 cells with HIV-1 strain NL43 by coculture.
Entity ID: 1, 2 / Source: NATURAL
Source (natural)Organism: Human immunodeficiency virus 1
Details of virusEmpty: NO / Enveloped: YES / Virus isolate: STRAIN / Virus type: VIRION
Natural hostOrganism: Homo sapiens
Buffer solutionpH: 7.4
Buffer componentName: PBS
SpecimenDetails: Viral particles were purified from cell culture supernatant by iodixanol gradient centrifugation.
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 / Grid type: C-flat
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 292 kelvins
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
MicroscopyMicroscope model: FEI TITAN KRIOS / Details: Nanoprobe
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 / Nominal defocus max: 6500 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 mm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 2.2 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Number of grids imaged: 1
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV
Image scansDimension width: 3710 / Dimension height: 3838 / Movie frames/image: 5

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Processing

EM software
IDNameCategoryImaging IDImage processing IDFitting ID
2SerialEMIMAGE ACQUISITION1
4IMODCTF CORRECTION1
7UCSF ChimeraMODEL FITTING1
12AV3FINAL EULER ASSIGNMENT1
13TOM ToolboxFINAL EULER ASSIGNMENT1
15AV3RECONSTRUCTION1
16TOM ToolboxRECONSTRUCTION1
Image processingDetails: Frames were aligned using MotionCorr. Tilts in a tilt series were exposure filtered for cumulative electron dose. Tomograms were reconstructed using IMOD.
CTF correctionDetails: CTF correction was performed using the ctfphaseflip program in IMOD prior to backprojection.
Type: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C1
3D reconstructionResolution: 8.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 9273
Details: The final reconstruction is obtained by averaging, without further alignment, subtomograms that were selected based on the local curvature of the hexameric lattice. This reconstruction has hexamer-hexamer curvature parameters: tilt=17, twist=12.
Number of class averages: 1 / Symmetry type: POINT
EM volume selectionDetails: Subtomograms were extracted along the manually rendered core surface of each viral particle.
Number of tomograms: 103 / Number of volumes extracted: 652618 / Reference model: reference free
Atomic model buildingRef protocol: RIGID BODY FIT / Ref space: REAL / Target criteria: Cross-correlation coefficient

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