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- PDB-5md1: The structure of the mature HIV-1 CA hexameric lattice with curva... -

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Basic information

Entry
Database: PDB / ID: 5md1
TitleThe structure of the mature HIV-1 CA hexameric lattice with curvature parameters: tilt=5, twist=0
DescriptorCapsid protein p24
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 (8.2 A resolution / 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 StrPapers
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

DateDeposition: Nov 10, 2016 / Release: Dec 28, 2016

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Assembly

Deposited unit
A: Capsid protein p24
B: Capsid protein p24
F: Capsid protein p24
W: Capsid protein p24
a: Capsid protein p24
b: Capsid protein p24
f: Capsid protein p24
C: Capsid protein p24
D: Capsid protein p24
E: Capsid protein p24
G: Capsid protein p24
H: Capsid protein p24
I: Capsid protein p24
J: Capsid protein p24


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)
Capsid protein p24


Mass: 8370.568 Da / Num. of mol.: 8 / Fragment: C-terminal domain, UNP residues 141-214
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)
Capsid protein p24


Mass: 16301.689 Da / Num. of mol.: 6 / Fragment: N-terminal domain, UNP residues 123-269
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 experimentReconstruction method: SUBTOMOGRAM AVERAGING

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Sample preparation

ComponentName: Human immunodeficiency virus 1
Details: HIV-1 particles were produced by infection of MT-4 cells with HIV-1 strain NL43 by coculture.
Type: VIRUS
Details of the virusEmpty: NO / Enveloped: YES / Virus isolate: STRAIN / Virus type: VIRION
Specimen supportGrid material: COPPER / Grid mesh size: 300 / Grid type: C-Flat
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 %
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 / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 / Nominal defocus max: 6500 / Nominal defocus min: 2000 / Cs: 2.7
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER

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Processing

3D reconstructionResolution: 8.2 / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 16208
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=5, twist=0.
Number of class averages: 1
Atomic model buildingRef protocol: RIGID BODY FIT / Ref space: REAL / Target criteria: Correlation coefficient

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