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- PDB-3j4f: Structure of HIV-1 capsid protein by cryo-EM -

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Basic information

Entry
Database: PDB / ID: 3j4f
TitleStructure of HIV-1 capsid protein by cryo-EM
Descriptorcapsid protein
KeywordsVIRAL PROTEIN / HIV-1 capsid / core / all-atom model / MDFF / tubular assembly / hexamer
Specimen sourceHuman immunodeficiency virus 1 / virus / HIV-1 / ヒト免疫不全ウイルス 1
MethodElectron microscopy (8.6 Å resolution / Helical array / Helical)
AuthorsZhao, G. / Perilla, J.R. / Meng, X. / Schulten, K. / Zhang, P.
CitationNature, 2013, 497, 643-646

Nature, 2013, 497, 643-646 StrPapers
Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics.
Gongpu Zhao / Juan R Perilla / Ernest L Yufenyuy / Xin Meng / Bo Chen / Jiying Ning / Jinwoo Ahn / Angela M Gronenborn / Klaus Schulten / Christopher Aiken / Peijun Zhang

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 11, 2013 / Release: Jul 24, 2013

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Structure visualization

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  • Biological unit as representative helical assembly
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-5582
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Assembly

Deposited unit
A: capsid protein
B: capsid protein
C: capsid protein
D: capsid protein
E: capsid protein
F: capsid protein


Theoretical massNumber of molelcules
Total (without water)154,2156
Polyers154,2156
Non-polymers00
Water0
#1
A: capsid protein
B: capsid protein
C: capsid protein
D: capsid protein
E: capsid protein
F: capsid protein
x 35


Theoretical massNumber of molelcules
Total (without water)5,397,523210
Polyers5,397,523210
Non-polymers00
Water0
TypeNameSymmetry operationNumber
helical symmetry operation35
#2


  • idetical with deposited unit in distinct coordinate
  • helical asymmetric unit
TypeNameSymmetry operationNumber
helical symmetry operation1
#3


  • idetical with deposited unit in distinct coordinate
  • helical asymmetric unit, std helical frame
TypeNameSymmetry operationNumber
transform to helical frame1

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Components

#1: Polypeptide(L)
capsid protein


Mass: 25702.490 Da / Num. of mol.: 6 / Fragment: UNP residues 133-363 / Mutation: A92E
Source: (gene. exp.) Human immunodeficiency virus 1 / virus / ヒト免疫不全ウイルス 1
References: UniProt: Q79791

Cellular component

Molecular function

Biological process

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / Reconstruction method: HELICAL

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Sample preparation

ComponentName: HIV-1 capsid protein / Type: COMPLEX / Details: hexamer / Synonym: HIV CA
Molecular weightValue: 0.025 deg. / Units: MEGADALTONS / Experimental value: NO
Buffer solutionName: 1 M NaCl, 50 mM Tris-HCl / Details: 1 M NaCl, 50 mM Tris-HCl / pH: 8
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 200 mesh quantifoil R2/1 copper grid
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temp: 95 K / Humidity: 80 %
Details: With 2.5 uL sample on carbon side, add 3 uL dilution buffer (100 mM NaCl, 50 mM Tris, pH 8.0) to back side. Blot 3-5 seconds from back side and plunge into liquid ethane with a homemade plunger.
Method: With 2.5 uL sample on carbon side, add 3 uL dilution buffer (100 mM NaCl, 50 mM Tris, pH 8.0) to back side. Blot 3-5 seconds from back side.

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI POLARA 300 / Date: Dec 11, 2010
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 / Calibrated magnification: 58257 / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Cs: 2 mm / Camera length: 0 mm
Specimen holderSpecimen holder model: OTHER / Specimen holder type: Polara cartridge / Temperature: 82 kelvins / Temperature (max): 85 kelvins / Temperature (min): 80 kelvins / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
Image recordingElectron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNumber digital images: 27
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1MDFFMODEL FITTING
2FrealignRECONSTRUCTION
CTF correctionDetails: each filament
Helical symmertyAngular rotation/subunit: 31.13 deg. / Axial rise/subunit: 7.247 Å / Axial symmetry: C1
3D reconstructionMethod: real space helical reconstruction / Resolution: 8.6 Å / Resolution method: FSC 0.5 CUT-OFF / Number of particles: 3210 / Actual pixel size: 1.09
Details: (Helical Details: The segments were aligned and reconstructed using Frealign. Twofold symmetry was imposed using IHRSR++.)
Symmetry type: HELICAL
Atomic model building
IDDetailsRef protocolRef space
1METHOD--Seven hexamers were docked into density then solvated into 1M NaCl. Secondary structure restraints were applied to helices 1 to 11. MDFF was run for 10 ns with symmetry restraints between CA monomers along the chiral axis. The center hexamer was then extracted. PDB entries 3H47 and 2KOD were the starting structures. REFINEMENT PROTOCOL--flexibleFLEXIBLE FITREAL
2METHOD--Seven hexamers were docked into density then solvated into 1M NaCl. Secondary structure restraints were applied to helices 1 to 11. MDFF was run for 10 ns with symmetry restraints between CA monomers along the chiral axis. The center hexamer was then extracted. PDB entries 3H47 and 2KOD were the starting structures. REFINEMENT PROTOCOL--flexibleFLEXIBLE FITREAL
Atomic model building
IDPDB-ID 3D fitting ID
12KOD1
23H472
Number of atoms included #LASTProtein: 10799 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 10799

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