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- EMDB-8595: CryoEM Structure Refinement by Integrating NMR Chemical Shifts wi... -

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Basic information

Entry
Database: EMDB / ID: 8595
TitleCryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations
SampleHIV-1 Capsid Protein Assembly
SourceHuman immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) / virus
Map dataHIV-1 CA hexamer
Methodhelical reconstruction, at 5 Å resolution
AuthorsZhao G / Zhang P
CitationJ Phys Chem B, 2017, 121, 3853-3863

J Phys Chem B, 2017, 121, 3853-3863 StrPapers
CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations.
Juan R Perilla / Gongpu Zhao / Manman Lu / Jiying Ning / Guangjin Hou / In-Ja L Byeon / Angela M Gronenborn / Tatyana Polenova / Peijun Zhang

DateDeposition: Feb 4, 2017 / Header (metadata) release: Mar 1, 2017 / Map release: Mar 1, 2017 / Last update: Feb 4, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.035
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5upw
  • Surface level: 0.035
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

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Map

Fileemd_8595.map.gz (map file in CCP4 format, 379276 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
456 pix
1.22 Å/pix.
= 556.32 Å
456 pix
1.22 Å/pix.
= 556.32 Å
456 pix
1.22 Å/pix.
= 556.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.22 Å
Density
Contour Level:0.035 (by author), 0.035 (movie #1):
Minimum - Maximum-0.025930129 - 0.092899546
Average (Standard dev.)3.2771706E-5 (0.0012119777)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions456456456
Origin000
Limit455455455
Spacing456456456
CellA=B=C: 556.32 Å
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z1.221.221.22
M x/y/z456456456
origin x/y/z0.0000.0000.000
length x/y/z556.320556.320556.320
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS456456456
D min/max/mean-0.0260.0930.000

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Supplemental data

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Sample components

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Entire HIV-1 Capsid Protein Assembly

EntireName: HIV-1 Capsid Protein Assembly / Number of components: 2

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Component #1: protein, HIV-1 Capsid Protein Assembly

ProteinName: HIV-1 Capsid Protein Assembly / Recombinant expression: No
SourceSpecies: Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) / virus
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #2: protein, Gag polyprotein

ProteinName: Gag polyprotein / Recombinant expression: No
MassTheoretical: 24.654268 kDa
Source (engineered)Expression System: Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) / virus

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Experimental details

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Sample preparation

Specimen statehelical array
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 6.94 Å / Delta phi: -31.13 deg.
Sample solutionSpecimen conc.: 2 mg/ml / pH: 8
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 295 K / Humidity: 100 %
Details: The assembled sample (1.5 microliter) was applied to the carbon side of a glow discharged perforated Quantifoil grid, followed by application of 3 microliter of low salt buffer (100 milimolar NaCl, 50 milimolar Tris pH 8.0) on the back side of the grid, and blotting, from the back side, with a filter paper, before plunge-freezing in liquid ethane

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 41 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 31000 X (nominal) / Cs: 2.2 mm / Imaging mode: BRIGHT FIELD / Defocus: 700 - 2200 nm
Specimen HolderModel: SIDE ENTRY, EUCENTRIC
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 523

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionAlgorithm: FOURIER SPACE / Software: relion / Resolution: 5 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Refinement space: REAL
Input PDB model: 4XFX
Output model

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