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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
Map dataHIV-1 CA hexamer
SampleHIV-1 Capsid Protein Assembly:
Gag polyproteinGroup-specific antigen
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 type 1 (NEW YORK-5 ISOLATE)
Methodhelical reconstruction / cryo EM / 5 Å resolution
AuthorsZhao G / Zhang P
CitationJournal: J Phys Chem B / Year: 2017
Title: CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations.
Authors: Juan R Perilla / Gongpu Zhao / Manman Lu / Jiying Ning / Guangjin Hou / In-Ja L Byeon / Angela M Gronenborn / Tatyana Polenova / Peijun Zhang
Validation ReportPDB-ID: 5upw

SummaryFull reportAbout validation report
DateDeposition: Feb 4, 2017 / Header (metadata) release: Mar 1, 2017 / Map release: Mar 1, 2017 / Last update: Dec 6, 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
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  • Surface view with fitted model
  • Atomic models: : PDB-5upw
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8595.png

Downloads & links

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Map

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

Image control

Size
Brightness
Contrast
Others
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.

Voxel sizeX=Y=Z: 1.22 Å
Density

Histogram

Histogram (log scale)
Contour Level:0.035 (by author), 0.035 (movie #1):
Minimum - Maximum-0.025930129 - 0.092899546
Average (Standard dev.)0.000032771706 (0.0012119777)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions456456456
Origin0.00.00.0
Limit455.0455.0455.0
Spacing456456456
CellA=B=C: 556.32 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/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
α/β/γ90.00090.00090.000
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
MassTheoretical: 24 MDa
SourceSpecies: Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, Gag polyprotein

ProteinName: Gag polyproteinGroup-specific antigen / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 24.654268 kDa
SourceSpecies: Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: helical array / Method: cryo EM
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: 31000.0 X (nominal) / Cs: 2.2 mm / Imaging mode: BRIGHT FIELD / Defocus: 700.0 - 2200.0 nm
Specimen HolderModel: SIDE ENTRY, EUCENTRIC
CameraDetector: GATAN K2 SUMMIT (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 estimation)

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Atomic model buiding

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

4xfx

Output model

5upw

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