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- EMDB-3076: Cyclophilin A Stabilize HIV-1 Capsid through a Novel Non-canonica... -

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Entry
Database: EMDB / ID: 3076
TitleCyclophilin A Stabilize HIV-1 Capsid through a Novel Non-canonical Binding Site
SampleHelical assembly of HIV-1 capsid protein and host cell factor Cyclophilin A
SourceHuman immunodeficiency virus 1 / virus / ヒト免疫不全ウイルス 1
Map dataReconstruction by aligning both CA and Cypa
Methodhelical reconstruction, at 8 Å resolution
AuthorsLiu C / Perilla JR / Ning J / Lu M / Hou G / Ramalhu R / Bedwell GJ / Ahn J / Shi J / Gronenborn AM / Prevelige Jr PE / Rousso I / Aiken C / Polenova T / Schulten K / Zhang P
CitationNat Commun, 2016, 7, 10714-10714

Nat Commun, 2016, 7, 10714-10714 StrPapers
Cyclophilin A stabilizes the HIV-1 capsid through a novel non-canonical binding site.
Chuang Liu / Juan R Perilla / Jiying Ning / Manman Lu / Guangjin Hou / Ruben Ramalho / Benjamin A Himes / Gongpu Zhao / Gregory J Bedwell / In-Ja Byeon / Jinwoo Ahn / Angela M Gronenborn / Peter E Prevelige / Itay Rousso / Christopher Aiken / Tatyana Polenova / Klaus Schulten / Peijun Zhang

Validation ReportPDB-ID: 5fjb

SummaryFull reportAbout validation report
DateDeposition: Jul 5, 2015 / Header (metadata) release: Jul 29, 2015 / Map release: Mar 16, 2016 / Last update: Apr 6, 2016

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 15
  • Imaged by UCSF CHIMERA
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  • Surface view colored by cylindrical radius
  • Surface level: 15
  • Imaged by UCSF CHIMERA
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  • Surface view colored by cylindrical radius
  • Surface level: 15
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5fjb
  • Surface level: 15
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5fjb
  • Surface level: 15
  • Imaged by UCSF CHIMERA
  • Download
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Map

Fileemd_3076.map.gz (map file in CCP4 format, 193068 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
260 pix
1.06 Å/pix.
= 275.6 Å
436 pix
1.06 Å/pix.
= 462.16 Å
436 pix
1.06 Å/pix.
= 462.16 Å

Surface

Projections

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Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.06 Å
Density
Contour Level:20 (by author), 15 (movie #1):
Minimum - Maximum-44.91537476 - 57.38076782
Average (Standard dev.)0.24355465 (11.38533211)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions436436260
Origin000
Limit435435259
Spacing436436260
CellA: 462.15997 Å / B: 462.15997 Å / C: 275.59998 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z436436260
origin x/y/z0.0000.0000.000
length x/y/z462.160462.160275.600
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS436436260
D min/max/mean-44.91557.3810.244

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Supplemental data

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Sample components

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Entire Helical assembly of HIV-1 capsid protein and host cell factor Cyc...

EntireName: Helical assembly of HIV-1 capsid protein and host cell factor Cyclophilin A
Number of components: 1 / Oligomeric State: hexamer
MassTheoretical: 42 kDa / Experimental: 42 kDa

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Component #1: protein, Human immunodeficiency virus 1

ProteinName: Human immunodeficiency virus 1 / a.k.a: HIV-1 capsid protein with CypA / Oligomeric Details: Hexamer / Recombinant expression: Yes
MassTheoretical: 42 kDa / Experimental: 42 kDa
SourceSpecies: Human immunodeficiency virus 1 / virus / ヒト免疫不全ウイルス 1
Source (engineered)Expression System: Escherichia coli bl21(de3) / bacteria / image: Escherichia coli

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Experimental details

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Sample preparation

Specimen statehelical array
Helical parametersAxial symmetry: C1 (asymmetric) / Hand: LEFT HANDED / Delta z: 7.393 Å / Delta phi: 138.133 deg.
Sample solutionSpecimen conc.: 2 mg/ml / Buffer solution: 1m NaCl,50mM Tris-Hcl / pH: 8
Support filmGlow discharged perforated Quantifoil R2/1 grid
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 120 K / Humidity: 100 %
Method: With 2.5 uL sample on carbon side, add 3 uL dilution buffer (100 mM NaCl,50mM 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 F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20 / Date: Jun 20, 2013
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 15 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 59000 X (nominal) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 3500 nm
Specimen HolderHolder: side entry / Model: GATAN LIQUID NITROGEN
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 19 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 6.349 microns / Bit depth: 32

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Image processing

ProcessingMethod: helical reconstruction / Details: The particles were aligned using IHRSR
3D reconstructionSoftware: SPIDER, IHRSR / CTF correction: Each particle / Resolution: 8 Å / Resolution method: FSC 0.5, gold-standard

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Atomic model buiding

Modeling #1Software: Chimera / Refinement protocol: rigid body / Refinement space: REAL
Input PDB model: 3J4F
Modeling #2Software: Chimera / Refinement protocol: rigid body / Refinement space: REAL
Input PDB model: 1AK4
Output model

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