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- EMDB-5294: 3D reconstruction of frozen hydrated HIV-1 integrase dimer in com... -

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Basic information

Entry
Database: EMDB / ID: 5294
Title3D reconstruction of frozen hydrated HIV-1 integrase dimer in complex with two Fabs.
KeywordsHIV-1 integrase dimer / Fab
SampleHIV-1 integrase - Fab complex
SourceHuman immunodeficiency virus 1 / virus / HIV-1 / ヒト免疫不全ウイルス 1
Map dataThis is 3D reconstruction of frozen hydrated HIV-1 integrase dimer in complex with 2 Fabs.
Methodsingle particle reconstruction, at 9.6 A resolution
AuthorsWu S / Avila-Sakar A / Kim J / Booth DS / Greenberg CH / Rossi A / Liao M / Alian A / Griner SL / Juge N / Mergel CM / Chaparro-Riggers J / Strop P / Tampe R / Edwards RH / Stroud RM / Craik CS / Cheng Y
CitationStructure, 2012, 20, 582-592

Structure, 2012, 20, 582-592 StrPapers
Fabs enable single particle cryoEM studies of small proteins.
Shenping Wu / Agustin Avila-Sakar / JungMin Kim / David S Booth / Charles H Greenberg / Andrea Rossi / Maofu Liao / Xueming Li / Akram Alian / Sarah L Griner / Narinobu Juge / Yadong Yu / Claudia M Mergel / Javier Chaparro-Riggers / Pavel Strop / Robert Tampé / Robert H Edwards / Robert M Stroud / Charles S Craik / Yifan Cheng

DateDeposition: May 22, 2011 / Header (metadata) release: Oct 26, 2011 / Map release: May 29, 2012 / Last update: May 22, 2011

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_5294.map.gz (map file in CCP4 format, 12665 KB)
Projections & slices
Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
148 pix
1.8 A/pix
= 266.4 A
148 pix
1.8 A/pix
= 266.4 A
148 pix
1.8 A/pix
= 266.4 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.8 A
Density
Contour Level:1 (by author), 1 (movie #1):
Minimum - Maximum-1.03870511 - 3.12253904
Average (Standard dev.)-0.00818645 (0.18489794)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions148148148
Origin-74-54-74
Limit739373
Spacing148148148
CellA=B=C: 266.4 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z1.81.81.8
M x/y/z148148148
origin x/y/z0.0000.0000.000
length x/y/z266.400266.400266.400
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-54-74-74
NC/NR/NS148148148
D min/max/mean-1.0393.123-0.008

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Supplemental data

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Sample components

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Entire HIV-1 integrase - Fab complex

EntireName: HIV-1 integrase - Fab complex / Number of components: 2 / Oligomeric State: 2 Fabs bind to one integrase dimer
MassTheoretical: 160 kDa / Experimental: 160 kDa

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Component #1: protein, integrase

ProteinName: integrase / Oligomeric Details: dimer / Details: dimer, total molecular weight 65kDa / Recombinant expression: Yes / Number of Copies: 2
MassTheoretical: 32 kDa / Experimental: 32 kDa
SourceSpecies: Human immunodeficiency virus 1 / virus / HIV-1 / ヒト免疫不全ウイルス 1
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Experimental details

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Sample preparation

Specimen stateparticle
Support film200 mesh Quantifoil
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 100 K / Humidity: 100 % / Details: Vitrification instrument: Vitrobot

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI F20 / Date: Feb 1, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 30 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 80000 X (nominal) / Cs: 2.1 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000 - 5000 nm
Specimen HolderHolder: CT3500 / Model: GATAN LIQUID NITROGEN
CameraDetector: TVIPS TEMCAM-F816 (8k x 8k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 14000 / Applied symmetry: C2 (2 fold cyclic)
3D reconstructionAlgorithm: Fourier space / Software: Frealign / CTF correction: Each particle / Resolution: 9.6 A / Resolution method: FSC 0.143

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Atomic model buiding

Modeling #1Software: Chimera / Refinement protocol: rigid body / Refinement space: REAL / Details: Protocol: rigid body
Input PDB model: 1EXQ
Modeling #2Software: Chimera / Refinement protocol: rigid body / Refinement space: REAL / Details: Protocol: rigid body
Input PDB model: 1M71

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