3D Electron Microscopy (3D-EM) Data Navigator [English / 日本語]
Top Gallery List Diagram Statistics Viewer Documents
Movie pageYodrodumi (structure viewer)
PDBj>EM Navigator>Detail page - EMDB-5294

3D reconstruction of frozen hydrated HIV-1 integrase dimer in complex with two Fabs.

by single particle reconstruction, at 9.6 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 1, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 1, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5294
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
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 1, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 1, Made by UCSF CHIMERA

Supplemental images

EMDB figure
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

EMDB-5295
Cite

Cite: data citing same article

Similar strucutres (beta)

Diagram

PDB-2hil

EMDB-1105

PDB-3izd
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleStructure, Vol. 20, Issue 4, Page 582-92, Year 2012
TitleFabs enable single particle cryoEM studies of small proteins.
AuthorsShenping 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
The W.M. Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California San Francisco, 600 16th Street, San Francisco, CA 94158, USA.
KeywordsCryoelectron Microscopy (methods), Escherichia coli, Escherichia coli Proteins (chemistry), Humans, Image Processing, Computer-Assisted, Immunoglobulin Fab Fragments (chemistry), Models, Molecular, Molecular Weight, PCSK9 protein, human (3.4.21.-), Peptide Library, Proprotein Convertases (chemistry, 3.4.-), Protein Conformation, Recombinant Proteins (chemistry), Serine Endopeptidases (chemistry, 3.4.21.-), Vesicular Glutamate Transport Proteins (chemistry)
LinksPII: S0969-2126(12)00097-4, DOI: 10.1016/j.str.2012.02.017, PubMed: 22483106, PMC: PMC3322386
Map
FileEMD-5294.map ( map file in CCP4 format, 12969 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density

Histogram

Histogram (log scale)
Contour Level:1.0 (by author), 1 (movie #1):
Minimum - Maximum: -1.03870511 - 3.12253904
Average (Standard dev.): -0.00818645 (0.18489794)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis Order : X Y Z
Dimensions : 148 148 148
Origin : -54 -74 -74
Limit : 93 73 73
Spacing : 148 148 148
Unit CellA = 266.4 A , B = 266.4 A , C = 266.4 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees
Pixel SpacingX = 1.8 A , Y = 1.8 A , Z = 1.8 A
CCP4 map header info
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
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-1.0393.123-0.008
Annotation DetailsThis is 3D reconstruction of frozen hydrated HIV-1 integrase dimer in complex with 2 Fabs.
Supplement
Sample
NameHIV-1 integrase - Fab complex
Number of Components2
Oligomeric State2 Fabs bind to one integrase dimer
Theoretical Mass0.16 MDa
Experimental Mass0.16 MDa
Component #1: protein - integrase
Scientific nameintegrase
Theoretical Mass0.032 MDa
Experimental Mass0.032 MDa
Detailsdimer, total molecular weight 65kDa
Oligomeric Detailsdimer
Number of Copies2
Scientific Name of SpeciesHuman immunodeficiency virus 1 (NCBI Taxonomy: 11676)
Common Name of SpeciesHIV-1
Recombinant expressionYes
Engineered SourceExp System: Escherichia coli (NCBI Taxonomy: 562)
Experiment
Sample Preparation
Specimen Support Details200 mesh Quantifoil
Specimen Stateparticle
Vitrification
Cryogen NameETHANE
DetailsVitrification instrument: Vitrobot
Humidity100
InstrumentFEI VITROBOT
Temperature100 Kelvin
Imaging
MicroscopeFEI TECNAI F20
Date01-FEB-2011
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose30 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 80000 X,
Nominal Cs2.1 mm
Imaging ModeBRIGHT FIELD
Defocus2000 nm - 5000 nm
Specimen Holder
HolderCT3500 ( GATAN LIQUID NITROGEN )
Tilt Angle0 degrees - 0 degrees
Camera
DetectorTemF816
Image Acquisition
Processing
Methodsingle particle reconstruction
3 D reconstruction
AlgorithmFourier space
SoftwareFrealign
CTF CorrectionEach particle
Resolution By Author9.6
Resolution MethodFSC at 0.143
Single Particle
Number of Projections14000
Atomic Model Fitting
Model #0
DetailsProtocol: rigid body
Refinement Protocolrigid body
Refinement SpaceREAL
SoftwareChimera
Model #1
Refinement SpaceREAL
Refinement Protocolrigid body
DetailsProtocol: rigid body
SoftwareChimera
Download
Data from EMDB
Header (meta data in XML format)emd-5294.xml (7.6 KB)
Map dataemd_5294.map.gz (10.8 MB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5294
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 5.3 MB
Session file for UCSF-Chimera, 26.8 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.8 MB
Session file for UCSF-Chimera, 26.8 KB