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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, Image by UCSF CHIMERA

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

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5294
Title3D reconstruction of frozen hydrated HIV-1 integrase dimer in complex with two Fabs.
MapThis is 3D reconstruction of frozen hydrated HIV-1 integrase dimer in complex with 2 Fabs.
SampleHIV-1 integrase - Fab complex
KeywordsHIV-1 integrase dimer, Fab
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
DateDeposition: 2011-05-22, Header release: 2011-10-26, Map release: 2012-05-29, Last update: 2012-05-29
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

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

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

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
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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.gz ( map file in CCP4 format, 12665 KB )
Projections & SlicesSize of images:
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.

Density
Contour Level:1 (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 orderXYZ
Dimensions148148148
Origin-74-54-74
Limit739373
Spacing148148148
Unit CellA= B= C: 266.4 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= 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
Images
Images
Sample
NameHIV-1 integrase - Fab complex
Number of Components2
Oligomeric State2 Fabs bind to one integrase dimer
Theoretical Mass0.16MDa
Experimental Mass0.16MDa
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
Common Name of SpeciesHIV-1
NCBI taxonomy11676
Recombinant expressionYes
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
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
Nominal Cs2.1 mm
Imaging ModeBRIGHT FIELD
Defocus2000 nm - 5000 nm
Specimen Holder
HolderCT3500
ModelGATAN LIQUID NITROGEN
Tilt Angle0 degrees - 0 degrees
Camera
DetectorTVIPS TEMCAM-F816 (8k x 8k)
Processing
Methodsingle particle reconstruction
3D reconstruction
AlgorithmFourier space
SoftwareFrealign
CTF CorrectionEach particle
Resolution By Author9.6 A
Resolution MethodFSC 0.143
Single Particle
Number of Projections14000
Applied SymmetryC2 (2 fold cyclic)
Atomic Model Fitting
Model #0
DetailsProtocol: rigid body
Refinement Protocolrigid body
Refinement SpaceREAL
SoftwareChimera
PDB Entry ID1EXQ
Model #1
Refinement SpaceREAL
Refinement Protocolrigid body
DetailsProtocol: rigid body
SoftwareChimera
PDB Entry ID1M71
Download
Data from EMDB
Header (meta data in XML format)emd-5294.xml (7.6 KB)
Map dataemd_5294.map.gz (10.8 MB)
Imagesemd_5294_1.jpg (20.1 KB)
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