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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
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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
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