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3D reconstruction of negatively stained PCSK9 in complex with a Fab

by single particle reconstruction, at 25 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.5, Made by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 0.5, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5295
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: 0.5, Made by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 0.5, Made by UCSF CHIMERA

Supplemental images

EMDB figure
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Related Structure Data
Related Entries

EMDB-5294
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Cite: data citing same article

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Diagram

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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-5295.map ( map file in CCP4 format, 866 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:0.5 (by author), 0.5 (movie #1):
Minimum - Maximum: -0.82391357 - 3.13429093
Average (Standard dev.): 0.00072357 (0.15620080)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis Order : X Y Z
Dimensions : 60 60 60
Origin : 0 0 0
Limit : 59 59 59
Spacing : 60 60 60
Unit CellA = 255.6 A , B = 255.6 A , C = 255.6 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees
Pixel SpacingX = 4.26 A , Y = 4.26 A , Z = 4.26 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z4.264.264.26
M x/y/z606060
origin x/y/z0.0000.0000.000
length x/y/z255.600255.600255.600
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS606060
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.8243.1340.001
Annotation Details3D reconstruction of negatively stained PCSK9-Fab complex
Supplement
Sample
Namehuman PCSK9 in complex with a Fab
Number of Components2
Oligomeric Statemonomer
Theoretical Mass0.12 MDa
Experimental Mass0.12 MDa
Component #1: protein - PCSK9
Scientific namePCSK9
Theoretical Mass0.12 MDa
Experimental Mass0.12 MDa
Oligomeric Detailsmonomer
Number of Copies2
Scientific Name of SpeciesHomo sapiens (NCBI Taxonomy: 9606)
Common Name of Specieshuman
Recombinant expressionYes
Engineered SourceExp System: Escherichia coli (NCBI Taxonomy: 562)
Experiment
Sample Preparation
Staininguranyl formate
Specimen Support Details200 mesh copper grid
Specimen Stateparticle
Vitrification
Cryogen NameNONE
InstrumentNONE
Imaging
MicroscopeFEI TECNAI 20
Electron Gun
Electron SourceLAB6
Accelerating Voltage120 kV
Electron Dose30 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000 X, Calibrated: 50000 X
Astigmatismeach particle
Nominal Cs2.0 mm
Imaging ModeBRIGHT FIELD
Defocus1.5 nm - 1.5 nm
Specimen Holder
Holdersingle tilt ( SIDE ENTRY, EUCENTRIC )
Tilt Angle0 degrees - 60 degrees
Camera
DetectorUS4000 CCD
Image Acquisition
Processing
Methodsingle particle reconstruction
3 D reconstruction
AlgorithmFourier space
SoftwareFrealign
CTF Correctioneach particle
Resolution By Author25
Resolution Method0.5
Single Particle
Number of Projections3876
Atomic Model Fitting
Model #0
Refinement SpaceREAL
Download
Data from EMDB
Header (meta data in XML format)emd-5295.xml (6.9 KB)
Map dataemd_5295.map.gz (799.7 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5295
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5.3 MB
Session file for UCSF-Chimera, 26.7 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 4.4 MB
Session file for UCSF-Chimera, 26.9 KB