EMDB-5295: 3D reconstruction of negatively stained PCSK9 in compl...

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 5295
Title	3D reconstruction of negatively stained PCSK9 in complex with a Fab
Map	3D reconstruction of negatively stained PCSK9-Fab complex
Sample	human PCSK9 in complex with a Fab
Keywords	PCSK9-Fab complex
Authors	Wu 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
Date	Deposition: 2011-05-23, Header release: 2011-10-26, Map release: 2012-05-29, Last update: 2012-05-29
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
Movies	Movie 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
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries	EMDB-5294 Cite Cite: data citing same article
Similar strucutres (beta)	Diagram EMDB-1646 PDB-3j15 EMDB-5013 EMDB-5017 List of similar structure data about Omokage system

Article
Citation - Primary
Article	Structure, Vol. 20, Issue 4, Page 582-92, Year 2012
Title	Fabs enable single particle cryoEM studies of small proteins.
Authors	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 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.
Keywords	Cryoelectron 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)
Links	PII: S0969-2126(12)00097-4, DOI: 10.1016/j.str.2012.02.017, PubMed: 22483106, PMC: PMC3322386

File

Projections & Slices

Size of images:

Images are generated by Spider package.

Density

Data Type

Image stored as Reals

Space Group Number

Map Geometry

Unit Cell

A= B= C: 255.6 A
Alpha=beta=gamma: 90 degrees

Pixel Spacing

X= Y= Z: 4.26 A

CCP4 map header info

Annotation Details

3D reconstruction of negatively stained PCSK9-Fab complex

Sample
Name	human PCSK9 in complex with a Fab
Number of Components	2
Oligomeric State	monomer
Theoretical Mass	0.12MDa
Experimental Mass	0.12MDa
Component #1: protein - PCSK9
Scientific name	PCSK9
Theoretical Mass	0.12 MDa
Experimental Mass	0.12 MDa
Oligomeric Details	monomer
Number of Copies	2
Scientific Name of Species	Homo sapiens
Common Name of Species	human
NCBI taxonomy	9606
Recombinant expression	Yes
Engineered Source	NCBI taxonomy: 562 Expression system: Escherichia coli

Processing
Method	single particle reconstruction
3D reconstruction
Algorithm	Fourier space
Software	Frealign
CTF Correction	each particle
Resolution By Author	25 A
Resolution Method	0.5
Single Particle
Number of Projections	3876
Atomic Model Fitting
Model #0
Refinement Space	REAL
PDB Entry ID	2PMW PDB-2pmw

Data from EMDB

Header (meta data in XML format)

Map data

FTP directory

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