EMDB-5346: 3D map of Cholesteryl Ester Transfer Protein (CETP, 53...

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 5346
Authors	Zhang L, Yan F, Zhang S, Lei D, Charles MA, Cavigiolio G, Oda M, Krauss RM, Weisgraber KH, Rye KA, Pownall HJ, Qiu X, Ren G
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
Movies	Movie 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 viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries	EMDB-5347 Cite Cite: data citing same article
Similar strucutres (beta)	Diagram PDB-2vaz EMDB-1495 PDB-3cre PDB-2bk2 List of similar structure data about Omokage system

Article
Citation - Primary
Article	Nat. Chem. Biol., Vol. 8, Issue 4, Page 342-9, Year 2012
Title	Structural basis of transfer between lipoproteins by cholesteryl ester transfer protein.
Authors	Lei Zhang, Feng Yan, Shengli Zhang, Dongsheng Lei, M Arthur Charles, Giorgio Cavigiolio, Michael Oda, Ronald M Krauss, Karl H Weisgraber, Kerry-Anne Rye, Henry J Pownall, Xiayang Qiu, Gang Ren Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Keywords	CETP protein, human, Cholesterol Ester Transfer Proteins (chemistry), Cryoelectron Microscopy, Humans, Hydrophobic and Hydrophilic Interactions, Lipoproteins (chemistry), Lipoproteins, HDL (chemistry), Lipoproteins, LDL (chemistry), Lipoproteins, VLDL (chemistry), Microscopy, Electron, Models, Molecular, Molecular Dynamics Simulation, Protein Conformation, Protein Structure, Tertiary
Links	DOI: 10.1038/nchembio.796, PubMed: 22344176

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 = 179.968 A , B = 179.968 A , C = 179.968 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees

Pixel Spacing

X = 1.406 A , Y = 1.406 A , Z = 1.406 A

CCP4 map header info

Annotation Details

This is 3D reconstruction of CETP by cryo-positive-staining EM

Sample
Name	Recombinant human CETP (about 53 kDa before post-translational modifications) was expressed in the dihydrofolate reductase-deficient Chinese hamster ovary cell line DG44.
Number of Components	2
Oligomeric State	monomeric CETP
Theoretical Mass	0.053 MDa
Details	The CETP sample was thawed from storage at -70 degrees Celcius before being used.
Mass-estimation Method	Sedimentation
Experimental Mass	0.074 MDa
Component #1: protein - CETP
Scientific name	Cholesteryl ester transfer protein
Common Name	CETP
Theoretical Mass	0.053 MDa
Experimental Mass	0.074 MDa
Details	Cryo-positive-staining method was used for CETP reconstruction
Oligomeric Details	monomer
Number of Copies	1
Scientific Name of Species	Homo sapiens (NCBI Taxonomy: 9606)
Common Name of Species	human
Recombinant expression	Yes
Natural Source	Organ Or Tissue: plasma
Engineered Source	Exp System: Cricetulus griseus (NCBI Taxonomy: 10029)

Experiment
Sample Preparation
Staining	CETP specimens were also prepared by a cryo-positive-staining EM (cryo-PS-EM) method (reported in the primary citation).
Specimen Conc	0.005 mg/ml
Specimen Support Details	CETP (holey thin-carbon-film-coated 300-mesh Copper grid (Cu-300HN, Pacific Grid-Tech, USA)
Specimen State	particle
Buffer	Details: DPBS buffer pH: 7.4
Vitrification
Method	Blot for 3 seconds before plunging
Cryogen Name	ETHANE
Details	Vitrification instrument: Vitrobot
Humidity	90
Instrument	FEI VITROBOT
Temperature	5 Kelvin
Imaging
Microscope	FEI TECNAI 20
Details	Lose dose mode
Electron Gun
Electron Source	LAB6
Accelerating Voltage	200 kV
Electron Dose	50 e/A**2
Illumination Mode	OTHER
Lens
Magnification	Nominal: 80000 X,
Nominal Cs	2.0 mm
Imaging Mode	BRIGHT FIELD
Defocus	100 nm - 700 nm
Specimen Holder
Holder	Gatan 626 ( GATAN LIQUID NITROGEN )
Temperature	96 Kelvin ( 94 Kelvin - 99 Kelvin )
Camera
Detector	Gatan UltraScan 4K x 4K CCD
Image Acquisition

Processing
Method	single particle reconstruction
3 D reconstruction
Algorithm	Class average
Software	EMAN
CTF Correction	ctffind3 in the FREALIGN software package, and corrected by EMAN
Resolution By Author	14
Resolution Method	FSC at 0.5 cut-off
Single Particle
Number of Class Averages	317
Number of Projections	8879
Details	The particles were initially selected using an automatic selection program, boxer, then manually adjusted by deleted the obviously poor quality particles.
Atomic Model Fitting
Model #0
Target Criteria	cross-correlation
Details	Protocol: Chimera Rigid Body Docking
Software	Chimera
Refinement Protocol	rigid body
Refinement Space	REAL

Data from EMDB

Header (meta data in XML format)

Map data

FTP directory

Movie files

movie #1

	.mp4 (H.264/MPEG-4 AVC format), 3.5 MB .webm (WebM/VP8 format), 4.9 MB Session file for UCSF-Chimera, 26.6 KB

movie #2

	.mp4 (H.264/MPEG-4 AVC format), 3.2 MB .webm (WebM/VP8 format), 4.2 MB Session file for UCSF-Chimera, 26.7 KB