3D Electron Microscopy (3D-EM) Data Navigator [English / 日本語]
Top Gallery List Diagram Statistics Viewer Documents
Movie pageYodrodumi (structure viewer)
PDBj>EM Navigator>Detail page - EMDB-5345

CryoEM Structure of the Human Propionyl-CoA Carboxylase

by single particle reconstruction, at 15 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.423, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.423, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5345
AuthorsZhou ZH, Deng B, Shen Y, Tong L
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.423, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.423, Made by UCSF CHIMERA

Supplemental images

EMDB figure
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

PDB-3n6r
Cite

Cite: data citing same article

Similar strucutres (beta)

Diagram

EMDB-1727

PDB-2vdc
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleNature, Vol. 466, Issue 7309, Page 1001-5, Year 2010
TitleCrystal structure of the alpha(6)beta(6) holoenzyme of propionyl-coenzyme A carboxylase.
AuthorsChristine S Huang, Kianoush Sadre-Bazzaz, Yang Shen, Binbin Deng, Z Hong Zhou, Liang Tong
Department of Biological Sciences, Columbia University, New York, New York 10027, USA.
KeywordsAcetyl-CoA Carboxylase (chemistry, 6.4.1.2), Biocatalysis, Biotin (metabolism, 58-85-5), Carbon-Nitrogen Ligases (chemistry, 6.3.-), Carrier Proteins (chemistry), Catalytic Domain, Cryoelectron Microscopy, Crystallography, X-Ray, Fatty Acid Synthetase Complex, Type II (6.-), Holoenzymes (chemistry), Humans, Methylmalonyl-CoA Decarboxylase (chemistry, 4.1.1.41), Models, Molecular, Mutation (genetics), Propionic Acidemia (enzymology), Protein Binding, Protein Structure, Quaternary, Protein Structure, Tertiary, Protein Subunits (chemistry), Rhodobacteraceae (enzymology), Structure-Activity Relationship, biotin carboxyl carrier protein (6.4.1.2), biotin carboxylase (6.3.4.14)
LinksDOI: 10.1038/nature09302, PubMed: 20725044, PMC: PMC2925307
Map
FileEMD-5345.map ( map file in CCP4 format, 5621 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:0.423 (by author), 0.423 (movie #1):
Minimum - Maximum: -3.60469 - 3.74047
Average (Standard dev.): -1.26603e-09 (0.385184)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis Order : X Y Z
Dimensions : 112 112 112
Origin : -56 -56 -56
Limit : 55 55 55
Spacing : 112 112 112
Unit CellA = 313.6 A , B = 313.6 A , C = 313.6 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees
Pixel SpacingX = 2.8 A , Y = 2.8 A , Z = 2.8 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z2.82.82.8
M x/y/z112112112
origin x/y/z0.0000.0000.000
length x/y/z313.600313.600313.600
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-56-56-56
NC/NR/NS112112112
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-3.6053.740-0.000
Annotation DetailsThis is the volume.
Supplement
Sample
NameHuman Propionyl-CoA Carboxylase holoenzyme
Number of Components2
Oligomeric Statedodecamer (six alpha and six beta subunits)
Theoretical Mass0.768 MDa
DetailsThe sample was monodisperse
Mass-estimation MethodSDS PAGE
Experimental Mass0.75 MDa
Component #1: protein - Human Propionyl-CoA Carboxylase
Scientific nameHuman Propionyl-CoA Carboxylase
Theoretical Mass0.768 MDa
Experimental Mass0.75 MDa
DetailsPCC in solution
Oligomeric Detailsdodecamer
Number of Copies6
Scientific Name of SpeciesHomo sapiens (NCBI Taxonomy: 9606)
Common Name of SpeciesHuman
Recombinant expressionYes
Natural SourceCell Location: cytoplasm
Engineered SourceVector: pET-26b
Exp System: Escherichia coli (NCBI Taxonomy: 562)
Experiment
Sample Preparation
Specimen Conc0.07 mg/ml
Specimen Support Details300 mesh copper quantifoil grid
Specimen Stateparticle
BufferDetails: 25 mM Tris, 250 mM NaCl, 2 mM DTT, 5% v/v glycerol
pH: 7.4
Vitrification
Methodblot for 2 seconds before plunging
Cryogen NameNITROGEN
DetailsVitrification instrument: home-made plunger
Humidity40
InstrumentHOMEMADE PLUNGER
Temperature90 Kelvin
Imaging
MicroscopeJEOL 1200EX
Electron Gun
Electron SourceLAB6
Accelerating Voltage100 kV
Electron Dose10 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000 X, Calibrated: 50000 X
Astigmatismcorrected at 100,000 times mag
Nominal Cs4.1 mm
Imaging ModeBRIGHT FIELD
Defocus500 nm - 1500 nm
Specimen Holder
Holdereucentric ( GATAN LIQUID NITROGEN )
Temperature90 Kelvin ( 77 Kelvin - 100 Kelvin )
Camera
DetectorKodak SO163 film
Image Acquisition
ScannerZEISS SCAI
Sampling Size14 microns
Quant Bit Number12
Processing
Methodsingle particle reconstruction
3 D reconstruction
Algorithmprojection matching
SoftwareEMAN
CTF Correctioneach particle
Resolution By Author15
Resolution MethodFSC at 0.5 cut-off
Single Particle
Number of Projections1000
Download
Data from EMDB
Header (meta data in XML format)emd-5345.xml (7.6 KB)
Map dataemd_5345.map.gz (4.3 MB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5345
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.4 MB
Session file for UCSF-Chimera, 26.7 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