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PDBj>EM Navigator>Detail page - EMDB-2038

Mammalian AAA ATPase p97 A232E mutant

by single particle reconstruction, at 23 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 13.8, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 13.8, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 2038
AuthorsNiwa H, Ewens CA, Tsang C, Yeung HO, Zhang X, Freemont PS
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 13.8, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 13.8, Made by UCSF CHIMERA

Supplemental images

2038.tif
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Similar strucutres (beta)

Diagram

EMDB-1193

EMDB-2163

EMDB-1981

EMDB-1290
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleJ. Biol. Chem., Vol. 287, Issue 11, Page 8561-70, Year 2012
TitleThe role of the N-domain in the ATPase activity of the mammalian AAA ATPase p97/VCP.
AuthorsHajime Niwa, Caroline A Ewens, Chun Tsang, Heidi O Yeung, Xiaodong Zhang, Paul S Freemont
Centre for Structural Biology, Division of Molecular Biosciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United Kingdom.
KeywordsAdenosine Triphosphatases (chemistry, 3.6.1.-), Adenosine Triphosphate (chemistry, 56-65-5), Amino Acid Substitution, CDC48 protein (3.6.1.-), Cell Cycle Proteins (chemistry), Frontotemporal Dementia, Humans, Hydrolysis, Models, Molecular, Mutagenesis, Mutation, Missense, Osteitis Deformans (genetics), Protein Structure, Tertiary, Structure-Activity Relationship
LinksDOI: 10.1074/jbc.M111.302778, PubMed: 22270372, PMC: PMC3318706
Map
FileEMD-2038.map ( map file in CCP4 format, 8390 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:13.8 (by author), 13.8 (movie #1):
Minimum - Maximum: 0E-8 - 141.23155212
Average (Standard dev.): 0.63924396 (6.21090364)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis Order : X Y Z
Dimensions : 128 128 128
Origin : -64 -64 -64
Limit : 63 63 63
Spacing : 128 128 128
Unit CellA = 450.56 A , B = 450.56 A , C = 450.56 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees
Pixel SpacingX = 3.52 A , Y = 3.52 A , Z = 3.52 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z3.523.523.52
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z450.560450.560450.560
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-64-64-64
NC/NR/NS128128128
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.000141.2320.639
Annotation Detailsp97 A232E
Supplement
Images
Images

2038.tif
Sample
NameFull length p97 IBMPFD mutant A232E
Number of Components1
Oligomeric Stateone p97 homohexamer
Theoretical Mass0.54 MDa
Experimental Mass0.54 MDa
Component #1: protein - p97
Scientific namep97
Oligomeric DetailsHexamer
Number of Copies6
Scientific Name of SpeciesMus musculus (NCBI Taxonomy: 10090)

Common Name of SpeciesHouse mouse
Recombinant expressionYes
Engineered SourceExp System: Escherichia coli (NCBI Taxonomy: 562)
Experiment
Sample Preparation
Specimen Conc0.5 mg/ml
Specimen Support Detailsholey carbon film on copper
Specimen Stateparticle
BufferDetails: 250 mM KCl, 25 mM HEPES
pH: 7.5
Vitrification
Cryogen NameETHANE
Humidity100
InstrumentNONE
Imaging
MicroscopeFEI/PHILIPS CM200FEG
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose10 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000 X,
Imaging ModeBRIGHT FIELD
Defocus2 nm - 5 nm
Specimen Holder
HolderEucentric ( GATAN LIQUID NITROGEN )
Camera
Image Acquisition
Number of Digital Images50
Processing
Methodsingle particle reconstruction
3 D reconstruction
Softwareimagic
CTF CorrectionParticles
Resolution By Author23
Resolution MethodFSC 0.5 bit cut off
Single Particle
Number of Projections1029
Download
Data from EMDB
Header (meta data in XML format)emd-2038.xml (6.3 KB)
Map dataemd_2038.map.gz (429.6 KB)
Images2038.tif (734.2 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-2038
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 5.2 MB
Session file for UCSF-Chimera, 26.1 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.1 MB
.webm (WebM/VP8 format), 4.6 MB
Session file for UCSF-Chimera, 26.7 KB