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CryoEM map of the p97-Ufd1-Npl4 complex in the two-binding-sites conformation

by single particle reconstruction, at 25 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.3, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.3, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 2015
AuthorsBebeacua C, Forster A, McKeown C, Meyer HH, 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: 0.3, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.3, Made by UCSF CHIMERA

Supplemental images

emd2015fig.png
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

EMDB-2013
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EMDB-2014
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EMDB-2016
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Cite: data citing same article

Similar strucutres (beta)

Diagram

EMDB-2016

EMDB-5324

EMDB-1727
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleProc. Natl. Acad. Sci. U.S.A., Vol. 109, Issue 4, Page 1098-103, Year 2012
TitleDistinct conformations of the protein complex p97-Ufd1-Npl4 revealed by electron cryomicroscopy.
AuthorsCecilia Bebeacua, Andreas Förster, Ciarán McKeown, Hemmo H Meyer, Xiaodong Zhang, Paul S Freemont
Centre for Structural Biology and Centre for Biomolecular Electron Microscopy, Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, United Kingdom.
KeywordsAdenosine Triphosphatases (ultrastructure, 3.6.1.-), CDC48 protein (3.6.1.-), Carrier Proteins (ultrastructure), Cell Cycle Proteins (ultrastructure), Cryoelectron Microscopy (methods), Escherichia coli, Image Processing, Computer-Assisted, Imaging, Three-Dimensional, Models, Molecular, Multiprotein Complexes (ultrastructure), Npl4 protein, rat, Protein Conformation, Proteins (ultrastructure), Ufd1l protein, mouse
LinksDOI: 10.1073/pnas.1114341109, PubMed: 22232657, PMC: PMC3268311
Map
FileEMD-2015.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:0.3 (by author), 0.3 (movie #1):
Minimum - Maximum: -1.92153 - 16.6492
Average (Standard dev.): 0.0840537 (0.725828)
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 = 451.84 A , B = 451.84 A , C = 451.84 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees
Pixel SpacingX = 3.53 A , Y = 3.53 A , Z = 3.53 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z3.533.533.53
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z451.840451.840451.840
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-1.92216.6490.084
Annotation Detailsp97-Ufd1-Npl4 complex in the two-binding-sites conformation
Supplement
Images
Images

emd2015fig.png
Sample
Namep97-Ufd1-Npl4
Number of Components3
Oligomeric StateOne hexamer of p97 binds to one Ufd1-Npl4 dimer
Theoretical Mass0.623 MDa
Experimental Mass0.623 MDa
Component #1: protein - p97
Scientific namep97
DetailsThis corresponds to the p97-Ufd1-Npl4 complex
Number of Copies1
Scientific Name of SpeciesMus musculus (NCBI Taxonomy: 10090)

Common Name of SpeciesHouse mouse
Recombinant expressionYes
Natural SourceCell Location: Cytoplasm
Engineered SourceExp System: Escherichia coli Rosetta strain D3
Component #2: protein - Ufd1
Scientific nameUfd1
DetailsThis corresponds to the p97-Ufd1-Npl4 complex
Number of Copies1
Scientific Name of SpeciesMus musculus (NCBI Taxonomy: 10090)
Common Name of SpeciesHouse mouse
Recombinant expressionYes
Natural SourceCell Location: Cytoplasm
Engineered SourceExp System: Escherichia coli Rosetta strain D3
Component #3: protein - Npl4
Scientific nameNpl4
DetailsThis corresponds to the p97-Ufd1-Npl4 complex
Number of Copies1
Scientific Name of SpeciesMus musculus (NCBI Taxonomy: 10090)
Common Name of SpeciesHouse mouse
Recombinant expressionYes
Natural SourceCell Location: Cytoplasm
Engineered SourceExp System: Escherichia coli Rosetta strain D3
Experiment
Sample Preparation
Specimen Conc0.5 mg/ml
Specimen Support Details200 mesh copper grid
Specimen Stateparticle
BufferDetails: 150 mM KCL, 25 mL Tris, 2.5 mM MgCl2
pH: 8
Vitrification
MethodBlot for 2 seconds before plunging
Cryogen NameETHANE
DetailsVitrification instrument: Vitrobot
Humidity100
InstrumentFEI VITROBOT
Imaging
MicroscopeFEI/PHILIPS CM200FEG
Date01-JUL-2009
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose10 e/A**2
Illumination ModeOTHER
Lens
MagnificationNominal: 50000 X, Calibrated: 50000 X
AstigmatismObjective lens astigmatism was corrected at 100,000 times magnification
Nominal Cs2.2 mm
Imaging ModeBRIGHT FIELD
Defocus1500 nm - 3000 nm
Energy FilterType: FEI , Window:
Specimen Holder
HolderEucentric ( GATAN LIQUID NITROGEN )
Camera
DetectorCCD
Image Acquisition
Number of Digital Images100
Processing
Methodsingle particle reconstruction
3 D reconstruction
AlgorithmBack Projection
SoftwareIMAGIC
Resolution By Author25
Resolution MethodFSC
Single Particle
Number of Projections5000
Atomic Model Fitting
Model #0
Target CriteriaCross Correlation
DetailsProtocol: Rigid Body. The protomers were fitted individually and the N-domains fitted by manual docking and refined automatically
SoftwareChimera
Refinement Protocolrigid body
Refinement SpaceREAL
Download
Data from EMDB
Header (meta data in XML format)emd-2015.xml (9.2 KB)
Map dataemd_2015.map.gz (699.1 KB)
Imagesemd2015fig.png (113.7 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-2015
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 5.2 MB
Session file for UCSF-Chimera, 26.7 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.1 MB
.webm (WebM/VP8 format), 4.5 MB
Session file for UCSF-Chimera, 26.7 KB