3D Electron Microscopy (3D-EM) Data Navigator [English / [日本語]]
Top Gallery List Statistics Shape search Viewer
Movie pageYodrodumi (structure viewer)
PDBj>EM Navigator>Detail page - EMDB-3523

This page is a legacy version and will be discarded in future. The new page is here.

cryoEM Structure of Polycystin-2 in complex with cations and lipids

by single particle reconstruction, at 4.3 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.0345, Imaged by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.0345, Imaged by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-5mke, Surface level: 0.0345, Imaged by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 3523
TitlecryoEM Structure of Polycystin-2 in complex with cations and lipids
SamplePolycystin-2
AuthorsWilkes M, Madej MG
DateDeposition: 2016-12-04, Header release: 2016-12-28, Map release: 2017-01-18, Last update: 2017-02-15
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.0345, Imaged by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.0345, Imaged by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-5mke, Surface level: 0.0345, Imaged by UCSF CHIMERA

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

PDB-5mke

CiteFit

Cite: data citing same article

Fit: output model of fitting

Similar-shape strucutres
Search for similar-shape assemblies throgh:
EMDB + EM entries in PDB
all of EMDB & PDB (Omokage search)
Article
Citation - Primary
ArticleNat. Struct. Mol. Biol., Vol. 24, Issue 2, Page 123-130, Year 2017
TitleMolecular insights into lipid-assisted Ca(2+) regulation of the TRP channel Polycystin-2.
AuthorsMartin Wilkes, M Gregor Madej, Lydia Kreuter, Daniel Rhinow, Veronika Heinz, Silvia De Sanctis, Sabine Ruppel, Rebecca M Richter, Friederike Joos, Marina Grieben, Ashley C W Pike, Juha T Huiskonen, Elisabeth P Carpenter, Werner Kühlbrandt, Ralph Witzgall, Christine Ziegler
Max Planck Institute of Biophysics, Department of Structural Biology, Frankfurt, Germany.
Biophysics II, Faculty of Biology and Preclinical Medicine, Regensburg, Germany.
Structural Genomics Consortium, University of Oxford, Oxford, UK.
Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
Department of Anatomy, Faculty of Biology and Preclinical Medicine, Regensburg, Germany.
KeywordsBinding Sites, Calcium (chemistry), Calcium Signaling, Cryoelectron Microscopy, Glycosylation, HEK293 Cells, Humans, Models, Molecular, Phosphatidic Acids (chemistry), Phosphatidylcholines (chemistry), Protein Binding, Protein Conformation, alpha-Helical, Protein Domains, Protein Processing, Post-Translational, Protein Structure, Quaternary, TRPP Cation Channels (chemistry), polycystic kidney disease 2 protein
LinksPubMed: 28092368, DOI: 10.1038/nsmb.3357
Map
Fileemd_3523.map.gz ( map file in CCP4 format, 18967 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
168 pix
1.14 A/pix
= 191.52 A
168 pix
1.14 A/pix
= 191.52 A
168 pix
1.14 A/pix
= 191.52 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.0345 (by author), 0.0345 (movie #1):
Minimum - Maximum: -0.06904477 - 0.09819269
Average (Standard dev.): 0.001177011 (0.0061609545)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions168168168
Origin000
Limit167167167
Spacing168168168
Unit CellA= B= C: 191.52 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 1.14 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z1.141.141.14
M x/y/z168168168
origin x/y/z0.0000.0000.000
length x/y/z191.520191.520191.520
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS168168168
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.0690.0980.001
Supplement
Images
Images
Sample
NamePolycystin-2
Number of Components7
Component #1: protein - Polycystin-2
Scientific namePolycystin-2
Scientific Name of Specieshomo sapiens
NCBI taxonomy9606
Recombinant expressionNo
Engineered SourceNCBI taxonomy: 9606
Expression system: homo sapiens
Component #2: protein - Polycystin-2
Scientific namePolycystin-2
Theoretical Mass0.109820086 MDa
Recombinant expressionNo
Engineered SourceNCBI taxonomy: 9606
Expression system: Homo sapiens
Component #3: ligand - N-ACETYL-D-GLUCOSAMINE
Scientific nameN-ACETYL-D-GLUCOSAMINE
Theoretical Mass0.000221208 MDa
Number of Copies16
Recombinant expressionNo
Component #4: ligand - 4-AMINO-5-CYCLOHEXYL-3-HYDROXY-PENTANOIC ACID
Scientific name4-AMINO-5-CYCLOHEXYL-3-HYDROXY-PENTANOIC ACID
Theoretical Mass0.000215289 MDa
Number of Copies8
Recombinant expressionNo
Component #5: ligand - 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE
Scientific name1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE
Theoretical Mass0.000647883 MDa
Number of Copies4
Recombinant expressionNo
Component #6: ligand - PALMITIC ACID
Scientific namePALMITIC ACID
Theoretical Mass0.000256424 MDa
Number of Copies12
Recombinant expressionNo
Component #7: ligand - CALCIUM ION
Scientific nameCALCIUM ION
Theoretical Mass4.0078e-05 MDa
Number of Copies2
Recombinant expressionNo
Experiment
Sample Preparation
Specimen Stateparticle
BufferpH: 7.5
Vitrification
Cryogen NameETHANE
Imaging
MicroscopeJEOL 3200FSC
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage300 kV
Electron Dose1.8 e/A**2
Illumination ModeFLOOD BEAM
Lens
Nominal Cs4.1 mm
Imaging ModeBRIGHT FIELD
Specimen Holder
ModelOTHER
Camera
DetectorGATAN K2 (4k x 4k)
Processing
Methodsingle particle reconstruction
3D reconstruction
Resolution By Author4.3 A
Resolution MethodFSC 0.143 CUT-OFF
Single Particle
Applied SymmetryC4 (4 fold cyclic)
Number of Projections42268
Atomic Model Fitting
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-3523-v19.xml (7.8 KB)
emd-3523-v20.xml (12.3 KB)
emd-3523.xml (7.8 KB)
Map dataemd_3523.map.gz (4 MB)
Imagesemd_3523.png (97.8 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-3523
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 5.9 MB
Session file for UCSF-Chimera, 27 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.1 MB
.webm (WebM/VP8 format), 6.1 MB
Session file for UCSF-Chimera, 26.8 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 7.6 MB
Session file for UCSF-Chimera, 1.8 MB