[English] 日本語
Yorodumi
- EMDB-7786: human PKD2 F604P mutant -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 7786
Titlehuman PKD2 F604P mutant
Map dataHuman PKD2 F604P mutant
SamplePKD2Polycystin 2:
Polycystin-2Polycystin 2 / ligand
Function / homologyPolycystin cation channel, PKD1/PKD2 / VxPx cargo-targeting to cilium / EF-hand calcium-binding domain profile. / EF-hand domain / Polycystin cation channel / Polycystic kidney disease type 2 protein / Voltage-dependent channel domain superfamily / EF-hand domain pair / metanephric smooth muscle tissue development / metanephric cortex development ...Polycystin cation channel, PKD1/PKD2 / VxPx cargo-targeting to cilium / EF-hand calcium-binding domain profile. / EF-hand domain / Polycystin cation channel / Polycystic kidney disease type 2 protein / Voltage-dependent channel domain superfamily / EF-hand domain pair / metanephric smooth muscle tissue development / metanephric cortex development / cellular response to hydrostatic pressure / metanephric cortical collecting duct development / detection of nodal flow / metanephric distal tubule development / cell-cell signaling by wnt / mesonephric tubule development / mesonephric duct development / polycystin complex / metanephric ascending thin limb development / determination of liver left/right asymmetry / metanephric part of ureteric bud development / integral component of cytoplasmic side of endoplasmic reticulum membrane / renal tubule morphogenesis / calcium-induced calcium release activity / positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / basal cortex / inorganic cation transmembrane transport / renal artery morphogenesis / cation channel complex / metanephric mesenchyme development / metanephric S-shaped body morphogenesis / non-motile cilium / HLH domain binding / outward rectifier potassium channel activity / cellular response to osmotic stress / placenta blood vessel development / regulation of calcium ion import / voltage-gated sodium channel activity / detection of mechanical stimulus / cytoplasmic sequestering of transcription factor / aorta development / sodium ion transmembrane transport / motile cilium / voltage-gated ion channel activity / determination of left/right symmetry / actinin binding / ciliary membrane / cation channel activity / voltage-gated cation channel activity / muscle alpha-actinin binding / ciliary basal body / receptor signaling pathway via JAK-STAT / neural tube development / negative regulation of G1/S transition of mitotic cell cycle / potassium channel activity / spinal cord development / potassium ion transmembrane transport / branching involved in ureteric bud morphogenesis / heart looping / voltage-gated calcium channel activity / voltage-gated potassium channel activity / release of sequestered calcium ion into cytosol / negative regulation of ryanodine-sensitive calcium-release channel activity / embryonic placenta development / centrosome duplication / calcium channel activity / calcium ion transmembrane transport / basal plasma membrane / cilium / calcium ion transport / cellular response to calcium ion / positive regulation of cell cycle arrest / cytoskeletal protein binding / mitotic spindle / cellular response to cAMP / cellular response to reactive oxygen species / cytoplasmic vesicle membrane / phosphoprotein binding / liver development / cellular response to fluid shear stress / integral component of lumenal side of endoplasmic reticulum membrane / protein heterotetramerization / cell-cell junction / cell cycle arrest / protein tetramerization / regulation of cell population proliferation / lamellipodium / protein homotetramerization / ATPase binding / heart development / positive regulation of nitric oxide biosynthetic process / ion channel binding / negative regulation of cell population proliferation / endoplasmic reticulum membrane / signaling receptor binding / calcium ion binding / endoplasmic reticulum / integral component of plasma membrane / Golgi apparatus / positive regulation of transcription by RNA polymerase II
Function and homology information
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 3.54 Å resolution
AuthorsZheng W / Yang X / Bulkley D / Chen XZ / Cao E
CitationJournal: Nat Commun / Year: 2018
Title: Hydrophobic pore gates regulate ion permeation in polycystic kidney disease 2 and 2L1 channels.
Authors: Wang Zheng / Xiaoyong Yang / Ruikun Hu / Ruiqi Cai / Laura Hofmann / Zhifei Wang / Qiaolin Hu / Xiong Liu / David Bulkey / Yong Yu / Jingfeng Tang / Veit Flockerzi / Ying Cao / Erhu Cao / Xing-Zhen Chen
Validation ReportPDB-ID: 6d1w

SummaryFull reportAbout validation report
DateDeposition: Apr 12, 2018 / Header (metadata) release: Jun 27, 2018 / Map release: Jun 27, 2018 / Last update: Jun 27, 2018

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6d1w
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_7786.map.gz (map file in CCP4 format, 28312 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
192 pix
1.22 Å/pix.
= 233.395 Å
192 pix
1.22 Å/pix.
= 233.395 Å
192 pix
1.22 Å/pix.
= 233.395 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2156 Å
Density
Contour Level:0.04 (by author), 0.04 (movie #1):
Minimum - Maximum-0.12531123 - 0.21940334
Average (Standard dev.)0.0012095302 (0.008277643)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions192192192
Origin0.0.0.
Limit191.191.191.
Spacing192192192
CellA=B=C: 233.3952 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.21559895833331.21559895833331.2155989583333
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z233.395233.395233.395
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.1250.2190.001

-
Supplemental data

-
Sample components

-
Entire PKD2

EntireName: PKD2 / Number of components: 3

-
Component #1: cellular-component, PKD2

Cellular-componentName: PKD2Polycystin 2 / Recombinant expression: No
MassTheoretical: 300 MDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK293S

-
Component #2: protein, Polycystin-2

ProteinName: Polycystin-2Polycystin 2 / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 84.996336 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

-
Component #3: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 12 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 2 mg/ml / pH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 4 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 387454
3D reconstructionResolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links: EMDB at EBI / Contact to PDBj

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more