[English] 日本語
Yorodumi
- EMDB-6877: Cryo-EM structure of polycystic kidney disease-like channel PKD2L1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-6877
TitleCryo-EM structure of polycystic kidney disease-like channel PKD2L1
Map data
Sample
  • Complex: PKD2L1
    • Protein or peptide: Polycystic kidney disease 2-like 1 protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordschannel / cryo-EM / MEMBRANE PROTEIN
Function / homology
Function and homology information


detection of chemical stimulus involved in sensory perception of sour taste / detection of chemical stimulus involved in sensory perception of taste / osmolarity-sensing monoatomic cation channel activity / pH-gated monoatomic ion channel activity / response to water / calcium-activated potassium channel activity / muscle alpha-actinin binding / cellular response to pH / cation channel complex / cellular response to acidic pH ...detection of chemical stimulus involved in sensory perception of sour taste / detection of chemical stimulus involved in sensory perception of taste / osmolarity-sensing monoatomic cation channel activity / pH-gated monoatomic ion channel activity / response to water / calcium-activated potassium channel activity / muscle alpha-actinin binding / cellular response to pH / cation channel complex / cellular response to acidic pH / calcium-activated cation channel activity / non-motile cilium / inorganic cation transmembrane transport / ciliary membrane / smoothened signaling pathway / sodium channel activity / monoatomic cation transport / monoatomic cation channel activity / calcium channel complex / protein tetramerization / calcium channel activity / actin cytoskeleton / cytoplasmic vesicle / protein homotetramerization / transmembrane transporter binding / receptor complex / calcium ion binding / endoplasmic reticulum / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Ferredoxin I 4Fe-4S cluster domain / : / Polycystic kidney disease type 2 protein / Polycystin domain / Polycystin domain / Polycystin cation channel, PKD1/PKD2 / Polycystin cation channel / Voltage-dependent channel domain superfamily / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Polycystin-2-like protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.38 Å
AuthorsZhang YQ
CitationJournal: Nat Commun / Year: 2018
Title: Cryo-EM structure of the polycystic kidney disease-like channel PKD2L1.
Authors: Qiang Su / Feizhuo Hu / Yuxia Liu / Xiaofei Ge / Changlin Mei / Shengqiang Yu / Aiwen Shen / Qiang Zhou / Chuangye Yan / Jianlin Lei / Yanqing Zhang / Xiaodong Liu / Tingliang Wang /
Abstract: PKD2L1, also termed TRPP3 from the TRPP subfamily (polycystic TRP channels), is involved in the sour sensation and other pH-dependent processes. PKD2L1 is believed to be a nonselective cation channel ...PKD2L1, also termed TRPP3 from the TRPP subfamily (polycystic TRP channels), is involved in the sour sensation and other pH-dependent processes. PKD2L1 is believed to be a nonselective cation channel that can be regulated by voltage, protons, and calcium. Despite its considerable importance, the molecular mechanisms underlying PKD2L1 regulations are largely unknown. Here, we determine the PKD2L1 atomic structure at 3.38 Å resolution by cryo-electron microscopy, whereby side chains of nearly all residues are assigned. Unlike its ortholog PKD2, the pore helix (PH) and transmembrane segment 6 (S6) of PKD2L1, which are involved in upper and lower-gate opening, adopt an open conformation. Structural comparisons of PKD2L1 with a PKD2-based homologous model indicate that the pore domain dilation is coupled to conformational changes of voltage-sensing domains (VSDs) via a series of π-π interactions, suggesting a potential PKD2L1 gating mechanism.
History
DepositionDec 28, 2017-
Header (metadata) releaseMar 28, 2018-
Map releaseMar 28, 2018-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.09
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.09
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5z1w
  • Surface level: 0.09
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6877.png

Downloads & links

-
Map

FileDownload / File: emd_6877.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 300 pix.
= 264. Å		0.88 Å/pix.
x 300 pix.
= 264. Å		0.88 Å/pix.
x 300 pix.
= 264. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09 / Movie #1: 0.09
Minimum - Maximum-0.22843578 - 0.45770916
Average (Standard dev.)0.0011068488 (±0.016226148)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 264.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.880.880.88
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z264.000264.000264.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.2280.4580.001

-
Supplemental data

-
Sample components

-
Entire : PKD2L1

EntireName: PKD2L1
Components
  • Complex: PKD2L1
    • Protein or peptide: Polycystic kidney disease 2-like 1 protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: PKD2L1

SupramoleculeName: PKD2L1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

-
Macromolecule #1: Polycystic kidney disease 2-like 1 protein

MacromoleculeName: Polycystic kidney disease 2-like 1 protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 65.600883 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TLVSSCCLHI CRSIRGLWGT TLTENTAENR ELYVKTTLRE LVVYIVFLVD ICLLTYGMTS SSAYYYTKVM SELFLHTPSD SGVSFQTIS SMSDFWDFAQ GPLLDSLYWT KWYNNQSLGR GSHSFIYYEN LLLGAPRLRQ LRVRNDSCVV HEDFREDILN C YDVYSPDK ...String:
TLVSSCCLHI CRSIRGLWGT TLTENTAENR ELYVKTTLRE LVVYIVFLVD ICLLTYGMTS SSAYYYTKVM SELFLHTPSD SGVSFQTIS SMSDFWDFAQ GPLLDSLYWT KWYNNQSLGR GSHSFIYYEN LLLGAPRLRQ LRVRNDSCVV HEDFREDILN C YDVYSPDK EDQLPFGPQN GTAWTYHSQN ELGGSSHWGR LTSYSGGGYY LDLPGSRQAS AEALQGLQEG LWLDRGTRVV FI DFSVYNA NINLFCILRL VVEFPATGGT IPSWQIRTVK LIRYVNNWDF FIVGCEVVFC VFIFYYVVEE ILEIHLHRLR YLS SVWNIL DLVVILLSIV AVGFHIFRTL EVNRLMGKLL QQPDTYADFE FLAFWQTQYN NMNAVNLFFA WIKIFKYISF NKTM TQLSS TLARCAKDIL GFAIMFFIVF FAYAQLGYLL FGTQVENFST FVKCIFTQFR IILGDFDYNA IDNANRILGP VYFVT YVFF VFFVLLNMFL AIINDTYSEV KEELAGQKDQ LQLSDFLKQS YNKTLLRLRL RKERVSDVQK VLKGGEPEIQ FEDFTS TLR ELG

UniProtKB: Polycystin-2-like protein 1

-
Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 12 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.001 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 22296
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
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.
  • 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 Accession Codes are Changing Soon! / 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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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