[English] 日本語
Yorodumi
- EMDB-6991: Structure of the human PKD1/PKD2 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-6991
TitleStructure of the human PKD1/PKD2 complex
Map dataNone
Sample
  • Complex: the structure of an asymmetric complex
    • Protein or peptide: Polycystin-2
    • Protein or peptide: Polycystin-1
KeywordsAsymmetric complex / polycystic kidney disease / MEMBRANE PROTEIN
Function / homology
Function and homology information


metanephric distal tubule morphogenesis / nitrogen cycle metabolic process / detection of nodal flow / metanephric smooth muscle tissue development / metanephric cortex development / metanephric cortical collecting duct development / metanephric distal tubule development / polycystin complex / mesonephric tubule development / mesonephric duct development ...metanephric distal tubule morphogenesis / nitrogen cycle metabolic process / detection of nodal flow / metanephric smooth muscle tissue development / metanephric cortex development / metanephric cortical collecting duct development / metanephric distal tubule development / polycystin complex / mesonephric tubule development / mesonephric duct development / metanephric part of ureteric bud development / renal tubule morphogenesis / determination of liver left/right asymmetry / HLH domain binding / lung epithelium development / metanephric ascending thin limb development / lymph vessel morphogenesis / metanephric mesenchyme development / metanephric S-shaped body morphogenesis / basal cortex / renal artery morphogenesis / mitocytosis / positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / metanephric proximal tubule development / calcium-induced calcium release activity / calcium-independent cell-matrix adhesion / Wnt receptor activity / migrasome / cilium organization / VxPx cargo-targeting to cilium / genitalia development / detection of mechanical stimulus / muscle alpha-actinin binding / regulation of calcium ion import / voltage-gated monoatomic ion channel activity / placenta blood vessel development / response to fluid shear stress / cellular response to hydrostatic pressure / Golgi-associated vesicle membrane / cation channel complex / cellular response to fluid shear stress / metanephric collecting duct development / outward rectifier potassium channel activity / actinin binding / cellular response to osmotic stress / non-motile cilium / digestive tract development / determination of left/right symmetry / inorganic cation transmembrane transport / voltage-gated monoatomic cation channel activity / aorta development / cartilage development / neural tube development / motile cilium / voltage-gated sodium channel activity / ciliary membrane / cartilage condensation / branching involved in ureteric bud morphogenesis / protein heterotetramerization / branching morphogenesis of an epithelial tube / skin development / negative regulation of G1/S transition of mitotic cell cycle / spinal cord development / establishment of cell polarity / cytoplasmic side of endoplasmic reticulum membrane / homophilic cell adhesion via plasma membrane adhesion molecules / heart looping / regulation of G1/S transition of mitotic cell cycle / centrosome duplication / voltage-gated potassium channel activity / cell surface receptor signaling pathway via JAK-STAT / anatomical structure morphogenesis / potassium channel activity / lateral plasma membrane / embryonic placenta development / voltage-gated calcium channel activity / regulation of cell adhesion / transcription regulator inhibitor activity / monoatomic cation channel activity / cytoskeletal protein binding / cellular response to cAMP / regulation of proteasomal protein catabolic process / release of sequestered calcium ion into cytosol / potassium ion transmembrane transport / calcium channel complex / sodium ion transmembrane transport / regulation of mitotic spindle organization / cytoplasmic vesicle membrane / cellular response to calcium ion / protein export from nucleus / liver development / basal plasma membrane / cell-matrix adhesion / kidney development / lumenal side of endoplasmic reticulum membrane / cellular response to reactive oxygen species / establishment of localization in cell / phosphoprotein binding / protein tetramerization / calcium ion transmembrane transport
Similarity search - Function
Polycystic kidney disease type 1 protein / PKD/REJ-like domain / Polycystin cation channel / REJ domain / REJ domain / REJ domain profile. / Polycystin-1 like, PLAT/LH2 domain / Carbohydrate-binding WSC / WSC domain / WSC domain profile. ...Polycystic kidney disease type 1 protein / PKD/REJ-like domain / Polycystin cation channel / REJ domain / REJ domain / REJ domain profile. / Polycystin-1 like, PLAT/LH2 domain / Carbohydrate-binding WSC / WSC domain / WSC domain profile. / present in yeast cell wall integrity and stress response component proteins / PKD domain / Ferredoxin I 4Fe-4S cluster domain / : / Polycystic kidney disease type 2 protein / Polycystin domain / Polycystin domain / Lipoxygenase homology 2 (beta barrel) domain / PLAT/LH2 domain / PLAT/LH2 domain superfamily / PLAT/LH2 domain / PLAT domain profile. / Polycystic kidney disease (PKD) domain profile. / GPS motif / GAIN-B domain profile. / G-protein-coupled receptor proteolytic site domain / PKD domain / Polycystin cation channel, PKD1/PKD2 / Polycystin cation channel / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Voltage-dependent channel domain superfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Immunoglobulin-like fold
Similarity search - Domain/homology
Polycystin-1 / Polycystin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsSu Q / Hu F / Ge X / Lei J / Yu S / Wang T / Zhou Q / Mei C / Shi Y
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China31621092 China
National Natural Science Foundation of China31621092 China
National Natural Science Foundation of China31630017 China
CitationJournal: Science / Year: 2018
Title: Structure of the human PKD1-PKD2 complex.
Authors: Qiang Su / Feizhuo Hu / Xiaofei Ge / Jianlin Lei / Shengqiang Yu / Tingliang Wang / Qiang Zhou / Changlin Mei / Yigong Shi /
Abstract: Mutations in two genes, and , account for most cases of autosomal dominant polycystic kidney disease, one of the most common monogenetic disorders. Here we report the 3.6-angstrom cryo-electron ...Mutations in two genes, and , account for most cases of autosomal dominant polycystic kidney disease, one of the most common monogenetic disorders. Here we report the 3.6-angstrom cryo-electron microscopy structure of truncated human PKD1-PKD2 complex assembled in a 1:3 ratio. PKD1 contains a voltage-gated ion channel (VGIC) fold that interacts with PKD2 to form the domain-swapped, yet noncanonical, transient receptor potential (TRP) channel architecture. The S6 helix in PKD1 is broken in the middle, with the extracellular half, S6a, resembling pore helix 1 in a typical TRP channel. Three positively charged, cavity-facing residues on S6b may block cation permeation. In addition to the VGIC, a five-transmembrane helix domain and a cytosolic PLAT domain were resolved in PKD1. The PKD1-PKD2 complex structure establishes a framework for dissecting the function and disease mechanisms of the PKD proteins.
History
DepositionJun 29, 2018-
Header (metadata) releaseAug 15, 2018-
Map releaseAug 15, 2018-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6a70
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6991.png

Downloads & links

-
Map

FileDownload / File: emd_6991.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 256 pix.
= 279.296 Å		1.09 Å/pix.
x 256 pix.
= 279.296 Å		1.09 Å/pix.
x 256 pix.
= 279.296 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.091 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.032889903 - 0.08508097
Average (Standard dev.)0.0006551257 (±0.004800811)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 279.296 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0911.0911.091
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z279.296279.296279.296
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0330.0850.001

-
Supplemental data

-
Sample components

-
Entire : the structure of an asymmetric complex

EntireName: the structure of an asymmetric complex
Components
  • Complex: the structure of an asymmetric complex
    • Protein or peptide: Polycystin-2
    • Protein or peptide: Polycystin-1

-
Supramolecule #1: the structure of an asymmetric complex

SupramoleculeName: the structure of an asymmetric complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Samples were obtained by co-expression in 293F cells. A complex contains one PKD1 subunit and three PKD2 subunits.
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 310 KDa

-
Macromolecule #1: Polycystin-2

MacromoleculeName: Polycystin-2 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 66.623406 KDa
Recombinant expressionOrganism: HOMO SAPIENS (human)
SequenceString: MGSAGWSHPQ FEKGGGSGGG SGGSAWSHPQ FEKGSAAAPR VAWAERLVRG LRGLWGTRLM EESSTNREKY LKSVLRELVT YLLFLIVLC ILTYGMMSSN VYYYTRMMSQ LFLDTPVSKT EKTNFKTLSS MEDFWKFTEG SLLDGLYWKM QPSNQTEADN R SFIFYENL ...String:
MGSAGWSHPQ FEKGGGSGGG SGGSAWSHPQ FEKGSAAAPR VAWAERLVRG LRGLWGTRLM EESSTNREKY LKSVLRELVT YLLFLIVLC ILTYGMMSSN VYYYTRMMSQ LFLDTPVSKT EKTNFKTLSS MEDFWKFTEG SLLDGLYWKM QPSNQTEADN R SFIFYENL LLGVPRIRQL RVRNGSCSIP QDLRDEIKEC YDVYSVSSED RAPFGPRNGT AWIYTSEKDL NGSSHWGIIA TY SGAGYYL DLSRTREETA AQVASLKKNV WLDRGTRATF IDFSVYNANI NLFCVVRLLV EFPATGGVIP SWQFQPLKLI RYV TTFDFF LAACEIIFCF FIFYYVVEEI LEIRIHKLHY FRSFWNCLDV VIVVLSVVAI GINIYRTSNV EVLLQFLEDQ NTFP NFEHL AYWQIQFNNI AAVTVFFVWI KLFKFINFNR TMSQLSTTMS RCAKDLFGFA IMFFIIFLAY AQLAYLVFGT QVDDF STFQ ECIFTQFRII LGDINFAEIE EANRVLGPIY FTTFVFFMFF ILLNMFLAII NDTYSEVKSD LAQQKAEMEL SDLIRK GYH KALVKLKLKK NTVD

UniProtKB: Polycystin-2

-
Macromolecule #2: Polycystin-1

MacromoleculeName: Polycystin-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 127.024836 KDa
Recombinant expressionOrganism: HOMO SAPIENS (human)
SequenceString: MGSAGDYKDH DGDYKDHDID YKDDDDKGSA AATAFGASLF VPPSHVRFVF PEPTADVNYI VMLTCAVCLV TYMVMAAILH KLDQLDASR GRAIPFCGQR GRFKYEILVK TGWGRGSGTT AHVGIMLYGV DSRSGHRHLD GDRAFHRNSL DIFRIATPHS L GSVWKIRV ...String:
MGSAGDYKDH DGDYKDHDID YKDDDDKGSA AATAFGASLF VPPSHVRFVF PEPTADVNYI VMLTCAVCLV TYMVMAAILH KLDQLDASR GRAIPFCGQR GRFKYEILVK TGWGRGSGTT AHVGIMLYGV DSRSGHRHLD GDRAFHRNSL DIFRIATPHS L GSVWKIRV WHDNKGLSPA WFLQHVIVRD LQTARSAFFL VNDWLSVETE ANGGLVEKEV LAASDAALLR FRRLLVAELQ RG FFDKHIW LSIWDRPPRS RFTRIQRATC CVLLICLFLG ANAVWYGAVG DSAYSTGHVS RLSPLSVDTV AVGLVSSVVV YPV YLAILF LFRMSRSKVA GSPSPTPAGQ QVLDIDSCLD SSVLDSSFLT FSGLHAEQAF VGQMKSDLFL DDSKSLVCWP SGEG TLSWP DLLSDPSIVG SNLRQLARGQ AGHGLGPEED GFSLASPYSP AKSFSASDED LIQQVLAEGV SSPAPTQDTH METDL LSSL SSTPGEKTET LALQRLGELG PPSPGLNWEQ PQAARLSRTG LVEGLRKRLL PAWCASLAHG LSLLLVAVAV AVSGWV GAS FPPGVSVAWL LSSSASFLAS FLGWEPLKVL LEALYFSLVA KRLHPDEDDT LVESPAVTPV SARVPRVRPP HGFALFL AK EEARKVKRLH GMLRSLLVYM LFLLVTLLAS YGDASCHGHA YRLQSAIKQE LHSRAFLAIT RSEELWPWMA HVLLPYVH G NQSSPELGPP RLRQVRLQEA LYPDPPGPRV HTCSAAGGFS TSDYDVGWES PHNGSGTWAY SAPDLLGAWS WGSCAVYDS GGYVQELGLS LEESRDRLRF LQLHNWLDNR SRAVFLELTR YSPAVGLHAA VTLRLEFPAA GRALAALSVR PFALRRLSAG LSLPLLTSV CLLLFAVHFA VAEARTWHRE GRWRVLRLGA WARWLLVALT AATALVRLAQ LGAADRQWTR FVRGRPRRFT S FDQVAQLS SAARGLAASL LFLLLVKAAQ QLRFVRQWSV FGKTLCRALP ELLGVTLGLV VLGVAYAQLA ILLVSSCVDS LW SVAQALL VLCPGTGLST LCPAESWHLS PLLCVGLWAL RLWGALRLGA VILRWRYHAL RGELYRPAWE PQDYEMVELF LRR LRLWMG LSKVKEFRHK VRFEGMEPLP SRSSRGS

UniProtKB: Polycystin-1

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration10 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
20.0 mMHEPESHEPES 7.5
0.06 %digitonindigitonin
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was monodisperse.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5t4d

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 27296
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

+
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