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- EMDB-6991: Structure of the human PKD1/PKD2 complex -

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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-2Polycystin 2
    • Protein or peptide: Polycystin-1
KeywordsAsymmetric complex / polycystic kidney disease / MEMBRANE PROTEIN
Function / homology
Function and homology information


metanephric distal tubule morphogenesis / 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 / 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 / determination of liver left/right asymmetry / renal tubule morphogenesis / metanephric ascending thin limb development / HLH domain binding / lung epithelium development / metanephric proximal tubule development / lymph vessel morphogenesis / basal cortex / metanephric mesenchyme development / metanephric S-shaped body morphogenesis / renal artery morphogenesis / positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / mitocytosis / migrasome / calcium-independent cell-matrix adhesion / cilium organization / Wnt receptor activity / VxPx cargo-targeting to cilium / establishment of epithelial cell polarity / genitalia development / detection of mechanical stimulus / regulation of calcium ion import / response to fluid shear stress / cation channel complex / calcium-induced calcium release activity / muscle alpha-actinin binding / placenta blood vessel development / Golgi-associated vesicle membrane / voltage-gated monoatomic ion channel activity / cellular response to hydrostatic pressure / outward rectifier potassium channel activity / voltage-gated monoatomic cation channel activity / non-motile cilium / digestive tract development / cellular response to fluid shear stress / metanephric collecting duct development / cellular response to osmotic stress / voltage-gated sodium channel activity / transcription regulator inhibitor activity / actinin binding / motile cilium / inorganic cation transmembrane transport / cartilage development / determination of left/right symmetry / neural tube development / aorta development / protein heterotetramerization / ciliary membrane / skin development / branching involved in ureteric bud morphogenesis / cartilage condensation / negative regulation of G1/S transition of mitotic cell cycle / spinal cord development / branching morphogenesis of an epithelial tube / heart looping / homophilic cell adhesion via plasma membrane adhesion molecules / regulation of G1/S transition of mitotic cell cycle / cytoplasmic side of endoplasmic reticulum membrane / voltage-gated potassium channel activity / cell surface receptor signaling pathway via JAK-STAT / potassium channel activity / centrosome duplication / sodium ion transmembrane transport / negative regulation of ryanodine-sensitive calcium-release channel activity / lateral plasma membrane / anatomical structure morphogenesis / voltage-gated calcium channel activity / embryonic placenta development / regulation of proteasomal protein catabolic process / regulation of cell adhesion / regulation of mitotic spindle organization / monoatomic cation channel activity / cellular response to cAMP / release of sequestered calcium ion into cytosol / potassium ion transmembrane transport / calcium channel complex / cellular response to calcium ion / cytoskeletal protein binding / protein export from nucleus / basal plasma membrane / cell-matrix adhesion / ciliary basal body / liver development / kidney development / establishment of localization in cell / lumenal side of endoplasmic reticulum membrane / calcium ion transmembrane transport / protein tetramerization / phosphoprotein binding
Similarity search - Function
Polycystic kidney disease type 1 protein / Polycystin cation channel / REJ domain / REJ domain profile. / PKD/REJ-like domain / REJ domain / Polycystin-1 like, PLAT/LH2 domain / Carbohydrate-binding WSC / WSC domain / WSC domain profile. ...Polycystic kidney disease type 1 protein / Polycystin cation channel / REJ domain / REJ domain profile. / PKD/REJ-like domain / REJ domain / 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 / Polycystin domain / Polycystin domain / Polycystic kidney disease type 2 protein / Polycystic kidney disease (PKD) domain profile. / Polycystin cation channel, PKD1/PKD2 / Polycystin cation channel / PKD domain / Lipoxygenase homology 2 (beta barrel) domain / PLAT/LH2 domain / PLAT/LH2 domain superfamily / PLAT/LH2 domain / PLAT domain profile. / GPS motif / GPS domain profile. / G-protein-coupled receptor proteolytic site domain / 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

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Structure visualization

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

emd_6991.png

Downloads & links

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Map

FileDownload / File: emd_6991.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Voxel sizeX=Y=Z: 1.091 Å
Density
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

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Supplemental data

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Sample components

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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-2Polycystin 2
    • Protein or peptide: Polycystin-1

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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

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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

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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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration10 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chloridesodium 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.

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Electron microscopy

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

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Image processing

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

5t4d

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

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