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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-6991 | ||||||||||||
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Title | Structure of the human PKD1/PKD2 complex | ||||||||||||
![]() | None | ||||||||||||
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![]() | Asymmetric complex / polycystic kidney disease / MEMBRANE PROTEIN | ||||||||||||
Function / homology | ![]() 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 ...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 / mitocytosis / lymph vessel morphogenesis / basal cortex / metanephric mesenchyme development / metanephric S-shaped body morphogenesis / renal artery morphogenesis / metanephric proximal tubule development / positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / migrasome / calcium-independent cell-matrix adhesion / Wnt receptor activity / cilium organization / VxPx cargo-targeting to cilium / genitalia development / establishment of epithelial cell polarity / detection of mechanical stimulus / calcium-induced calcium release activity / regulation of calcium ion import / cation channel complex / muscle alpha-actinin binding / response to fluid shear stress / placenta blood vessel development / voltage-gated monoatomic ion channel activity / Golgi-associated vesicle membrane / cellular response to hydrostatic pressure / outward rectifier potassium channel activity / cellular response to fluid shear stress / metanephric collecting duct development / voltage-gated monoatomic cation channel activity / digestive tract development / non-motile cilium / cellular response to osmotic stress / actinin binding / motile cilium / transcription regulator inhibitor activity / cartilage development / determination of left/right symmetry / aorta development / inorganic cation transmembrane transport / neural tube development / ciliary membrane / voltage-gated sodium channel activity / protein heterotetramerization / skin development / branching involved in ureteric bud morphogenesis / cartilage condensation / negative regulation of G1/S transition of mitotic cell cycle / branching morphogenesis of an epithelial tube / spinal cord development / heart looping / homophilic cell adhesion via plasma membrane adhesion molecules / negative regulation of ryanodine-sensitive calcium-release channel activity / voltage-gated potassium channel activity / cytoplasmic side of endoplasmic reticulum membrane / regulation of G1/S transition of mitotic cell cycle / cell surface receptor signaling pathway via JAK-STAT / centrosome duplication / potassium channel activity / lateral plasma membrane / anatomical structure morphogenesis / sodium ion transmembrane transport / embryonic placenta development / voltage-gated calcium channel activity / regulation of cell adhesion / monoatomic cation channel activity / regulation of proteasomal protein catabolic process / cellular response to cAMP / release of sequestered calcium ion into cytosol / regulation of mitotic spindle organization / potassium ion transmembrane transport / calcium channel complex / cellular response to calcium ion / cytoskeletal protein binding / protein export from nucleus / cell-matrix adhesion / basal plasma membrane / ciliary basal body / liver development / kidney development / establishment of localization in cell / lumenal side of endoplasmic reticulum membrane / phosphoprotein binding / calcium ion transmembrane transport / protein tetramerization / cytoplasmic vesicle membrane Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||||||||
![]() | Su Q / Hu F / Ge X / Lei J / Yu S / Wang T / Zhou Q / Mei C / Shi Y | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 58.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.5 KB 14.5 KB | Display Display | ![]() |
Images | ![]() | 238.9 KB | ||
Filedesc metadata | ![]() | 6.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6a70MC ![]() 6992C C: citing same article ( M: atomic model generated by this map |
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Similar structure data | |
EM raw data | ![]() Data #1: Autopicked particles of PKD1/PKD2 complex [picked particles - multiframe - unprocessed]) |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.091 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : the structure of an asymmetric complex
Entire | Name: the structure of an asymmetric complex |
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Components |
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-Supramolecule #1: the structure of an asymmetric complex
Supramolecule | Name: 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. |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 310 KDa |
-Macromolecule #1: Polycystin-2
Macromolecule | Name: Polycystin-2 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 66.623406 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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
Macromolecule | Name: Polycystin-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 127.024836 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 10 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV | ||||||||||||
Details | This sample was monodisperse. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DARK FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 27296 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |