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- EMDB-62719: Structure of gain-of-function polycystin-1/polycystin-2 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-62719
TitleStructure of gain-of-function polycystin-1/polycystin-2 complex
Map data
Sample
  • Complex: Structure of Polycystic kidney disease protein 1/2 complex
    • Complex: Polycystin-1
      • Protein or peptide: Polycystin-1
    • Complex: Polycystin-2
      • Protein or peptide: Polycystin-2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsADPKD / polycystin-1 / polycystin-2 / ion channel / 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 / 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 / metanephric proximal tubule development / HLH domain binding / calcium-induced calcium release activity / calcium-independent cell-matrix adhesion / Wnt receptor activity / VxPx cargo-targeting to cilium / cilium organization / genitalia development / migrasome / muscle alpha-actinin binding / detection of mechanical stimulus / regulation of calcium ion import / voltage-gated monoatomic ion channel activity / placenta blood vessel development / cellular response to hydrostatic pressure / Golgi-associated vesicle membrane / response to fluid shear stress / cation channel complex / metanephric collecting duct development / cellular response to fluid shear stress / outward rectifier potassium channel activity / cartilage development / cellular response to osmotic stress / non-motile cilium / determination of left/right symmetry / actinin binding / digestive tract development / motile cilium / : / neural tube development / voltage-gated monoatomic cation channel activity / voltage-gated sodium channel activity / aorta development / branching involved in ureteric bud morphogenesis / cartilage condensation / ciliary membrane / skin development / branching morphogenesis of an epithelial tube / negative regulation of G1/S transition of mitotic cell cycle / protein heterotetramerization / spinal cord development / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytoplasmic side of endoplasmic reticulum membrane / heart looping / establishment of cell polarity / homophilic cell-cell adhesion / centrosome duplication / regulation of G1/S transition of mitotic cell cycle / lateral plasma membrane / voltage-gated potassium channel activity / anatomical structure morphogenesis / embryonic placenta development / potassium channel activity / voltage-gated calcium channel activity / cell surface receptor signaling pathway via JAK-STAT / regulation of cell adhesion / monoatomic cation channel activity / transcription regulator inhibitor activity / cytoskeletal protein binding / regulation of proteasomal protein catabolic process / release of sequestered calcium ion into cytosol / potassium ion transmembrane transport / calcium channel complex / protein export from nucleus / cellular response to calcium ion / cellular response to cAMP / basal plasma membrane / cytoplasmic vesicle membrane / sodium ion transmembrane transport / regulation of mitotic spindle organization / establishment of localization in cell / cell-matrix adhesion / cellular response to reactive oxygen species / lumenal side of endoplasmic reticulum membrane / kidney development / protein tetramerization / liver development / phosphoprotein binding / 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 / Ferredoxin I 4Fe-4S cluster domain / : / Polycystic kidney disease type 2 protein / Polycystin domain / PKD 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 / G-protein-coupled receptor proteolytic site domain / GAIN-B domain profile. / 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: 3.34 Å
AuthorsChen MY / Su Q
Funding support China, 4 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31930059 China
National Natural Science Foundation of China (NSFC)81970633 China
National Natural Science Foundation of China (NSFC)U1904146 China
National Natural Science Foundation of China (NSFC)81920108015 China
CitationJournal: To Be Published
Title: Structure of gain-of-function polycystin-1/polycystin-2 complex.
Authors: Chen M / Su Q / Shi Y
History
DepositionDec 12, 2024-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62719.png

Downloads & links

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Map

FileDownload / File: emd_62719.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 240 pix.
= 260.88 Å		1.09 Å/pix.
x 240 pix.
= 260.88 Å		1.09 Å/pix.
x 240 pix.
= 260.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.03650603 - 0.084327936
Average (Standard dev.)0.00041842752 (±0.0033316875)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 260.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_62719_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62719_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Structure of Polycystic kidney disease protein 1/2 complex

EntireName: Structure of Polycystic kidney disease protein 1/2 complex
Components
  • Complex: Structure of Polycystic kidney disease protein 1/2 complex
    • Complex: Polycystin-1
      • Protein or peptide: Polycystin-1
    • Complex: Polycystin-2
      • Protein or peptide: Polycystin-2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Structure of Polycystic kidney disease protein 1/2 complex

SupramoleculeName: Structure of Polycystic kidney disease protein 1/2 complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Polycystin-1

SupramoleculeName: Polycystin-1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Polycystin-2

SupramoleculeName: Polycystin-2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Polycystin-1

MacromoleculeName: Polycystin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 138.627828 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKG ASLFVPPSHV RFVFPEPTAD VNYIVMLTCA VCLVTYMVMA AILHKLDQLD ASRGRAIPFC GQRGRFKYEI LVKTGWGRG SGTTAHVGIM LYGVDSRSGH RHLDGDRAFH RNSLDIFRIA TPHSLGSVWK IRVWHDNKGL SPAWFLQHVI V RDLQTARS ...String:
MDYKDDDDKG ASLFVPPSHV RFVFPEPTAD VNYIVMLTCA VCLVTYMVMA AILHKLDQLD ASRGRAIPFC GQRGRFKYEI LVKTGWGRG SGTTAHVGIM LYGVDSRSGH RHLDGDRAFH RNSLDIFRIA TPHSLGSVWK IRVWHDNKGL SPAWFLQHVI V RDLQTARS AFFLVNDWLS VETEANGGLV EKEVLAASDA ALLRFRRLLV AELQRGFFDK HIWLSIWDRP PRSRFTRIQR AT CCVLLIC LFLGANAVWY GAVGDSAYST GHVSRLSPLS VDTVAVGLVS SVVVYPVYLA ILFLFRMSRS KVAGSPSPTP AGQ QVLDID SCLDSSVLDS SFLTFSGLHA EQAFVGQMKS DLFLDDSKSL VCWPSGEGTL SWPDLLSDPS IVGSNLRQLA RGQA GHGLG PEEDGFSLAS PYSPAKSFSA SDEDLIQQVL AEGVSSPAPT QDTHMETDLL SSLSSTPGEK TETLALQRLG ELGPP SPGL NWEQPQAARL SRTGLVEGLR KRLLPAWCAS LAHGLSLLLV AVAVAVSGWV GASFPPGVSV AWLLSSSASF LASFLG WEP LKVLLEALYF SLVAKRLHPD EDDTLVESPA VTPVSARVPR VRPPHGFALF LAKEEARKVK RLHGMLRSLL VYMLFLL VT LLASYGDASC HGHAYRLQSA IKQELHSRAF LAITRSEELW PWMAHVLLPY VHGNQSSPEL GPPRLRQVRL QEALYPDP P GPRVHTCSAA GGFSTSDYDV GWESPHNGSG TWAYSAPDLL GAWSWGSCAV YDSGGYVQEL GLSLEESRDR LRFLQLHNW LDNRSRAVFL ELTRYSPAVG LHAAVTLRLE FPAAGRALAA LSVRPFALRR LSAGLSLPLL TSVCLLLFAV HFAVAEARTW HREGRWRVL RLGAWARWLL VALTAATALV RLAQLGAADR QWTRFVRGRP RRFTSFDQVA QLSSAARGLA ASLLFLLLVK A AQQLRFVR QWSVFGKTLC RALPELLGVT LGLVVLGVAY AQLAILLVSS CVDSLWSVAQ ALLVLCPGTG LSTLCPAESW HL SPLLCVG LWALRLWGAL RLGAVILRWR YHALRGELYR PAWEPQDYEM VELFLRRLRL WMGLSKVKEF RHKVRFEGME PLP SRSSRG SKVSPDVPPP SAGSDASHPS TSSSQLDGLS VSLGRLGTRC EPEPSRLQAV FEALLTQFDR LNQATEDVYQ LEQQ LHSLQ GRRSSRAPAG SSRGPSPGLR PALPSRLARA SRGVDLATGP SRTPLRAKNK VHPSSTL

UniProtKB: Polycystin-1

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Macromolecule #2: Polycystin-2

MacromoleculeName: Polycystin-2 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 113.313727 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGASSAWSHP QFEKGGGSGG GSGGSAWSHP QFEKGGSMVN SSRVQPQQPG DAKRPPAPRA PDPGRLMAGC AAVGASLAAP GGLCEQRGL EIEMQRIRQA AARDPPAGAA ASPSPPLSSC SRQAWSRDNP GFEAEEEEEE VEGEEGGMVV EMDVEWRPGS R RSAASSAV ...String:
MGASSAWSHP QFEKGGGSGG GSGGSAWSHP QFEKGGSMVN SSRVQPQQPG DAKRPPAPRA PDPGRLMAGC AAVGASLAAP GGLCEQRGL EIEMQRIRQA AARDPPAGAA ASPSPPLSSC SRQAWSRDNP GFEAEEEEEE VEGEEGGMVV EMDVEWRPGS R RSAASSAV SSVGARSRGL GGYHGAGHPS GRRRRREDQG PPCPSPVGGG DPLHRHLPLE GQPPRVAWAE RLVRGLRGLW GT RLMEESS TNREKYLKSV LRELVTYLLF LIVLCILTYG MMSSNVYYYT RMMSQLFLDT PVSKTEKTNF KTLSSMEDFW KFT EGSLLD GLYWKMQPSN QTEADNRSFI FYENLLLGVP RIRQLRVRNG SCSIPQDLRD EIKECYDVYS VSSEDRAPFG PRNG TAWIY TSEKDLNGSS HWGIIATYSG AGYYLDLSRT REETAAQVAS LKKNVWLDRG TRATFIDFSV YNANINLFCV VRLLV EFPA TGGVIPSWQF QPLKLIRYVT TFDFFLAACE IIFCFFIFYY VVEEILEIRI HKLHYFRSFW NCLDVVIVVL SVVAIG INI YRTSNVEVLL QFLEDQNTFP NFEHLAYWQI QFNNIAAVTV FFVWIKLFKF INFNRTMSQL STTMSRCAKD LFGFAIM FF IIFLAYAQLA YLVFGTQVDD FSTFQECIFT QFRIILGDIN FAEIEEANRV LGPIYFTTFV FFMFFILLNM FAAIIADT Y SEVKSDLAQQ KAEMELSDLI RKGYHKALVK LKLKKNTVDD ISESLRQGGG KLNFDELRQD LKGKGHTDAE IEAIFTKYD QDGDQELTEH EHQQMRDDLE KEREDLDLDH SSLPRPMSSR SFPRSLDDSE EDDDEDSGHS SRRRGSISSG VSYEEFQVLV RRVDRMEHS IGSIVSKIDA VIVKLEIMER AKLKRREVLG RLLDGVAEDE RLGRDSEIHR EQMERLVREE LERWESDDAA S QISHGLGT PVGLNGQPRP RSSRPSSSQS TEGMEGAGGN GSSNVHV

UniProtKB: Polycystin-2

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 6 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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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

Concentration5 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k 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: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 192205
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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