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- EMDB-30607: Structure of PKD1L3-CTD/PKD2L1 in calcium-bound state -

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Basic information

Entry
Database: EMDB / ID: EMD-30607
TitleStructure of PKD1L3-CTD/PKD2L1 in calcium-bound state
Map dataCa
Sample
  • Complex: Mouse PKD1L3 in complex with PKD2L1 in presence of 20 mM calcium
    • Protein or peptide: Polycystic kidney disease 2-like 1 protein
    • Protein or peptide: Polycystic kidney disease protein 1-like 3
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
KeywordsHeterotetrameric TRP channel / Calcium / Primary cilia / PKD / TRANSPORT 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 / pH-gated monoatomic ion channel activity / response to water / osmolarity-sensing monoatomic cation channel activity / calcium-activated potassium channel activity / cellular response to pH / muscle alpha-actinin binding / calcium-activated cation channel activity / cation channel complex ...detection of chemical stimulus involved in sensory perception of sour taste / detection of chemical stimulus involved in sensory perception of taste / pH-gated monoatomic ion channel activity / response to water / osmolarity-sensing monoatomic cation channel activity / calcium-activated potassium channel activity / cellular response to pH / muscle alpha-actinin binding / calcium-activated cation channel activity / cation channel complex / cellular response to acidic pH / 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 ion transmembrane transport / calcium channel activity / actin cytoskeleton / carbohydrate binding / cytoplasmic vesicle / protein homotetramerization / transmembrane transporter binding / receptor complex / calcium ion binding / endoplasmic reticulum / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Polycystin-1 like, PLAT/LH2 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 ...Polycystin-1 like, PLAT/LH2 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. / GAIN domain superfamily / GPCR proteolysis site, GPS, motif / GPS motif / GAIN-B domain profile. / G-protein-coupled receptor proteolytic site domain / Polycystin cation channel, PKD1/PKD2 / Polycystin cation channel / C-type lectin-like/link domain superfamily / C-type lectin fold / 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 / Polycystin-1-like protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsSu Q / Shi YG
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31930059 China
National Natural Science Foundation of China (NSFC)81920108015 China
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis for Ca activation of the heteromeric PKD1L3/PKD2L1 channel.
Authors: Qiang Su / Mengying Chen / Yan Wang / Bin Li / Dan Jing / Xiechao Zhan / Yong Yu / Yigong Shi /
Abstract: The heteromeric complex between PKD1L3, a member of the polycystic kidney disease (PKD) protein family, and PKD2L1, also known as TRPP2 or TRPP3, has been a prototype for mechanistic characterization ...The heteromeric complex between PKD1L3, a member of the polycystic kidney disease (PKD) protein family, and PKD2L1, also known as TRPP2 or TRPP3, has been a prototype for mechanistic characterization of heterotetrametric TRP-like channels. Here we show that a truncated PKD1L3/PKD2L1 complex with the C-terminal TRP-fold fragment of PKD1L3 retains both Ca and acid-induced channel activities. Cryo-EM structures of this core heterocomplex with or without supplemented Ca were determined at resolutions of 3.1 Å and 3.4 Å, respectively. The heterotetramer, with a pseudo-symmetric TRP architecture of 1:3 stoichiometry, has an asymmetric selectivity filter (SF) guarded by Lys2069 from PKD1L3 and Asp523 from the three PKD2L1 subunits. Ca-entrance to the SF vestibule is accompanied by a swing motion of Lys2069 on PKD1L3. The S6 of PKD1L3 is pushed inward by the S4-S5 linker of the nearby PKD2L1 (PKD2L1-III), resulting in an elongated intracellular gate which seals the pore domain. Comparison of the apo and Ca-loaded complexes unveils an unprecedented Ca binding site in the extracellular cleft of the voltage-sensing domain (VSD) of PKD2L1-III, but not the other three VSDs. Structure-guided mutagenic studies support this unconventional site to be responsible for Ca-induced channel activation through an allosteric mechanism.
History
DepositionOct 3, 2020-
Header (metadata) releaseSep 1, 2021-
Map releaseSep 1, 2021-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7d7f
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30607.png

Downloads & links

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Map

FileDownload / File: emd_30607.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCa
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: 0.018 / Movie #1: 0.02
Minimum - Maximum-0.064338274 - 0.1254934
Average (Standard dev.)0.00056496 (±0.0045815594)
SymmetrySpace group: 1
Details

EMDB XML:

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

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0871.0871.087
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z260.880260.880260.880
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0640.1250.001

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Supplemental data

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Sample components

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Entire : Mouse PKD1L3 in complex with PKD2L1 in presence of 20 mM calcium

EntireName: Mouse PKD1L3 in complex with PKD2L1 in presence of 20 mM calcium
Components
  • Complex: Mouse PKD1L3 in complex with PKD2L1 in presence of 20 mM calcium
    • Protein or peptide: Polycystic kidney disease 2-like 1 protein
    • Protein or peptide: Polycystic kidney disease protein 1-like 3
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION

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Supramolecule #1: Mouse PKD1L3 in complex with PKD2L1 in presence of 20 mM calcium

SupramoleculeName: Mouse PKD1L3 in complex with PKD2L1 in presence of 20 mM calcium
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Mus musculus (house mouse)

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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: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 69.234734 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGSAGWSHPQ FEKGGGSGGG SGGSAWSHPQ FEKGSAAATL VSSCCLHICR SIRGLWGTTL TENTAENREL YVKTTLRELV VYIVFLVDI CLLTYGMTSS SAYYYTKVMS ELFLHTPSDS GVSFQTISSM SDFWDFAQGP LLDSLYWTKW YNNQSLGRGS H SFIYYENL ...String:
MGSAGWSHPQ FEKGGGSGGG SGGSAWSHPQ FEKGSAAATL VSSCCLHICR SIRGLWGTTL TENTAENREL YVKTTLRELV VYIVFLVDI CLLTYGMTSS SAYYYTKVMS ELFLHTPSDS GVSFQTISSM SDFWDFAQGP LLDSLYWTKW YNNQSLGRGS H SFIYYENL LLGAPRLRQL RVRNDSCVVH EDFREDILNC YDVYSPDKED QLPFGPQNGT AWTYHSQNEL GGSSHWGRLT SY SGGGYYL DLPGSRQASA EALQGLQEGL WLDRGTRVVF IDFSVYNANI NLFCILRLVV EFPATGGTIP SWQIRTVKLI RYV NNWDFF IVGCEVVFCV FIFYYVVEEI LEIHLHRLRY LSSVWNILDL VVILLSIVAV GFHIFRTLEV NRLMGKLLQQ PDTY ADFEF LAFWQTQYNN MNAVNLFFAW IKIFKYISFN KTMTQLSSTL ARCAKDILGF AIMFFIVFFA YAQLGYLLFG TQVEN FSTF VKCIFTQFRI ILGDFDYNAI DNANRILGPV YFVTYVFFVF FVLLNMFLAI INDTYSEVKE ELAGQKDQLQ LSDFLK QSY NKTLLRLRLR KERVSDVQKV LKGGEPEIQF EDFTSTLREL G

UniProtKB: Polycystin-2-like protein 1

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Macromolecule #2: Polycystic kidney disease protein 1-like 3

MacromoleculeName: Polycystic kidney disease protein 1-like 3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 62.541914 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGSAGDYKDH DGDYKDHDID YKDDDDKGSA AAPIYTAPAM NNLAKPTRKA WKKQLSKLTG GTLVQILFLT LLMTTVYSAK DSSRFFLHR AIWKRFSHRF SEIKTVEDFY PWANGTLLPN LYGDYRGFIT DGNSFLLGNV LIRQTRIPND IFFPGSLHKQ M KSPPQHQE ...String:
MGSAGDYKDH DGDYKDHDID YKDDDDKGSA AAPIYTAPAM NNLAKPTRKA WKKQLSKLTG GTLVQILFLT LLMTTVYSAK DSSRFFLHR AIWKRFSHRF SEIKTVEDFY PWANGTLLPN LYGDYRGFIT DGNSFLLGNV LIRQTRIPND IFFPGSLHKQ M KSPPQHQE DRENYGAGWV PPDTNITKVD SIWHYQNQES LGGYPIQGEL ATYSGGGYVV RLGRNHSAAT RVLQHLEQRR WL DHCTKAL FVEFTVFNAN VNLLCAVTLI LESSGVGTFL TSLQLDSLTS LQSSERGFAW IVSQVVYYLL VCYYAFIQGC RLK RQRLAF FTRKRNLLDT SIVLISFSIL GLSMQSLSLL HKKMQQYHCD RDRFISFYEA LRVNSAVTHL RGFLLLFATV RVWD LLRHH AQLQVINKTL SKAWDEVLGF ILIIVVLLSS YAMTFNLLFG WSISDYQSFF RSIVTVVGLL MGTSKHKEVI ALYPI LGSL LVLSSIILMG LVIINLFVSA ILIAFGKERK ACEKEATLTD MLLQKLSSLL GIRLHQNPSE EHADNTG

UniProtKB: Polycystin-1-like protein 3

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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: 10 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 5 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 149903
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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