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- EMDB-7786: human PKD2 F604P mutant -

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Basic information

Entry
Database: EMDB / ID: EMD-7786
Titlehuman PKD2 F604P mutant
Map dataHuman PKD2 F604P mutant
Sample
  • Organelle or cellular component: PKD2
    • Protein or peptide: Polycystin-2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsIon Channel / TRP channel / PKD2 / PC2 / TRPP2 / TRANSPORT PROTEIN
Function / homology
Function and homology information


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 ...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 / metanephric ascending thin limb development / metanephric mesenchyme development / metanephric S-shaped body morphogenesis / basal cortex / renal artery morphogenesis / positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / calcium-induced calcium release activity / migrasome / cilium organization / VxPx cargo-targeting to cilium / detection of mechanical stimulus / muscle alpha-actinin binding / regulation of calcium ion import / voltage-gated monoatomic ion channel activity / placenta blood vessel development / cellular response to hydrostatic pressure / cation channel complex / cellular response to fluid shear stress / outward rectifier potassium channel activity / actinin binding / cellular response to osmotic stress / non-motile cilium / determination of left/right symmetry / inorganic cation transmembrane transport / voltage-gated monoatomic cation channel activity / aorta development / neural tube development / motile cilium / voltage-gated sodium channel activity / ciliary membrane / branching involved in ureteric bud morphogenesis / protein heterotetramerization / negative regulation of G1/S transition of mitotic cell cycle / spinal cord development / cytoplasmic side of endoplasmic reticulum membrane / heart looping / centrosome duplication / voltage-gated potassium channel activity / cell surface receptor signaling pathway via JAK-STAT / potassium channel activity / embryonic placenta development / voltage-gated calcium channel activity / transcription regulator inhibitor activity / monoatomic cation channel activity / cytoskeletal protein binding / cellular response to cAMP / release of sequestered calcium ion into cytosol / potassium ion transmembrane transport / sodium ion transmembrane transport / cytoplasmic vesicle membrane / cellular response to calcium ion / liver development / basal plasma membrane / 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 / Wnt signaling pathway / intracellular calcium ion homeostasis / calcium ion transport / mitotic spindle / positive regulation of nitric oxide biosynthetic process / cell-cell junction / lamellipodium / regulation of cell population proliferation / heart development / ATPase binding / positive regulation of cytosolic calcium ion concentration / basolateral plasma membrane / protein homotetramerization / transmembrane transporter binding / cell surface receptor signaling pathway / regulation of cell cycle / ciliary basal body / cilium / signaling receptor binding / negative regulation of cell population proliferation / calcium ion binding / positive regulation of gene expression / endoplasmic reticulum membrane / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular exosome / identical protein binding
Similarity search - Function
Ferredoxin I 4Fe-4S cluster domain / : / Polycystic kidney disease type 2 protein / Polycystin domain / Polycystin domain / Polycystin cation channel, PKD1/PKD2 / Polycystin cation channel / Voltage-dependent channel domain superfamily / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.54 Å
AuthorsZheng W / Yang X
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01 DK110575-01 United States
CitationJournal: Nat Commun / Year: 2018
Title: Hydrophobic pore gates regulate ion permeation in polycystic kidney disease 2 and 2L1 channels.
Authors: Wang Zheng / Xiaoyong Yang / Ruikun Hu / Ruiqi Cai / Laura Hofmann / Zhifei Wang / Qiaolin Hu / Xiong Liu / David Bulkley / Yong Yu / Jingfeng Tang / Veit Flockerzi / Ying Cao / Erhu Cao / Xing-Zhen Chen /
Abstract: PKD2 and PKD1 genes are mutated in human autosomal dominant polycystic kidney disease. PKD2 can form either a homomeric cation channel or a heteromeric complex with the PKD1 receptor, presumed to ...PKD2 and PKD1 genes are mutated in human autosomal dominant polycystic kidney disease. PKD2 can form either a homomeric cation channel or a heteromeric complex with the PKD1 receptor, presumed to respond to ligand(s) and/or mechanical stimuli. Here, we identify a two-residue hydrophobic gate in PKD2L1, and a single-residue hydrophobic gate in PKD2. We find that a PKD2 gain-of-function gate mutant effectively rescues PKD2 knockdown-induced phenotypes in embryonic zebrafish. The structure of a PKD2 activating mutant F604P by cryo-electron microscopy reveals a π- to α-helix transition within the pore-lining helix S6 that leads to repositioning of the gate residue and channel activation. Overall the results identify hydrophobic gates and a gating mechanism of PKD2 and PKD2L1.
History
DepositionApr 12, 2018-
Header (metadata) releaseJun 27, 2018-
Map releaseJun 27, 2018-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.04
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  • Surface view with fitted model
  • Atomic models: PDB-6d1w
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7786.png

Downloads & links

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Map

FileDownload / File: emd_7786.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman PKD2 F604P mutant
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.22 Å/pix.
x 192 pix.
= 233.395 Å		1.22 Å/pix.
x 192 pix.
= 233.395 Å		1.22 Å/pix.
x 192 pix.
= 233.395 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2156 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.12531123 - 0.21940334
Average (Standard dev.)0.0012095302 (±0.008277643)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 233.3952 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.21559895833331.21559895833331.2155989583333
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z233.395233.395233.395
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.1250.2190.001

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Supplemental data

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Half map: Human PKD2 F604P mutant

Fileemd_7786_half_map_1.map
AnnotationHuman PKD2 F604P mutant
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Human PKD2 F604P mutant

Fileemd_7786_half_map_2.map
AnnotationHuman PKD2 F604P mutant
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PKD2

EntireName: PKD2
Components
  • Organelle or cellular component: PKD2
    • Protein or peptide: Polycystin-2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: PKD2

SupramoleculeName: PKD2 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 300 kDa/nm

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Macromolecule #1: Polycystin-2

MacromoleculeName: Polycystin-2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 84.996336 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIEMQRIRQA AARDPPAGAA ASPSPPLSSC SRQAWSRDNP GFEAEEEEEE VEGEEGGMVV EMDVEWRPGS RRSAASSAVS SVGARSRGL GGYHGAGHPS GRRRRREDQG PPCPSPVGGG DPLHRHLPLE GQPPRVAWAE RLVRGLRGLW GTRLMEESST N REKYLKSV ...String:
EIEMQRIRQA AARDPPAGAA ASPSPPLSSC SRQAWSRDNP GFEAEEEEEE VEGEEGGMVV EMDVEWRPGS RRSAASSAVS SVGARSRGL GGYHGAGHPS GRRRRREDQG PPCPSPVGGG DPLHRHLPLE GQPPRVAWAE RLVRGLRGLW GTRLMEESST N REKYLKSV LRELVTYLLF LIVLCILTYG MMSSNVYYYT RMMSQLFLDT PVSKTEKTNF KTLSSMEDFW KFTEGSLLDG LY WKMQPSN QTEADNRSFI FYENLLLGVP RIRQLRVRNG SCSIPQDLRD EIKECYDVYS VSSEDRAPFG PRNGTAWIYT SEK DLNGSS HWGIIATYSG AGYYLDLSRT REETAAQVAS LKKNVWLDRG TRATFIDFSV YNANINLFCV VRLLVEFPAT GGVI PSWQF QPLKLIRYVT TFDFFLAACE IIFCFFIFYY VVEEILEIRI HKLHYFRSFW NCLDVVIVVL SVVAIGINIY RTSNV EVLL QFLEDQNTFP NFEHLAYWQI QFNNIAAVTV FFVWIKLFKF INFNRTMSQL STTMSRCAKD LFGFAIMPFI IFLAYA QLA YLVFGTQVDD FSTFQECIFT QFRIILGDIN FAEIEEANRV LGPIYFTTFV FFMFFILLNM FLAIINDTYS EVKSDLA QQ KAEMELSDLI RKGYHKALVK LKLKKNTVDD ISESLRQGGG KLNFDELRQD LKGKGHTDAE IEAIFTKYDQ DGDQELTE H EHQQMRDDLE KEREDLDLD

UniProtKB: Polycystin-2

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 12 / 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

Concentration2 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 387454
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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