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- EMDB-49489: human polycystin-2 with clinical variant D511V -

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Basic information

Entry
Database: EMDB / ID: EMD-49489
Titlehuman polycystin-2 with clinical variant D511V
Map datamain map of human polycystin-2 53-792 with clinical variant D511V
Sample
  • Complex: human polycystin-2 53-792 with clinical variant D511V
    • Protein or peptide: Polycystin-2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsion channels / polycystic kidney disease / PKD / PKD2 / D511V / TRP / ADPKD / METAL TRANSPORT
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 / metanephric ascending thin limb development / metanephric mesenchyme development / metanephric S-shaped body morphogenesis / basal cortex / placenta blood vessel development / renal artery morphogenesis / HLH domain binding / VxPx cargo-targeting to cilium / cilium organization / migrasome / neural tube development / cellular response to fluid shear stress / regulation of calcium ion import / calcium-induced calcium release activity / detection of mechanical stimulus / determination of left/right symmetry / voltage-gated monoatomic ion channel activity / embryonic placenta development / cellular response to hydrostatic pressure / aorta development / cation channel complex / branching involved in ureteric bud morphogenesis / non-motile cilium / outward rectifier potassium channel activity / motile cilium / actinin binding / cellular response to osmotic stress / negative regulation of G1/S transition of mitotic cell cycle / voltage-gated sodium channel activity / heart looping / spinal cord development / ciliary membrane / voltage-gated monoatomic cation channel activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / protein heterotetramerization / cytoplasmic side of endoplasmic reticulum membrane / potassium channel activity / voltage-gated potassium channel activity / centrosome duplication / transcription regulator inhibitor activity / cell surface receptor signaling pathway via JAK-STAT / voltage-gated calcium channel activity / release of sequestered calcium ion into cytosol / monoatomic cation channel activity / cytoskeletal protein binding / cellular response to calcium ion / cellular response to cAMP / liver development / potassium ion transmembrane transport / basal plasma membrane / cytoplasmic vesicle membrane / sodium ion transmembrane transport / lumenal side of endoplasmic reticulum membrane / cellular response to reactive oxygen species / protein tetramerization / Wnt signaling pathway / phosphoprotein binding / mitotic spindle / positive regulation of nitric oxide biosynthetic process / calcium ion transmembrane transport / heart development / calcium ion transport / transmembrane transport / cell-cell junction / cilium / regulation of cell population proliferation / lamellipodium / ATPase binding / ciliary basal body / vesicle / protein homotetramerization / basolateral plasma membrane / regulation of cell cycle / transmembrane transporter binding / cell surface receptor signaling pathway / negative regulation of cell population proliferation / signaling receptor binding / positive regulation of gene expression / calcium ion binding / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / extracellular exosome / membrane / identical protein binding / plasma membrane / cytoplasm
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: 3.1 Å
AuthorsWang Q / Cao E
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: To Be Published
Title: human polycystin-2 with clinical variant D511V
Authors: Wang Q / Cao E
History
DepositionFeb 27, 2025-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49489.png

Downloads & links

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Map

FileDownload / File: emd_49489.map.gz / Format: CCP4 / Size: 65.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map of human polycystin-2 53-792 with clinical variant D511V
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.38 Å/pix.
x 258 pix.
= 356.04 Å		1.38 Å/pix.
x 258 pix.
= 356.04 Å		1.38 Å/pix.
x 258 pix.
= 356.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.38 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.32
Minimum - Maximum-11.658766999999999 - 15.822195000000001
Average (Standard dev.)-0.012232662 (±0.34657678)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions258258258
Spacing258258258
CellA=B=C: 356.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpened map of human polycystin-2 53-792 with clinical...

Fileemd_49489_additional_1.map
Annotationunsharpened map of human polycystin-2 53-792 with clinical variant D511V
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map of human polycystin-2 53-792 with clinical variant D511V

Fileemd_49489_half_map_1.map
Annotationhalf map of human polycystin-2 53-792 with clinical variant D511V
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map of human polycystin-2 53-792 with clinical variant D511V

Fileemd_49489_half_map_2.map
Annotationhalf map of human polycystin-2 53-792 with clinical variant D511V
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : human polycystin-2 53-792 with clinical variant D511V

EntireName: human polycystin-2 53-792 with clinical variant D511V
Components
  • Complex: human polycystin-2 53-792 with clinical variant D511V
    • Protein or peptide: Polycystin-2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: human polycystin-2 53-792 with clinical variant D511V

SupramoleculeName: human polycystin-2 53-792 with clinical variant D511V / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Over expressed in HEK293S cells and purified in detergent
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Polycystin-2

MacromoleculeName: Polycystin-2 / type: protein_or_peptide / ID: 1
Details: human polycystin-2 53-792 with clinical variant D511V
Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 85.433898 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GAMGSEIEMQ RIRQAAARDP PAGAAASPSP PLSSCSRQAW SRDNPGFEAE EEEEEVEGEE GGMVVEMDVE WRPGSRRSAA SSAVSSVGA RSRGLGGYHG AGHPSGRRRR REDQGPPCPS PVGGGDPLHR HLPLEGQPPR VAWAERLVRG LRGLWGTRLM E ESSTNREK ...String:
GAMGSEIEMQ RIRQAAARDP PAGAAASPSP PLSSCSRQAW SRDNPGFEAE EEEEEVEGEE GGMVVEMDVE WRPGSRRSAA SSAVSSVGA RSRGLGGYHG AGHPSGRRRR REDQGPPCPS PVGGGDPLHR HLPLEGQPPR VAWAERLVRG LRGLWGTRLM E ESSTNREK YLKSVLRELV TYLLFLIVLC ILTYGMMSSN VYYYTRMMSQ LFLDTPVSKT EKTNFKTLSS MEDFWKFTEG SL LDGLYWK MQPSNQTEAD NRSFIFYENL LLGVPRIRQL RVRNGSCSIP QDLRDEIKEC YDVYSVSSED RAPFGPRNGT AWI YTSEKD LNGSSHWGII ATYSGAGYYL DLSRTREETA AQVASLKKNV WLDRGTRATF IDFSVYNANI NLFCVVRLLV EFPA TGGVI PSWQFQPLKL IRYVTTFDFF LAACEIIFCF FIFYYVVEEI LEIRIHKLHY FRSFWNCLVV VIVVLSVVAI GINIY RTSN VEVLLQFLED QNTFPNFEHL AYWQIQFNNI AAVTVFFVWI KLFKFINFNR TMSQLSTTMS RCAKDLFGFA IMFFII FLA YAQLAYLVFG TQVDDFSTFQ ECIFTQFRII LGDINFAEIE EANRVLGPIY FTTFVFFMFF ILLNMFLAII NDTYSEV KS DLAQQKAEME LSDLIRKGYH KALVKLKLKK NTVDDISESL RQGGGKLNFD ELRQDLKGKG HTDAEIEAIF TKYDQDGD Q ELTEHEHQQM RDDLEKERED LDLD

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

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 59.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 54727
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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