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- EMDB-8912: Human Polycsytin 2-l1 -

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Basic information

Entry
Database: EMDB / ID: EMD-8912
TitleHuman Polycsytin 2-l1
Map dataHuman Polycsytin 2-l1, primary map
Sample
  • Organelle or cellular component: Human polycystic 2-l
    • Protein or peptide: Polycystic kidney disease 2-like 1 protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


sour taste receptor activity / detection of chemical stimulus involved in sensory perception of sour taste / detection of chemical stimulus involved in sensory perception of taste / sensory perception of sour taste / response to water / calcium-activated potassium channel activity / detection of mechanical stimulus / muscle alpha-actinin binding / cellular response to acidic pH / calcium-activated cation channel activity ...sour taste receptor activity / detection of chemical stimulus involved in sensory perception of sour taste / detection of chemical stimulus involved in sensory perception of taste / sensory perception of sour taste / response to water / calcium-activated potassium channel activity / detection of mechanical stimulus / muscle alpha-actinin binding / cellular response to acidic pH / calcium-activated cation channel activity / sodium channel activity / non-motile cilium / inorganic cation transmembrane transport / ciliary membrane / smoothened signaling pathway / alpha-actinin binding / monoatomic cation transport / sodium ion transmembrane transport / monoatomic cation channel activity / potassium ion transmembrane transport / calcium channel complex / cytoskeletal protein binding / calcium channel activity / actin cytoskeleton / cytoplasmic vesicle / protein homotetramerization / transmembrane transporter binding / receptor complex / intracellular membrane-bounded organelle / calcium ion binding / cell surface / endoplasmic reticulum / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Ferredoxin I 4Fe-4S cluster domain / Polycystin domain / Polycystin domain / Polycystic kidney disease type 2 protein / Polycystin cation channel, PKD1/PKD2 / Polycystin cation channel / Voltage-dependent channel domain superfamily
Similarity search - Domain/homology
Polycystin-2-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsHulse RE / Clapham DE / Li Z / Huang RK / Zhang J
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Elife / Year: 2018
Title: Cryo-EM structure of the polycystin 2-l1 ion channel.
Authors: Raymond E Hulse / Zongli Li / Rick K Huang / Jin Zhang / David E Clapham /
Abstract: We report the near atomic resolution (3.3 Å) of the human polycystic kidney disease 2-like 1 (polycystin 2-l1) ion channel. Encoded by PKD2L1, polycystin 2-l1 is a calcium and monovalent cation- ...We report the near atomic resolution (3.3 Å) of the human polycystic kidney disease 2-like 1 (polycystin 2-l1) ion channel. Encoded by PKD2L1, polycystin 2-l1 is a calcium and monovalent cation-permeant ion channel in primary cilia and plasma membranes. The related primary cilium-specific polycystin-2 protein, encoded by PKD2, shares a high degree of sequence similarity, yet has distinct permeability characteristics. Here we show that these differences are reflected in the architecture of polycystin 2-l1.
History
DepositionJun 20, 2018-
Header (metadata) releaseJul 4, 2018-
Map releaseJul 25, 2018-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.11
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.11
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6du8
  • Surface level: 0.11
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8912.png

Downloads & links

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Map

FileDownload / File: emd_8912.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman Polycsytin 2-l1, primary map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14 / Movie #1: 0.11
Minimum - Maximum-0.3621503 - 0.48114175
Average (Standard dev.)0.00011901388 (±0.029999765)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z266.240266.240266.240
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.3620.4810.000

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Supplemental data

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Mask #1

Fileemd_8912_msk_1.map
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 polycystic 2-l

EntireName: Human polycystic 2-l
Components
  • Organelle or cellular component: Human polycystic 2-l
    • Protein or peptide: Polycystic kidney disease 2-like 1 protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Human polycystic 2-l

SupramoleculeName: Human polycystic 2-l / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Homotetrameric assembly of polycystic 2-l1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 547 KDa
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant plasmid: pEG

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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: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 92.070633 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MNAVGSPEGQ ELQKLGSGAW DNPAYSGPPS PHGTLRVCTI SSTGPLQPQP KKPEDEPQET AYRTQVSSCC LHICQGIRGL WGTTLTENT AENRELYIKT TLRELLVYIV FLVDICLLTY GMTSSSAYYY TKVMSELFLH TPSDTGVSFQ AISSMADFWD F AQGPLLDS ...String:
MNAVGSPEGQ ELQKLGSGAW DNPAYSGPPS PHGTLRVCTI SSTGPLQPQP KKPEDEPQET AYRTQVSSCC LHICQGIRGL WGTTLTENT AENRELYIKT TLRELLVYIV FLVDICLLTY GMTSSSAYYY TKVMSELFLH TPSDTGVSFQ AISSMADFWD F AQGPLLDS LYWTKWYNNQ SLGHGSHSFI YYENMLLGVP RLRQLKVRND SCVVHEDFRE DILSCYDVYS PDKEEQLPFG PF NGTAWTY HSQDELGGFS HWGRLTSYSG GGYYLDLPGS RQGSAEALRA LQEGLWLDRG TRVVFIDFSV YNANINLFCV LRL VVEFPA TGGAIPSWQI RTVKLIRYVS NWDFFIVGCE VIFCVFIFYY VVEEILELHI HRLRYLSSIW NILDLVVILL SIVA VGFHI FRTLEVNRLM GKLLQQPNTY ADFEFLAFWQ TQYNNMNAVN LFFAWIKIFK YISFNKTMTQ LSSTLARCAK DILGF AVMF FIVFFAYAQL GYLLFGTQVE NFSTFIKCIF TQFRIILGDF DYNAIDNANR ILGPAYFVTY VFFVFFVLLN MFLAII NDT YSEVKEELAG QKDELQLSDL LKQGYNKTLL RLRLRKERVS DVQKVLQGGE QEIQFEDFTN TLRELGHAEH EITELTA TF TKFDRDGNRI LDEKEQEKMR QDLEEERVAL NTEIEKLGRS IVSSPQGKSG PEAARAGGWV SGEEFYMLTR RVLQLETV L EGVVSQIDAV GSKLKMLERK GWLAPSPGVK EQAIWKHPQP APAVTPDPWG VQGGQESEVP YKREEEALEE RRLSRGEIP TLQRS

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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: 4 / 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 state3D array

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Sample preparation

Concentration3.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMKCLPotassium Chloride
50.0 mMC8H18N2O4SHEPES
50.0 mMNaClSodium Chloride
1.0 mMCaCl2Calcium Chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: FORMVAR / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Detailspolycystic 2-l1 stabilized in amphipol PMAL-C8

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 8 / Applied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 119334
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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