+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8912 | |||||||||
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Title | Human Polycsytin 2-l1 | |||||||||
Map data | Human Polycsytin 2-l1, primary map | |||||||||
Sample |
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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 / non-motile cilium / inorganic cation transmembrane transport / sodium channel activity / 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 / identical protein binding / membrane / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.11 Å | |||||||||
Authors | Hulse RE / Clapham DE / Li Z / Huang RK / Zhang J | |||||||||
Funding support | United States, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8912.map.gz | 59.5 MB | EMDB map data format | |
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Header (meta data) | emd-8912-v30.xml emd-8912.xml | 12.4 KB 12.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8912_fsc.xml | 10.7 KB | Display | FSC data file |
Images | emd_8912.png | 3.3 MB | ||
Masks | emd_8912_msk_1.map | 64 MB | Mask map | |
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8912 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8912 | HTTPS FTP |
-Validation report
Summary document | emd_8912_validation.pdf.gz | 592.3 KB | Display | EMDB validaton report |
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Full document | emd_8912_full_validation.pdf.gz | 591.9 KB | Display | |
Data in XML | emd_8912_validation.xml.gz | 11 KB | Display | |
Data in CIF | emd_8912_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8912 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8912 | HTTPS FTP |
-Related structure data
Related structure data | 6du8MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8912.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Human Polycsytin 2-l1, primary map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_8912_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human polycystic 2-l
Entire | Name: Human polycystic 2-l |
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Components |
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-Supramolecule #1: Human polycystic 2-l
Supramolecule | Name: Human polycystic 2-l / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Homotetrameric assembly of polycystic 2-l1 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 547 KDa |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant plasmid: pEG |
-Macromolecule #1: Polycystic kidney disease 2-like 1 protein
Macromolecule | Name: Polycystic kidney disease 2-like 1 protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 92.070633 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 4 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | 3D array |
-Sample preparation
Concentration | 3.5 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: FORMVAR / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV | |||||||||||||||
Details | polycystic 2-l1 stabilized in amphipol PMAL-C8 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |