[English] 日本語
Yorodumi- EMDB-39753: Activation mechanism and novel binding site of the BKCa channel a... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-39753 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Activation mechanism and novel binding site of the BKCa channel activator CTIBD | ||||||||||||
Map data | |||||||||||||
Sample |
| ||||||||||||
Keywords | BKca channel / Slo1 / CTIBD / MEMBRANE PROTEIN | ||||||||||||
Function / homology | Function and homology information Acetylcholine inhibits contraction of outer hair cells / micturition / Ca2+ activated K+ channels / response to carbon monoxide / large conductance calcium-activated potassium channel activity / calcium-activated potassium channel activity / negative regulation of cell volume / smooth muscle contraction involved in micturition / intracellular potassium ion homeostasis / Sensory processing of sound by inner hair cells of the cochlea ...Acetylcholine inhibits contraction of outer hair cells / micturition / Ca2+ activated K+ channels / response to carbon monoxide / large conductance calcium-activated potassium channel activity / calcium-activated potassium channel activity / negative regulation of cell volume / smooth muscle contraction involved in micturition / intracellular potassium ion homeostasis / Sensory processing of sound by inner hair cells of the cochlea / response to osmotic stress / cGMP effects / voltage-gated potassium channel activity / voltage-gated potassium channel complex / potassium ion transmembrane transport / caveola / regulation of membrane potential / potassium ion transport / response to calcium ion / vasodilation / actin binding / postsynaptic membrane / response to hypoxia / positive regulation of apoptotic process / apical plasma membrane / identical protein binding / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||||||||
Authors | Lee N / Kim S / Jo H / Lee NY / Jin MS / Park CS | ||||||||||||
Funding support | Korea, Republic Of, 3 items
| ||||||||||||
Citation | Journal: To Be Published Title: Activation mechanism and novel binding site of the BKCa channel activator CTIBD Authors: Lee N / Kim S / Jo H / Lee NY / Jeong P / Pagire HS / Pagire SH / Ahn JH / Jin MS / Park CS | ||||||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_39753.map.gz | 28.3 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-39753-v30.xml emd-39753.xml | 20.4 KB 20.4 KB | Display Display | EMDB header |
Images | emd_39753.png | 108.8 KB | ||
Filedesc metadata | emd-39753.cif.gz | 7.1 KB | ||
Others | emd_39753_half_map_1.map.gz emd_39753_half_map_2.map.gz | 27.9 MB 27.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-39753 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-39753 | HTTPS FTP |
-Validation report
Summary document | emd_39753_validation.pdf.gz | 823.9 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_39753_full_validation.pdf.gz | 823.5 KB | Display | |
Data in XML | emd_39753_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | emd_39753_validation.cif.gz | 12.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-39753 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-39753 | HTTPS FTP |
-Related structure data
Related structure data | 8z3sMC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_39753.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.41 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: #2
File | emd_39753_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_39753_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Calcium-activated potassium channel subunit alpha-1 (Slo1)
Entire | Name: Calcium-activated potassium channel subunit alpha-1 (Slo1) |
---|---|
Components |
|
-Supramolecule #1: Calcium-activated potassium channel subunit alpha-1 (Slo1)
Supramolecule | Name: Calcium-activated potassium channel subunit alpha-1 (Slo1) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 500 KDa |
-Macromolecule #1: Calcium-activated potassium channel subunit alpha-1
Macromolecule | Name: Calcium-activated potassium channel subunit alpha-1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 125.541461 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MDALIIPVTM EVPCDSRGQR MWWAFLASSM VTFFGGLFII LLWRTLKYLW TVCCHCGGKT KEAQKINNGS SQADGTLKPV DEKEEAVAA EVGWMTSVKD WAGVMISAQT LTGRVLVVLV FALSIGALVI YFIDSSNPIE SCQNFYKDFT LQIDMAFNVF F LLYFGLRF ...String: MDALIIPVTM EVPCDSRGQR MWWAFLASSM VTFFGGLFII LLWRTLKYLW TVCCHCGGKT KEAQKINNGS SQADGTLKPV DEKEEAVAA EVGWMTSVKD WAGVMISAQT LTGRVLVVLV FALSIGALVI YFIDSSNPIE SCQNFYKDFT LQIDMAFNVF F LLYFGLRF IAANDKLWFW LEVNSVVDFF TVPPVFVSVY LNRSWLGLRF LRALRLIQFS EILQFLNILK TSNSIKLVNL LS IFISTWL TAAGFIHLVE NSGDPWENFQ NNQALTYWEC VYLLMVTMST VGYGDVYAKT TLGRLFMVFF ILGGLAMFAS YVP EIIELI GNRKKYGGSY SAVSGRKHIV VCGHITLESV SNFLKDFLHK DRDDVNVEIV FLHNISPNLE LEALFKRHFT QVEF YQGSV LNPHDLARVK IESADACLIL ANKYCADPDA EDASNIMRVI SIKNYHPKIR IITQMLQYHN KAHLLNIPSW NWKEG DDAI CLAELKLGFI AQSCLAQGLS TMLANLFSMR SFIKIEEDTW QKYYLEGVSN EMYTEYLSSA FVGLSFPTVC ELCFVK LKL LMIAIEYKSA NRESRILINP GNHLKIQEGT LGFFIASDAK EVKRAFFYCK ACHDDITDPK RIKKCGCKRP KMSIYKR MR RACCFDCGRS ERDCSCMSGR VRGNVDTLER AFPLSSVSVN DCSTSFRAFE DEQPSTLSPK KKQRNGGMRN SPNTSPKL M RHDPLLIPGN DQIDNMDSNV KKYDSTGMFH WCAPKEIEKV ILTRSEAAMT VLSGHVVVCI FGDVSSALIG LRNLVMPLR ASNFHYHELK HIVFVGSIEY LKREWETLHN FPKVSILPGT PLSRADLRAV NINLCDMCVI LSANQNNIDD TSLQDKECIL ASLNIKSMQ FDDSIGVLQA NSQGFTPPGM DRSSPDNSPV HGMLRQPSIT TGVNIPIITE LVNDTNVQFL DQDDDDDPDT E LYLTQPFA CGTAFAVSVL DSLMSATYFN DNILTLIRTL VTGGATPELE ALIAEENALR GGYSTPQTLA NRDRCRVAQL AL LDGPFAD LGDGGCYGDL FCKALKTYNM LCFGIYRLRD AHLSTPSQCT KRYVITNPPY EFELVPTDLI FCLMQFD UniProtKB: Calcium-activated potassium channel subunit alpha-1 |
-Macromolecule #2: 4-[4-(4-chlorophenyl)-3-(trifluoromethyl)-1,2-oxazol-5-yl]benzene...
Macromolecule | Name: 4-[4-(4-chlorophenyl)-3-(trifluoromethyl)-1,2-oxazol-5-yl]benzene-1,3-diol type: ligand / ID: 2 / Number of copies: 8 / Formula: A1L04 |
---|---|
Molecular weight | Theoretical: 355.696 Da |
-Macromolecule #3: CHOLESTEROL HEMISUCCINATE
Macromolecule | Name: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: Y01 |
---|---|
Molecular weight | Theoretical: 486.726 Da |
Chemical component information | ChemComp-Y01: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: MG |
---|---|
Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #5: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 8 / Formula: CA |
---|---|
Molecular weight | Theoretical: 40.078 Da |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5.5 mg/mL | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 8 Component:
| ||||||||||||||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 4806 / Average exposure time: 13.67 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 73000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |