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Yorodumi- EMDB-23309: Cryo-EM structure of human cGMP-bound open CNGA1 channel in Na+ -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23309 | |||||||||
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Title | Cryo-EM structure of human cGMP-bound open CNGA1 channel in Na+ | |||||||||
Map data | ||||||||||
Sample |
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Keywords | ALPHA-HELICAL / MEMBRANE PROTEIN / ION CHANNEL | |||||||||
Function / homology | Function and homology information intracellular cyclic nucleotide activated cation channel complex / intracellularly cGMP-activated cation channel activity / intracellularly cAMP-activated cation channel activity / rod photoreceptor outer segment / sodium channel activity / photoreceptor outer segment membrane / sodium ion transport / monoatomic cation transmembrane transport / cGMP binding / cAMP binding ...intracellular cyclic nucleotide activated cation channel complex / intracellularly cGMP-activated cation channel activity / intracellularly cAMP-activated cation channel activity / rod photoreceptor outer segment / sodium channel activity / photoreceptor outer segment membrane / sodium ion transport / monoatomic cation transmembrane transport / cGMP binding / cAMP binding / visual perception / calcium channel activity / Activation of the phototransduction cascade / calcium ion transport / Inactivation, recovery and regulation of the phototransduction cascade / protein-containing complex binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Xue J / Han Y | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Neuron / Year: 2021 Title: Structural mechanisms of gating and selectivity of human rod CNGA1 channel. Authors: Jing Xue / Yan Han / Weizhong Zeng / Yan Wang / Youxing Jiang / Abstract: Mammalian cyclic nucleotide-gated (CNG) channels play an essential role in the signal transduction of the visual and olfactory sensory systems. Here we reveal the structural mechanism of ligand ...Mammalian cyclic nucleotide-gated (CNG) channels play an essential role in the signal transduction of the visual and olfactory sensory systems. Here we reveal the structural mechanism of ligand gating in human rod CNGA1 channel by determining its cryo-EM structures in both the apo closed and cGMP-bound open states. Distinct from most other members of voltage-gated tetrameric cation channels, CNGA1 forms a central channel gate in the middle of the membrane, occluding the central cavity. Structural analyses of ion binding profiles in the selectivity filters of the wild-type channel and the E365Q filter mutant allow us to unambiguously define the two Ca binding sites inside the selectivity filter, providing structural insights into Ca blockage and permeation in CNG channels. The structure of the E365Q mutant also reveals two alternative side-chain conformations at Q365, providing a plausible explanation for the voltage-dependent gating of CNG channel acquired upon E365 mutation. | |||||||||
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_23309.map.gz | 85.1 MB | EMDB map data format | |
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Header (meta data) | emd-23309-v30.xml emd-23309.xml | 10.3 KB 10.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_23309_fsc.xml | 10.3 KB | Display | FSC data file |
Images | emd_23309.png | 169.6 KB | ||
Filedesc metadata | emd-23309.cif.gz | 5.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23309 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23309 | HTTPS FTP |
-Validation report
Summary document | emd_23309_validation.pdf.gz | 642.5 KB | Display | EMDB validaton report |
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Full document | emd_23309_full_validation.pdf.gz | 642.1 KB | Display | |
Data in XML | emd_23309_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | emd_23309_validation.cif.gz | 15.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23309 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23309 | HTTPS FTP |
-Related structure data
Related structure data | 7lfyMC 7lftC 7lfwC 7lfxC 7lg1C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_23309.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.829 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : cGMP-bound open CNGA1 homotetramer in Na+
Entire | Name: cGMP-bound open CNGA1 homotetramer in Na+ |
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Components |
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-Supramolecule #1: cGMP-bound open CNGA1 homotetramer in Na+
Supramolecule | Name: cGMP-bound open CNGA1 homotetramer in Na+ / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: cGMP-gated cation channel alpha-1
Macromolecule | Name: cGMP-gated cation channel alpha-1 / 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: 64.650434 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MDYKDDDDKG GSASKDKKEE EKKEVVVIDP SGNTYYNWLF CITLPVMYNW TMVIARACFD ELQSDYLEYW LILDYVSDIV YLIDMFVRT RTGYLEQGLL VKEELKLINK YKSNLQFKLD VLSLIPTDLL YFKLGWNYPE IRLNRLLRFS RMFEFFQRTE T RTNYPNIF ...String: MDYKDDDDKG GSASKDKKEE EKKEVVVIDP SGNTYYNWLF CITLPVMYNW TMVIARACFD ELQSDYLEYW LILDYVSDIV YLIDMFVRT RTGYLEQGLL VKEELKLINK YKSNLQFKLD VLSLIPTDLL YFKLGWNYPE IRLNRLLRFS RMFEFFQRTE T RTNYPNIF RISNLVMYIV IIIHWNACVF YSISKAIGFG NDTWVYPDIN DPEFGRLARK YVYSLYWSTL TLTTIGETPP PV RDSEYVF VVVDFLIGVL IFATIVGNIG SMISNMNAAR AEFQARIDAI KQYMHFRNVS KDMEKRVIKW FDYLWTNKKT VDE KEVLKY LPDKLRAEIA INVHLDTLKK VRIFADCEAG LLVELVLKLQ PQVYSPGDYI CKKGDIGREM YIIKEGKLAV VADD GVTQF VVLSDGSYFG EISILNIKGS KAGNRRTANI KSIGYSDLFC LSKDDLMEAL TEYPDAKTML EEKGKQILMK DGLLD LNIA NAGSDPKDLE EKVTRMEGSV DLLQTRFARI LAEYESMQQK LKQRLTKVEK FLKPLIDTEF SSIEGPGAES GPIDST UniProtKB: Cyclic nucleotide-gated channel alpha-1 |
-Macromolecule #2: CYCLIC GUANOSINE MONOPHOSPHATE
Macromolecule | Name: CYCLIC GUANOSINE MONOPHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: PCG |
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Molecular weight | Theoretical: 345.205 Da |
Chemical component information | ChemComp-PCG: |
-Macromolecule #3: SODIUM ION
Macromolecule | Name: SODIUM ION / type: ligand / ID: 3 / Number of copies: 3 |
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Molecular weight | Theoretical: 22.99 Da |
-Macromolecule #4: water
Macromolecule | Name: water / type: ligand / ID: 4 / Number of copies: 4 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |