[English] 日本語
![](img/lk-miru.gif)
- EMDB-24460: Cryo-EM structure of human rod CNGA1/B1 channel in cAMP-bound state -
+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-24460 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of human rod CNGA1/B1 channel in cAMP-bound state | ||||||||||||
![]() | |||||||||||||
![]() |
| ||||||||||||
![]() | ion channel / TRANSPORT PROTEIN | ||||||||||||
Function / homology | ![]() olfactory nerve maturation / non-motile cilium membrane / detection of chemical stimulus involved in sensory perception of smell / photoreceptor cell outer segment organization / protein localization to organelle / detection of light stimulus involved in visual perception / ion channel modulating, G protein-coupled receptor signaling pathway / response to odorant / VxPx cargo-targeting to cilium / rod photoreceptor outer segment ...olfactory nerve maturation / non-motile cilium membrane / detection of chemical stimulus involved in sensory perception of smell / photoreceptor cell outer segment organization / protein localization to organelle / detection of light stimulus involved in visual perception / ion channel modulating, G protein-coupled receptor signaling pathway / response to odorant / VxPx cargo-targeting to cilium / rod photoreceptor outer segment / intracellular cyclic nucleotide activated cation channel complex / intracellularly cGMP-activated cation channel activity / Golgi-associated vesicle membrane / intracellularly cAMP-activated cation channel activity / photoreceptor cell maintenance / retina homeostasis / sodium channel activity / ciliary membrane / photoreceptor outer segment membrane / sodium ion transport / monoatomic cation transmembrane transport / monoatomic cation transport / membrane depolarization / phototransduction / ligand-gated monoatomic ion channel activity / cGMP binding / photoreceptor outer segment / transmembrane transporter complex / cAMP binding / regulation of cytosolic calcium ion concentration / visual perception / potassium ion transport / Olfactory Signaling Pathway / Activation of the phototransduction cascade / calcium channel activity / terminal bouton / calcium ion transport / Inactivation, recovery and regulation of the phototransduction cascade / sensory perception of smell / positive regulation of gene expression / protein-containing complex binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.88 Å | ||||||||||||
![]() | Xue J / Han Y | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() Title: Structural mechanisms of assembly, permeation, gating, and pharmacology of native human rod CNG channel. Authors: Jing Xue / Yan Han / Weizhong Zeng / Youxing Jiang / ![]() Abstract: Mammalian cyclic nucleotide-gated (CNG) channels are nonselective cation channels activated by cGMP or cAMP and play essential roles in the signal transduction of the visual and olfactory sensory ...Mammalian cyclic nucleotide-gated (CNG) channels are nonselective cation channels activated by cGMP or cAMP and play essential roles in the signal transduction of the visual and olfactory sensory systems. CNGA1, the principal component of the CNG channel from rod photoreceptors, can by itself form a functional homotetrameric channel and has been used as the model system in the majority of rod CNG studies. However, the native rod CNG functions as a heterotetramer consisting of three A1 and one B1 subunits and exhibits different functional properties than the CNGA1 homomer. Here we present the functional analysis of human rod CNGA1/B1 heterotetramer and its cryo-EM structures in apo, cGMP-bound, cAMP-bound, and L-cis-Diltiazem-blocked states. These structures, with resolution ranging from 2.6 to 3.3 Å, elucidate the structural mechanisms underlying the 3:1 subunit stoichiometry, the asymmetrical gating upon cGMP activation, and the unique pharmacological property of the native rod CNG channel. | ||||||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 85.1 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 13.1 KB 13.1 KB | Display Display | ![]() |
Images | ![]() | 185 KB | ||
Filedesc metadata | ![]() | 5.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 625.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 625.5 KB | Display | |
Data in XML | ![]() | 6.3 KB | Display | |
Data in CIF | ![]() | 7.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7rhgMC ![]() 7rh9C ![]() 7rhhC ![]() 7rhiC ![]() 7rhjC ![]() 7rhkC ![]() 7rhlC C: citing same article ( M: atomic model generated by this map |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 0.841 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
-Entire : human rod CNGA1/B1 channel in cAMP-bound state
Entire | Name: human rod CNGA1/B1 channel in cAMP-bound state |
---|---|
Components |
|
-Supramolecule #1: human rod CNGA1/B1 channel in cAMP-bound state
Supramolecule | Name: human rod CNGA1/B1 channel in cAMP-bound state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
---|---|
Source (natural) | Organism: ![]() |
-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: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 64.650434 KDa |
Recombinant expression | Organism: ![]() |
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 nucleotide-gated cation channel beta-1
Macromolecule | Name: Cyclic nucleotide-gated cation channel beta-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 91.039305 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MDYKDDDDKG GSASSGVPAT KQHPEVQVED TDADSCPLMA EENPPSTVLP PPSPAKSDTL IVPSSASGTH RKKLPSEDDE AEELKALSP AESPVVAWSD PTTPKDTDGQ DRAASTASTN SAIINDRLQE LVKLFKERTE KVKEKLIDPD VTSDEESPKP S PAKKAPEP ...String: MDYKDDDDKG GSASSGVPAT KQHPEVQVED TDADSCPLMA EENPPSTVLP PPSPAKSDTL IVPSSASGTH RKKLPSEDDE AEELKALSP AESPVVAWSD PTTPKDTDGQ DRAASTASTN SAIINDRLQE LVKLFKERTE KVKEKLIDPD VTSDEESPKP S PAKKAPEP APDTKPAEAE PVEEEHYCDM LCCKFKHRPW KKYQFPQSID PLTNLMYVLW LFFVVMAWNW NCWLIPVRWA FP YQTPDNI HHWLLMDYLC DLIYFLDITV FQTRLQFVRG GDIITDKKDM RNNYLKSRRF KMDLLSLLPL DFLYLKVGVN PLL RLPRCL KYMAFFEFNS RLESILSKAY VYRVIRTTAY LLYSLHLNSC LYYWASAYQG LGSTHWVYDG VGNSYIRCYY FAVK TLITI GGLPDPKTLF EIVFQLLNYF TGVFAFSVMI GQMRDVVGAA TAGQTYYRSC MDSTVKYMNF YKIPKSVQNR VKTWY EYTW HSQGMLDESE LMVQLPDKMR LDLAIDVNYN IVSKVALFQG CDRQMIFDML KRLRSVVYLP NDYVCKKGEI GREMYI IQA GQVQVLGGPD GKSVLVTLKA GSVFGEISLL AVGGGNRRTA NVVAHGFTNL FILDKKDLNE ILVHYPESQK LLRKKAR RM LRSNNKPKEE KSVLILPPRA GTPKLFNAAL AMTGKMGGKG AKGGKLAHLR ARLKELAALE AAAKQQELVE QAKSSQDV K GEEGSAAPDQ HTHPKEAATD PPAPRTPPEP PGSPPSSPPP ASLGRPEGEE EGPAEPEEHS VRICMSPGPE PGEQILSVK MPEEREEKAE UniProtKB: Cyclic nucleotide-gated channel beta-1 |
-Macromolecule #3: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
Macromolecule | Name: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: CMP |
---|---|
Molecular weight | Theoretical: 329.206 Da |
Chemical component information | ![]() ChemComp-CMP: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 7.4 |
---|---|
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
-
Image processing
Startup model | Type of model: EMDB MAP |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 326371 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: RANDOM ASSIGNMENT |