[English] 日本語
Yorodumi- EMDB-32769: Cryo-EM structure of the Potassium channel AKT1 from Arabidopsis ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32769 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the Potassium channel AKT1 from Arabidopsis thaliana | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Function / homology | Function and homology information root hair elongation / regulation of stomatal closure / response to water deprivation / inward rectifier potassium channel activity / monoatomic ion channel complex / potassium ion import across plasma membrane / response to salt stress / potassium ion transport / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Yang GH / Lu YM / Zhang YM / Jia YT / Li XM / Lei JL | |||||||||
Funding support | 1 items
| |||||||||
Citation | Journal: Nat Commun / Year: 2022 Title: Structural basis for the activity regulation of a potassium channel AKT1 from Arabidopsis. Authors: Yaming Lu / Miao Yu / Yutian Jia / Fan Yang / Yanming Zhang / Xia Xu / Xiaomin Li / Fan Yang / Jianlin Lei / Yi Wang / Guanghui Yang / Abstract: The voltage-gated potassium channel AKT1 is responsible for primary K uptake in Arabidopsis roots. AKT1 is functionally activated through phosphorylation and negatively regulated by a potassium ...The voltage-gated potassium channel AKT1 is responsible for primary K uptake in Arabidopsis roots. AKT1 is functionally activated through phosphorylation and negatively regulated by a potassium channel α-subunit AtKC1. However, the molecular basis for the modulation mechanism remains unclear. Here we report the structures of AKT1, phosphorylated-AKT1, a constitutively-active variant, and AKT1-AtKC1 complex. AKT1 is assembled in 2-fold symmetry at the cytoplasmic domain. Such organization appears to sterically hinder the reorientation of C-linkers during ion permeation. Phosphorylated-AKT1 adopts an alternate 4-fold symmetric conformation at cytoplasmic domain, which indicates conformational changes associated with symmetry switch during channel activation. To corroborate this finding, we perform structure-guided mutagenesis to disrupt the dimeric interface and identify a constitutively-active variant Asp379Ala mediates K permeation independently of phosphorylation. This variant predominantly adopts a 4-fold symmetric conformation. Furthermore, the AKT1-AtKC1 complex assembles in 2-fold symmetry. Together, our work reveals structural insight into the regulatory mechanism for AKT1. | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_32769.map.gz | 113.8 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-32769-v30.xml emd-32769.xml | 11 KB 11 KB | Display Display | EMDB header |
Images | emd_32769.png | 49.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32769 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32769 | HTTPS FTP |
-Validation report
Summary document | emd_32769_validation.pdf.gz | 432.8 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_32769_full_validation.pdf.gz | 432.4 KB | Display | |
Data in XML | emd_32769_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | emd_32769_validation.cif.gz | 7.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32769 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32769 | HTTPS FTP |
-Related structure data
Related structure data | 7wswMC 7fcvC 7xufC 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_32769.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.0825 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Sample components
-Entire : The Potassium channel AKT1 from Arabidopsis thaliana
Entire | Name: The Potassium channel AKT1 from Arabidopsis thaliana |
---|---|
Components |
|
-Supramolecule #1: The Potassium channel AKT1 from Arabidopsis thaliana
Supramolecule | Name: The Potassium channel AKT1 from Arabidopsis thaliana / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
-Macromolecule #1: Potassium channel AKT1
Macromolecule | Name: Potassium channel AKT1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Molecular weight | Theoretical: 99.413938 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MASDYKDDDD KASDEVDAGT ATMRGGALLC GQVQDEIEQL SRESSHFSLS TGILPSLGAR SNRRVKLRRF VVSPYDHKYR IWEAFLVVL VVYTAWVSPF EFGFLRKPRP PLSITDNIVN AFFAIDIIMT FFVGYLDKST YLIVDDRKQI AFKYLRSWFL L DLVSTIPS ...String: MASDYKDDDD KASDEVDAGT ATMRGGALLC GQVQDEIEQL SRESSHFSLS TGILPSLGAR SNRRVKLRRF VVSPYDHKYR IWEAFLVVL VVYTAWVSPF EFGFLRKPRP PLSITDNIVN AFFAIDIIMT FFVGYLDKST YLIVDDRKQI AFKYLRSWFL L DLVSTIPS EAAMRISSQS YGLFNMLRLW RLRRVGALFA RLEKDRNFNY FWVRCAKLVC VTLFAVHCAA CFYYLIAARN SN PAKTWIG ANVANFLEES LWMRYVTSMY WSITTLTTVG YGDLHPVNTK EMIFDIFYML FNLGLTAYLI GNMTNLVVHG TSR TRNFRD TIQAASNFAH RNHLPPRLQD QMLAHLCLKY RTDSEGLQQQ ETLDALPKAI RSSISHFLFY SLMDKVYLFR GVSN DLLFQ LVSEMKAEYF PPKEDVILQN EAPTDFYILV NGTADLVDVD TGTESIVREV KAGDIIGEIG VLCYRPQLFT VRTKR LCQL LRMNRTTFLN IIQANVGDGT IIMNNLLQHL KEMNDPVMTN VLLEIENMLA RGKMDLPLNL CFAAIREDDL LLHQLL KRG LDPNESDNNG RTPLHIAASK GTLNCVLLLL EYHADPNCRD AEGSVPLWEA MVEGHEKVVK VLLEHGSTID AGDVGHF AC TAAEQGNLKL LKEIVLHGGD VTRPRATGTS ALHTAVCEEN IEMVKYLLEQ GADVNKQDMH GWTPRDLAEQ QGHEDIKA L FREKLHERRV HIETSSSVPI LKTGIRFLGR FTSEPNIRPA SREVSFRIRE TRARRKTNNF DNSLFGILAN QSVPKNGLA TVDEGRTGNP VRVTISCAEK DDIAGKLVLL PGSFKELLEL GSNKFGIVAT KVMNKDNNAE IDDVDVIRDG DHLIFATDS |
-Macromolecule #2: PHOSPHATIDYLETHANOLAMINE
Macromolecule | Name: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 2 / Number of copies: 4 / Formula: PTY |
---|---|
Molecular weight | Theoretical: 734.039 Da |
Chemical component information | ChemComp-PTY: |
-Macromolecule #3: POTASSIUM ION
Macromolecule | Name: POTASSIUM ION / type: ligand / ID: 3 / Number of copies: 3 / Formula: K |
---|---|
Molecular weight | Theoretical: 39.098 Da |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.5625 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 181714 |
---|---|
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |