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Yorodumi- EMDB-33467: Cryo-EM structure of the AKT1-AtKC1 complex from Arabidopsis thaliana -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33467 | |||||||||
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Title | Cryo-EM structure of the AKT1-AtKC1 complex from Arabidopsis thaliana | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Complex / Potassium channel / Membrane protein | |||||||||
Function / homology | Function and homology information root hair elongation / regulation of stomatal closure / response to nematode / response to water deprivation / inward rectifier potassium channel activity / monoatomic ion channel complex / voltage-gated potassium channel activity / potassium ion import across plasma membrane / potassium ion transmembrane transport / response to salt stress ...root hair elongation / regulation of stomatal closure / response to nematode / response to water deprivation / inward rectifier potassium channel activity / monoatomic ion channel complex / voltage-gated potassium channel activity / potassium ion import across plasma membrane / potassium ion transmembrane transport / response to salt stress / potassium ion transport / endoplasmic reticulum / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Yang GH / Lu YM / Jia YT / Yang F / Zhang YM / Xu X / Li XM / Lei JL | |||||||||
Funding support | 1 items
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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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33467.map.gz | 78.6 MB | EMDB map data format | |
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Header (meta data) | emd-33467-v30.xml emd-33467.xml | 15.9 KB 15.9 KB | Display Display | EMDB header |
Images | emd_33467.png | 70.1 KB | ||
Filedesc metadata | emd-33467.cif.gz | 6 KB | ||
Others | emd_33467_half_map_1.map.gz emd_33467_half_map_2.map.gz | 77.5 MB 77.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33467 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33467 | HTTPS FTP |
-Related structure data
Related structure data | 7xufMC 7fcvC 7wswC 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_33467.map.gz / Format: CCP4 / Size: 83.7 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: 0.86 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_33467_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33467_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Arabidopsis thaliana AKT1-AtKC1 complex
Entire | Name: Arabidopsis thaliana AKT1-AtKC1 complex |
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Components |
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-Supramolecule #1: Arabidopsis thaliana AKT1-AtKC1 complex
Supramolecule | Name: Arabidopsis thaliana AKT1-AtKC1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
-Macromolecule #1: Potassium channel KAT3
Macromolecule | Name: Potassium channel KAT3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Molecular weight | Theoretical: 75.688023 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MSTTTTEARS PLPLLLRRGR SSTALSASTA EARSPLSILQ FRRRSSKDVR NITSVSSSLL PAFGTFIEDD NPSSKPFIVL HFDRRYRLW ELFLVILVGY SAWASLFELA FEKAAEGALL TIDLVVDFFF AVDIILTFFV SYLDNTTYLN VTDHKLIAKR Y LKSVAFVM ...String: MSTTTTEARS PLPLLLRRGR SSTALSASTA EARSPLSILQ FRRRSSKDVR NITSVSSSLL PAFGTFIEDD NPSSKPFIVL HFDRRYRLW ELFLVILVGY SAWASLFELA FEKAAEGALL TIDLVVDFFF AVDIILTFFV SYLDNTTYLN VTDHKLIAKR Y LKSVAFVM DVASTLPIQF IYKTITGDVG RGQAFGFLNL LRLWRLRRVA ELFKRLEKDA HFNYFVIRVI KLLCVTIFWI HL AGCILYW IAYHYPRPTD TWIGSQVEDF KERSVWLGYT YSMYWSIVTL TTVGYGDLHA VNSREKTFNM FYMLFNIGLT SYI IGIMTN LVVHGALRTF AMRSAINDIL RYTSKNRLPD TMREQMLAHM QLKFKTAELR QEEVLQDLPK AIRSSINQHL FRSI IEEAY LFKGFPEGLL VQLVSQIQAE YFPPKMEIIL QNEIPTDFYV IVSGGVDIIA SKGVSEQVLA KLGPGSMAGE IGVVF NIPQ PFTVRTRRLS QVIRIGHHKF KEMVQSDNDV DAKMIIANFM TYLKGLNDEL KKEIPFLRDL LDDADAQVQE TVQSEE TPQ SNDEEIVTVS RHENGQIEER RREGVPKRVI IHGQAPPNQD NKNNGDSNGR LIILPDSIQL LFDLAEKKLG KRGSTIA MA DGAHVEQIDA LRENDHLYIF UniProtKB: Potassium channel KAT3 |
-Macromolecule #2: Potassium channel AKT1
Macromolecule | Name: Potassium channel AKT1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Molecular weight | Theoretical: 97.109625 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MRGGALLCGQ VQDEIEQLSR ESSHFSLSTG ILPSLGARSN RRVKLRRFVV SPYDHKYRIW EAFLVVLVVY TAWVSPFEFG FLRKPRPPL SITDNIVNAF FAIDIIMTFF VGYLDKSTYL IVDDRKQIAF KYLRSWFLLD LVSTIPSEAA MRISSQSYGL F NMLRLWRL ...String: MRGGALLCGQ VQDEIEQLSR ESSHFSLSTG ILPSLGARSN RRVKLRRFVV SPYDHKYRIW EAFLVVLVVY TAWVSPFEFG FLRKPRPPL SITDNIVNAF FAIDIIMTFF VGYLDKSTYL IVDDRKQIAF KYLRSWFLLD LVSTIPSEAA MRISSQSYGL F NMLRLWRL RRVGALFARL EKDRNFNYFW VRCAKLVCVT LFAVHCAACF YYLIAARNSN PAKTWIGANV ANFLEESLWM RY VTSMYWS ITTLTTVGYG DLHPVNTKEM IFDIFYMLFN LGLTAYLIGN MTNLVVHGTS RTRNFRDTIQ AASNFAHRNH LPP RLQDQM LAHLCLKYRT DSEGLQQQET LDALPKAIRS SISHFLFYSL MDKVYLFRGV SNDLLFQLVS EMKAEYFPPK EDVI LQNEA PTDFYILVNG TADLVDVDTG TESIVREVKA GDIIGEIGVL CYRPQLFTVR TKRLCQLLRM NRTTFLNIIQ ANVGD GTII MNNLLQHLKE MNDPVMTNVL LEIENMLARG KMDLPLNLCF AAIREDDLLL HQLLKRGLDP NESDNNGRTP LHIAAS KGT LNCVLLLLEY HADPNCRDAE GSVPLWEAMV EGHEKVVKVL LEHGSTIDAG DVGHFACTAA EQGNLKLLKE IVLHGGD VT RPRATGTSAL HTAVCEENIE MVKYLLEQGA DVNKQDMHGW TPRDLAEQQG HEDIKALFRE KLHERRVHIE TSSSVPIL K TGIRFLGRFT SEPNIRPASR EVSFRIRETR ARRKTNNFDN SLFGILANQS VPKNGLATVD EGRTGNPVRV TISCAEKDD IAGKLVLLPG SFKELLELGS NKFGIVATKV MNKDNNAEID DVDVIRDGDH LIFATDS UniProtKB: Potassium channel AKT1 |
-Macromolecule #3: POTASSIUM ION
Macromolecule | Name: POTASSIUM ION / type: ligand / ID: 3 / Number of copies: 3 / Formula: K |
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Molecular weight | Theoretical: 39.098 Da |
-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 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 1.5959 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
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 104142 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |