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- PDB-7cal: Cryo-EM Structure of the Hyperpolarization-Activated Inwardly Rec... -

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Basic information

Entry
Database: PDB / ID: 7cal
TitleCryo-EM Structure of the Hyperpolarization-Activated Inwardly Rectifying Potassium Channel KAT1 from Arabidopsis
ComponentsPotassium channel KAT1
KeywordsMEMBRANE PROTEIN / Hyperpolarization-Activated Inwardly Rectifying Potassium Channel
Function / homology
Function and homology information


inward rectifier potassium channel activity / monoatomic ion channel complex / identical protein binding / plasma membrane
Similarity search - Function
Potassium channel KAT/AKT / KHA domain / KHA, dimerisation domain of potassium ion channel / KHA domain profile. / Potassium channel, voltage-dependent, EAG/ELK/ERG / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily ...Potassium channel KAT/AKT / KHA domain / KHA, dimerisation domain of potassium ion channel / KHA domain profile. / Potassium channel, voltage-dependent, EAG/ELK/ERG / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / Potassium channel KAT1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLi, S.Y. / Yang, F. / Sun, D.M. / Zhang, Y. / Zhang, M.G. / Zhou, P. / Liu, S.L. / Zhang, Y.N. / Zhang, L.H. / Tian, C.L.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31600601 China
National Natural Science Foundation of China (NSFC)21778051 China
National Natural Science Foundation of China (NSFC)21825703 China
CitationJournal: Cell Res / Year: 2020
Title: Cryo-EM structure of the hyperpolarization-activated inwardly rectifying potassium channel KAT1 from Arabidopsis.
Authors: Siyu Li / Fan Yang / Demeng Sun / Yong Zhang / Mengge Zhang / Sanling Liu / Peng Zhou / Chaowei Shi / Longhua Zhang / Changlin Tian /
History
DepositionJun 9, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 18, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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Assembly

Deposited unit
A: Potassium channel KAT1
B: Potassium channel KAT1
C: Potassium channel KAT1
D: Potassium channel KAT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)316,4388
Polymers313,4464
Non-polymers2,9924
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Potassium channel KAT1


Mass: 78361.445 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: KAT1, At5g46240, MPL12.2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q39128
#2: Chemical
ChemComp-3PE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / 3-SN-PHOSPHATIDYLETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C41H82NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: KAT1 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: DIFFRACTION
Image recordingElectron dose: 57.6 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.14_3260refinement
PHENIX1.14_3260refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 111658 / Symmetry type: POINT
RefinementStereochemistry target values: CDL v1.2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.007114480
ELECTRON MICROSCOPYf_angle_d1.001719724
ELECTRON MICROSCOPYf_chiral_restr0.06042224
ELECTRON MICROSCOPYf_plane_restr0.00712452
ELECTRON MICROSCOPYf_dihedral_angle_d7.03048344

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