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- PDB-6hrb: Cryo-EM structure of the KdpFABC complex in an E2 inward-facing s... -

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Basic information

Entry
Database: PDB / ID: 6hrb
TitleCryo-EM structure of the KdpFABC complex in an E2 inward-facing state (state 2)
Components
  • Potassium-transporting ATPase ATP-binding subunit
  • Potassium-transporting ATPase KdpC subunit
  • Potassium-transporting ATPase KdpF subunit
  • Potassium-transporting ATPase potassium-binding subunit
KeywordsMEMBRANE PROTEIN / P-type ATPase superfamily of K+ transporters (SKT) potassium uptake system four subunit complex
Function / homologyhaloacid dehalogenase-like hydrolase / Potassium-transporting ATPase A chain / E1-E2 ATPase / E1-E2 ATPases phosphorylation site. / F subunit of K+-transporting ATPase (Potass_KdpF) / Potassium-transporting ATPase A subunit / K+-transporting ATPase, c chain / HAD-like superfamily / P-type ATPase, cytoplasmic domain N / P-type ATPase, transmembrane domain superfamily ...haloacid dehalogenase-like hydrolase / Potassium-transporting ATPase A chain / E1-E2 ATPase / E1-E2 ATPases phosphorylation site. / F subunit of K+-transporting ATPase (Potass_KdpF) / Potassium-transporting ATPase A subunit / K+-transporting ATPase, c chain / HAD-like superfamily / P-type ATPase, cytoplasmic domain N / P-type ATPase, transmembrane domain superfamily / HAD superfamily / P-type ATPase, phosphorylation site / K+ transporting P-type ATPase, F subunit / P-type ATPase, B chain, subfamily IA / P-type ATPase, A domain superfamily / Potassium-transporting ATPase C chain / P-type ATPase / potassium ion-transporting ATPase complex / potassium-transporting ATPase activity / P-type K+ transporter / ATP hydrolysis coupled cation transmembrane transport / regulation of ATPase activity / potassium ion transmembrane transport / potassium ion binding / potassium ion transport / integral component of plasma membrane / magnesium ion binding / integral component of membrane / ATP binding / plasma membrane / Potassium-transporting ATPase potassium-binding subunit / Potassium-transporting ATPase ATP-binding subunit / Potassium-transporting ATPase KdpC subunit / Potassium-transporting ATPase KdpF subunit
Function and homology information
Specimen sourceEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4 Å resolution
AuthorsStock, C. / Hielkema, L. / Tascon, I. / Wunnicke, D. / Oostergetel, G.T. / Azkargorta, M. / Paulino, C. / Haenelt, I.
CitationJournal: Nat Commun / Year: 2018
Title: Cryo-EM structures of KdpFABC suggest a K transport mechanism via two inter-subunit half-channels.
Authors: C Stock / L Hielkema / I Tascón / D Wunnicke / G T Oostergetel / M Azkargorta / C Paulino / I Hänelt
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 26, 2018 / Release: Dec 5, 2018

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Structure visualization

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Assembly

Deposited unit
A: Potassium-transporting ATPase potassium-binding subunit
B: Potassium-transporting ATPase ATP-binding subunit
C: Potassium-transporting ATPase KdpC subunit
D: Potassium-transporting ATPase KdpF subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,9585
Polyers154,9194
Non-polymers391
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA

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Components

#1: Protein/peptide Potassium-transporting ATPase potassium-binding subunit / ATP phosphohydrolase [potassium-transporting] A chain / Potassium-binding and translocating subunit A / Potassium-translocating ATPase A chain


Mass: 59218.613 Da / Num. of mol.: 1
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: kdpA, b0698, JW0686 / Production host: Escherichia coli (E. coli) / References: UniProt: P03959
#2: Protein/peptide Potassium-transporting ATPase ATP-binding subunit / ATP phosphohydrolase [potassium-transporting] B chain / Potassium-binding and translocating subunit B / Potassium-translocating ATPase B chain


Mass: 72347.844 Da / Num. of mol.: 1
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: kdpB, b0697, JW0685 / Production host: Escherichia coli (E. coli) / References: UniProt: P03960, EC: 3.6.3.12
#3: Protein/peptide Potassium-transporting ATPase KdpC subunit / ATP phosphohydrolase [potassium-transporting] C chain / Potassium-binding and translocating subunit C / Potassium-translocating ATPase C chain


Mass: 20281.035 Da / Num. of mol.: 1
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: kdpC, b0696, JW0684 / Production host: Escherichia coli (E. coli) / References: UniProt: P03961
#4: Protein/peptide Potassium-transporting ATPase KdpF subunit / ATP phosphohydrolase [potassium-transporting] F chain / Potassium-binding and translocating subunit F / Potassium-translocating ATPase F chain


Mass: 3071.714 Da / Num. of mol.: 1
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: kdpF, b4513, JW0687 / Production host: Escherichia coli (E. coli) / References: UniProt: P36937
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Formula: K / Potassium

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: KdpFABC / Type: COMPLEX / Entity ID: 1, 2, 3, 4 / Source: RECOMBINANT
Molecular weightValue: 0.157 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionDetails: 10 mM Tris-HCl pH 8, 10 mM MgCl2, 10 mM NaCl and 0.012% DDM
pH: 8
SpecimenConc.: 3.1 / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: at 5 mA / Grid material: GOLD / Grid mesh size: 300 / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 49407 / Calibrated magnification: 49407 / Nominal defocus max: 3000 / Nominal defocus min: 300 / Calibrated defocus min: 300 / Calibrated defocus max: 3000 / Cs: 2.7 / C2 aperture diameter: 100 / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 105 / Temperature (min): 90
Image recordingAverage exposure time: 9 / Electron dose: 52 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 9 / Number of real images: 7327
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20
Image scansWidth: 3838 / Height: 3710 / Movie frames/image: 60 / Used frames/image: 1-60

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM software
IDNameVersionCategory
2EPU1.9.1image acquisition
4CTFFIND4.1.8CTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10RELION2.1binitial Euler assignment
11RELION2.1bfinal Euler assignment
13RELION2.1b3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 826403
SymmetryPoint symmetry: C1
3D reconstructionResolution: 4 / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 104786 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingRef space: REAL
Atomic model buildingPDB-ID: 5MRW
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00810986
ELECTRON MICROSCOPYf_angle_d0.95014954
ELECTRON MICROSCOPYf_dihedral_angle_d6.7586533
ELECTRON MICROSCOPYf_chiral_restr0.0541803
ELECTRON MICROSCOPYf_plane_restr0.0071898

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