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- EMDB-0258: Cryo-EM structure of the KdpFABC complex in an E2 inward-facing s... -

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Basic information

Entry
Database: EMDB / ID: 0258
TitleCryo-EM structure of the KdpFABC complex in an E2 inward-facing state (state 2)
Map data
SampleKdpFABC
  • (Potassium-transporting ATPase ...) x 4
  • ligand
Function / homologyP-type ATPase, B chain, subfamily IA / Potassium-transporting ATPase A chain / 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, B chain, subfamily IA / Potassium-transporting ATPase A chain / 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, A domain superfamily / P-type ATPase / Potassium-transporting ATPase C chain / K+-transporting ATPase / potassium ion-transporting ATPase complex / potassium-transporting ATPase activity / 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
SourceEscherichia coli K-12 (bacteria) / Escherichia coli (strain K12) (bacteria)
Methodsingle particle reconstruction / cryo EM / 4 Å resolution
AuthorsStock C / Hielkema L / Tascon I / Wunnicke D / Oostergetel GT / 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 ReportPDB-ID: 6hrb

SummaryFull reportAbout validation report
DateDeposition: Sep 26, 2018 / Header (metadata) release: Dec 5, 2018 / Map release: Dec 5, 2018 / Last update: Dec 5, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0595
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0595
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6hrb
  • Surface level: 0.0595
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_0258.map.gz (map file in CCP4 format, 55297 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
240 pix
1.01 Å/pix.
= 242.88 Å
240 pix
1.01 Å/pix.
= 242.88 Å
240 pix
1.01 Å/pix.
= 242.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.012 Å
Density
Contour Level:0.0595 (by author), 0.0595 (movie #1):
Minimum - Maximum-0.07844194 - 0.18261603
Average (Standard dev.)0.0012946029 (0.008314866)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions240240240
Origin0.00.00.0
Limit239.0239.0239.0
Spacing240240240
CellA=B=C: 242.87999 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0121.0121.012
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z242.880242.880242.880
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0780.1830.001

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Supplemental data

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Mask #1

Fileemd_0258_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire KdpFABC

EntireName: KdpFABC / Number of components: 6

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Component #1: protein, KdpFABC

ProteinName: KdpFABC / Recombinant expression: No
MassTheoretical: 157 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, Potassium-transporting ATPase potassium-binding subunit

ProteinName: Potassium-transporting ATPase potassium-binding subunit
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 59.218613 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, Potassium-transporting ATPase ATP-binding subunit

ProteinName: Potassium-transporting ATPase ATP-binding subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 72.347844 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: protein, Potassium-transporting ATPase KdpC subunit

ProteinName: Potassium-transporting ATPase KdpC subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.281035 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #5: protein, Potassium-transporting ATPase KdpF subunit

ProteinName: Potassium-transporting ATPase KdpF subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 3.071714 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #6: ligand, POTASSIUM ION

LigandName: POTASSIUM IONPotassium / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 3.909805 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 3.1 mg/ml
Buffer solution: 10 mM Tris-HCl pH 8, 10 mM MgCl2, 10 mM NaCl and 0.012% DDM
pH: 8
Support filmat 5 mA
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 293 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 52 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 49407.0 X (nominal), 49407.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 300.0 - 3000.0 nm / Energy filter: GIF Bioquantum
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: K ( 90.0 - 105.0 K)
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 7327

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 104786
3D reconstructionAlgorithm: BACK PROJECTION / Software: RELION / Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Refinement space: REAL
Input PDB model: 5MRW
Output model

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