[English] 日本語
Yorodumi
- EMDB-1605: Solution structure of the KdpFABC P-type ATPase from Escherichia ... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 1605
TitleSolution structure of the KdpFABC P-type ATPase from Escherichia coli by electron microscopic single particle analysis
Map dataVolume of the KdpFABC P-type ATPase
SampleKdpFABC P-type ATPase
  • KdpA-subunit
  • KdpB-subunit
  • KdpC-subunit
  • KdpF-subunit
KeywordsKdpFABC / P-type ATPase / potassium transport / single particle analysis / electron microscopy.
SourceEscherichia coli / / bacteria /
Methodsingle particle reconstruction / negative staining / 19 Å resolution
AuthorsHeitkamp T / Bottcher B / Greie J-C
CitationJournal: J. Struct. Biol. / Year: 2009
Title: Solution structure of the KdpFABC P-type ATPase from Escherichia coli by electron microscopic single particle analysis.
Authors: Thomas Heitkamp / Bettina Böttcher / Jörg-Christian Greie
Abstract: The K+-translocating KdpFABC complex from Escherichia coli functions as a high affinity potassium uptake system and belongs to the superfamily of P-type ATPases, although it exhibits some unique ...The K+-translocating KdpFABC complex from Escherichia coli functions as a high affinity potassium uptake system and belongs to the superfamily of P-type ATPases, although it exhibits some unique features. It comprises four subunits, and the sites of ATP hydrolysis and substrate transport are located on two different polypeptides. No structural data are so far available for elucidating the correspondingly unique mechanism of coupling ion transport and catalysis in this P-type ATPase. By use of electron microscopy and single particle analysis of negatively stained, solubilized KdpFABC complexes, we solved the structure of the complex at a resolution of 19A, which allowed us to model the arrangement of subunits within the holoenzyme and, thus, to identify the interfaces between subunits. The model showed that the K+-translocating KdpA subunit is in close contact with the transmembrane region of the ATP-hydrolyzing subunit KdpB. The cytosolic C-terminal domain of the KdpC subunit, which is assumed to play a role in cooperative ATP binding together with KdpB, is located in close vicinity to the nucleotide binding domain of KdpB. Overall, the arrangement of subunits agrees with biochemical data and the predictions on subunit interactions.
DateDeposition: Mar 17, 2009 / Header (metadata) release: Apr 15, 2009 / Map release: Apr 24, 2009 / Last update: Oct 24, 2012

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 200
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 200
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_1605.map.gz (map file in CCP4 format, 1341 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
70 pix
2.8 Å/pix.
= 196. Å
70 pix
2.8 Å/pix.
= 196. Å
70 pix
2.8 Å/pix.
= 196. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.8 Å
Density
Contour Level:150 (by author), 200 (movie #1):
Minimum - Maximum-374.723 - 1448.24
Average (Standard dev.)15.9693 (95.5698)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions707070
Origin000
Limit696969
Spacing707070
CellA=B=C: 196 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.82.82.8
M x/y/z707070
origin x/y/z0.0000.0000.000
length x/y/z196.000196.000196.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-17-17-200
NX/NY/NZ123123401
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS707070
D min/max/mean-374.7231448.24115.969

-
Supplemental data

-
Sample components

-
Entire KdpFABC P-type ATPase

EntireName: KdpFABC P-type ATPase / Number of components: 1 / Oligomeric State: monomer
MassTheoretical: 154 kDa

-
Component #1: protein, KdpA-subunit

ProteinName: KdpA-subunit / a.k.a: KdpA-subunit / Oligomeric Details: monomer / Number of Copies: 1 / Recombinant expression: Yes
MassTheoretical: 59 kDa
SourceSpecies: Escherichia coli / / bacteria /
Source (engineered)Expression System: Escherichia coli / / bacteria / / Vector: pGS4
Source (natural)Location in cell: membrane

-
Component #2: protein, KdpB-subunit

ProteinName: KdpB-subunit / a.k.a: KdpB-subunit / Oligomeric Details: monomer / Recombinant expression: Yes / Number of Copies: 1
MassTheoretical: 72 kDa
SourceSpecies: Escherichia coli / / bacteria /
Source (engineered)Expression System: Escherichia coli / / bacteria / / Vector: pGS4
Source (natural)Location in cell: membrane

-
Component #3: protein, KdpC-subunit

ProteinName: KdpC-subunit / a.k.a: KdpC-subunit / Oligomeric Details: monomer / Number of Copies: 1 / Recombinant expression: Yes
MassTheoretical: 21 kDa
SourceSpecies: Escherichia coli / / bacteria /
Source (engineered)Expression System: Escherichia coli / / bacteria / / Vector: pGS4
Source (natural)Location in cell: membrane

-
Component #4: protein, KdpF-subunit

ProteinName: KdpF-subunit / a.k.a: KdpF-subunit / Oligomeric Details: monomer / Recombinant expression: Yes / Number of Copies: 1
MassTheoretical: 3 kDa
SourceSpecies: Escherichia coli / / bacteria /
Source (engineered)Expression System: Escherichia coli / / bacteria / / Vector: pGS4
Source (natural)Location in cell: membrane

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: negative staining
Sample solutionSpecimen conc.: 0.005 mg/ml
Buffer solution: 50 mM MES pH 6.0, 50 mM NaCl, 5 mM MgCl2, 5 mM CaCl2
pH: 6
Support film400 mesh copper grid, carbon coated
Stainingapplied to freshly glow-discharged carbon-coated copper grids (400 mesh). Staining with 2 % (w/v) uranylacetic acid
VitrificationInstrument: NONE / Cryogen name: NONE

-
Electron microscopy imaging

ImagingMicroscope: FEI/PHILIPS CM120T / Date: Jul 20, 2004
Electron gunElectron source: LAB6 / Accelerating voltage: 100 kV / Illumination mode: FLOOD BEAM
LensMagnification: 52000 X (nominal), 48000 X (calibrated) / Astigmatism: manually at 200000 on carbon film / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 432 - 864 nm
Specimen HolderHolder: room temperature holder / Model: SIDE ENTRY, EUCENTRIC / Temperature: 295 K ( 95 - 295 K)
CameraDetector: KODAK SO-163 FILM

-
Image acquisition

Image acquisitionNumber of digital images: 90 / Scanner: ZEISS SCAI / Sampling size: 14 microns / Bit depth: 8

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 10040
Details: started with angular reconstitution in IMAGIC (25 class averages) followed by projection matching in Spider (global search in 10 degree steps followed by local search in 2 degree steps)
Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: Sinogram Correlation followed by Projection Matching
Software: IMAGIC Spider / Resolution: 19 Å / Resolution method: FSC 0.5

+
About Yorodumi

-
News

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more