[English] 日本語
Yorodumi
- PDB-5y0b: PIG GASTRIC H+,K+ - ATPASE IN COMPLEX with BYK99 -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 5y0b
TitlePIG GASTRIC H+,K+ - ATPASE IN COMPLEX with BYK99
DescriptorPotassium-transporting ATPase alpha chain 1
Potassium-transporting ATPase subunit beta
KeywordsHYDROLASE / ion pump / h+ / k+-atpase / p-type atpase / membrane protein / Hydrolase / e2 / aluminium fluoride / ATP-binding / hydrogen ion transport / ion transport / magnesium / membrane / metal-binding / nucleotide-binding / phosphoprotein / potassium / potassium transport / transmembrane / transport / disulfide bond / glycoprotein / signal-anchor
Specimen sourceSus scrofa / mammal / Pig / イノシシ, いのしし, ニホンイノシシ, ブタ / image: Sus scrofa domestica
MethodElectron crystallography (6.5 Å resolution / 2d array / Crystallography)
AuthorsAbe, K. / Shimokawa, J. / Natio, M. / Munson, K. / Vagin, O. / Sachs, G. / Suzuki, H. / Tani, K. / Fujiyoshi, Y.
CitationSci Rep, 2017, 7, 6632-6632

Sci Rep, 2017, 7, 6632-6632 StrPapers
The cryo-EM structure of gastric H(+),K(+)-ATPase with bound BYK99, a high-affinity member of K(+)-competitive, imidazo[1,2-a]pyridine inhibitors.
Kazuhiro Abe / Jun Shimokawa / Mao Naito / Keith Munson / Olga Vagin / George Sachs / Hiroshi Suzuki / Kazutoshi Tani / Yoshinori Fujiyoshi

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 16, 2017 / Release: Aug 9, 2017

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide

Downloads & links

-
Assembly

Deposited unit
A: Potassium-transporting ATPase alpha chain 1
B: Potassium-transporting ATPase subunit beta


Theoretical massNumber of molelcules
Total (without water)147,5142
Polyers147,5142
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)4060
ΔGint (kcal/M)-24
Surface area (Å2)54910
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)142.600, 112.000, 320.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP 21 21 2

-
Components

#1: Polypeptide(L)Potassium-transporting ATPase alpha chain 1 / Gastric H+/K+ ATPase subunit alpha / Proton pump


Mass: 114399.688 Da / Num. of mol.: 1
Source: (natural) Sus scrofa / mammal / イノシシ, いのしし, ニホンイノシシ, ブタ / image: Sus scrofa domestica
References: UniProt: P19156, EC: 3.6.3.10
#2: Polypeptide(L)Potassium-transporting ATPase subunit beta / Gastric H+/K+ ATPase subunit beta / Proton pump beta chain / gp60-90


Mass: 33113.844 Da / Num. of mol.: 1
Source: (natural) Sus scrofa / mammal / イノシシ, いのしし, ニホンイノシシ, ブタ / image: Sus scrofa domestica
References: UniProt: P18434

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 2D ARRAY / Reconstruction method: CRYSTALLOGRAPHY
Crystal symmetryAngle gamma: 90 deg. / C sampling length: 320 Å / Length a: 142.6 Å / Length b: 112 Å / Length c: 320 Å / Space group name H-M: P 2 21 21

-
Sample preparation

ComponentName: PIG GASTRIC H+/ K+ - ATPASE IN COMPLEX WITH BYK99 / Type: COMPLEX / Entity ID: 1, 2 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Sus scrofa / Tissue: stomach
Buffer solutionpH: 4.8
SpecimenConc.: 6.5 mg/ml / Details: This sample is 2D crystal. / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: LEICA KF80 / Cryogen name: NITROGEN
Crystal growpH: 4.87

-
Data collection

MicroscopyMicroscope model: JEOL KYOTO-3000SFF
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 8 e/Å2 / Film or detector model: KODAK SO-163 FILM
EM diffractionCamera length: 1500 mm
EM diffraction shellFourier space coverage: 47.1 / High resolution: 6.5 Å / Low resolution: 200 Å / Multiplicity: 11.9 / Number of structure factors: 4974 / Phase residual: 33.1 deg.
EM diffraction statsFourier space coverage: 47.1 / High resolution: 6.5 Å / Number of intensities measured: 59212 / Number of structure factors: 4974 / Overall phase error: 33.1 deg. / Overall phase residual: 33.1 deg. / Phase error rejection criteria: 0 / R merge: 0.469 / R sym: 0.469

-
Processing

EM software
IDNameCategoryImaging IDImage processing IDFitting ID
1MRCIMAGE ACQUISITION1
3MRCCTF CORRECTION1
6SITUSMODEL FITTING1
12MRCRECONSTRUCTION1
13COOTMODEL REFINEMENT1
Crystal symmetryAngle gamma: 90 deg. / C sampling length: 320 Å / Length a: 142.6 Å / Length b: 112 Å / Length c: 320 Å / Space group name H-M: P 2 21 21
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 6.5 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 2D CRYSTAL
Atomic model buildingRef protocol: RIGID BODY FIT / Ref space: REAL / Target criteria: correlation coefficient
RefineCross valid method: THROUGHOUT
Least-squares processHighest resolution: 6.7 Å / Lowest resolution: 200 Å / Number reflection obs: 4974 / Percent reflection obs: 50.1
Number of atoms included #1Protein: 1044 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0

+
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 / Changes in new EM Navigator and Yorodumi

Read more