[English] 日本語
Yorodumi
- PDB-9g8k: Structure of K+-dependent Na+-PPase from Thermotoga maritima in c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9g8k
TitleStructure of K+-dependent Na+-PPase from Thermotoga maritima in complex with Ca2+ and Etidronate
ComponentsK(+)-stimulated pyrophosphate-energized sodium pump
KeywordsMEMBRANE PROTEIN / Complex / Inhibitor / enzyme / transport
Function / homology
Function and homology information


Na+-exporting diphosphatase / diphosphate hydrolysis-driven proton transmembrane transporter activity / sodium ion transmembrane transporter activity / inorganic diphosphate phosphatase activity / potassium ion binding / sodium ion transmembrane transport / calcium ion binding / magnesium ion binding / protein homodimerization activity / membrane / plasma membrane
Similarity search - Function
Pyrophosphate-energised proton pump / Inorganic H+ pyrophosphatase
Similarity search - Domain/homology
(1-hydroxyethane-1,1-diyl)bis(phosphonic acid) / K(+)-stimulated pyrophosphate-energized sodium pump
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsVidilaseris, K. / Liu, J. / Goldman, A.
Funding support Finland, United Kingdom, 5items
OrganizationGrant numberCountry
Academy of Finland308105 Finland
Academy of Finland1355187 Finland
Academy of Finland1322609 Finland
Academy of Finland13364501 Finland
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T006048/1 United Kingdom
Citation
Journal: Elife / Year: 2024
Title: Conformational dynamics and asymmetry in multimodal inhibition of membrane-bound pyrophosphatases
Authors: Liu, J. / Shah, A. / Ma, Y. / Hardman, K. / Johansson, N.G. / Ribeiro, O. / Brookfield, A. / Bowen, A. / Yli-Kauhaluoma, J. / Xhaard, H. / Jeuken, L.J. / Goldman, A. / Pliotas, C. / Vidilaseris, K.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionJul 23, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: K(+)-stimulated pyrophosphate-energized sodium pump
B: K(+)-stimulated pyrophosphate-energized sodium pump
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,16617
Polymers156,4342
Non-polymers1,73215
Water1086
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7730 Å2
ΔGint-190 kcal/mol
Surface area44850 Å2
Unit cell
Length a, b, c (Å)83.742, 111.663, 105.199
Angle α, β, γ (deg.)90.000, 106.670, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 3 through 7 or (resid 8...
d_2ens_1(chain "B" and (resid 3 through 27 or (resid 28...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11VALVALGLUGLUAA3 - 3012 - 39
d_12GLUGLULYSLYSAA33 - 11342 - 122
d_13ILEILEMETMETAA115 - 473124 - 482
d_14ASPASPILEILEAA477 - 577486 - 586
d_15TYRTYRGLUGLUAA596 - 672605 - 681
d_16LYSLYSPHEPHEAA676 - 726685 - 735
d_17ETDETDETDETDAC801
d_21VALVALLEULEUBB3 - 20712 - 216
d_22PROPROLYSLYSBB216 - 312225 - 321
d_23ASNASNILEILEBB316 - 577325 - 586
d_24TYRTYRPHEPHEBB596 - 726605 - 735
d_25ETDETDETDETDBD801

NCS oper: (Code: givenMatrix: (0.582622134635, 0.0240946401217, -0.812385928331), (0.024947374407, -0.999619637632, -0.0117562140895), (-0.812360189044, -0.013417465369, -0.583001625109)Vector: 25. ...NCS oper: (Code: given
Matrix: (0.582622134635, 0.0240946401217, -0.812385928331), (0.024947374407, -0.999619637632, -0.0117562140895), (-0.812360189044, -0.013417465369, -0.583001625109)
Vector: 25.4176655853, -26.6567174403, 48.6725007053)

-
Components

-
Protein / Sugars , 2 types, 4 molecules AB

#1: Protein K(+)-stimulated pyrophosphate-energized sodium pump / Membrane-bound sodium-translocating pyrophosphatase / Pyrophosphate-energized inorganic ...Membrane-bound sodium-translocating pyrophosphatase / Pyrophosphate-energized inorganic pyrophosphatase / Na(+)-PPase / Tm-PPase


Mass: 78217.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: hppA, TM_0174 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q9S5X0, EC: 7.2.3.-
#5: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

-
Non-polymers , 4 types, 19 molecules

#2: Chemical ChemComp-911 / (1-hydroxyethane-1,1-diyl)bis(phosphonic acid) / Etidronic acid


Mass: 206.028 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H8O7P2 / Comment: medication, detergent*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.2 M CaCl2, 0.1 M HEPES pH 7.0, and 33 % PEG400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 3.15→80.22 Å / Num. obs: 19273 / % possible obs: 91.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 109.19 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.041 / Rrim(I) all: 0.099 / Net I/σ(I): 9.7
Reflection shellResolution: 3.15→3.56 Å / Redundancy: 7 % / Rmerge(I) obs: 1.193 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 964 / CC1/2: 0.494 / % possible all: 59.3

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→80.22 Å / SU ML: 0.5046 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 40.7838
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2942 960 4.99 %
Rwork0.2693 18263 -
obs0.2706 19223 59.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 96.54 Å2
Refinement stepCycle: LAST / Resolution: 3.15→80.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10107 0 103 6 10216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003210406
X-RAY DIFFRACTIONf_angle_d0.691914198
X-RAY DIFFRACTIONf_chiral_restr0.04231734
X-RAY DIFFRACTIONf_plane_restr0.00481754
X-RAY DIFFRACTIONf_dihedral_angle_d15.11193465
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.30190924348 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.310.5403100.3665175X-RAY DIFFRACTION4.05
3.31-3.520.513370.3546579X-RAY DIFFRACTION13.44
3.52-3.790.344870.31581571X-RAY DIFFRACTION35.97
3.79-4.180.34081650.28113175X-RAY DIFFRACTION73.04
4.18-4.780.30552160.25413964X-RAY DIFFRACTION90.59
4.78-6.020.3142290.29184344X-RAY DIFFRACTION99.05
6.02-80.220.25052160.25534455X-RAY DIFFRACTION99.34

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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.
  • 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

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more