[English] 日本語
Yorodumi
- PDB-7ztk: NME1 in complex with CoA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ztk
TitleNME1 in complex with CoA
ComponentsNucleoside diphosphate kinase A
KeywordsTRANSFERASE / NME1 / complex / nucleoside diphosphate kinase 1 / coenzyme-A
Function / homology
Function and homology information


Azathioprine ADME / Ribavirin ADME / Interconversion of nucleotide di- and triphosphates / DNA nuclease activity / nucleoside-diphosphate kinase / mammary gland development / UTP biosynthetic process / CTP biosynthetic process / nucleoside diphosphate kinase activity / dTMP biosynthetic process ...Azathioprine ADME / Ribavirin ADME / Interconversion of nucleotide di- and triphosphates / DNA nuclease activity / nucleoside-diphosphate kinase / mammary gland development / UTP biosynthetic process / CTP biosynthetic process / nucleoside diphosphate kinase activity / dTMP biosynthetic process / GTP biosynthetic process / ribosomal small subunit binding / lactation / 3'-5' exonuclease activity / positive regulation of epithelial cell proliferation / ruffle membrane / endocytosis / myelin sheath / nervous system development / cell differentiation / early endosome / GTP binding / magnesium ion binding / mitochondrion / ATP binding / identical protein binding / nucleus / cytosol
Similarity search - Function
Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily
Similarity search - Domain/homology
COENZYME A / Nucleoside diphosphate kinase A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGarcia-Saez, I. / Iuso, D. / Khochbin, S. / Petosa, C.
Funding support France, 1items
OrganizationGrant numberCountry
Other government France
CitationJournal: Sci Adv / Year: 2023
Title: Nucleoside diphosphate kinases 1 and 2 regulate a protective liver response to a high-fat diet.
Authors: Iuso, D. / Garcia-Saez, I. / Coute, Y. / Yamaryo-Botte, Y. / Boeri Erba, E. / Adrait, A. / Zeaiter, N. / Tokarska-Schlattner, M. / Jilkova, Z.M. / Boussouar, F. / Barral, S. / Signor, L. / ...Authors: Iuso, D. / Garcia-Saez, I. / Coute, Y. / Yamaryo-Botte, Y. / Boeri Erba, E. / Adrait, A. / Zeaiter, N. / Tokarska-Schlattner, M. / Jilkova, Z.M. / Boussouar, F. / Barral, S. / Signor, L. / Couturier, K. / Hajmirza, A. / Chuffart, F. / Bourova-Flin, E. / Vitte, A.L. / Bargier, L. / Puthier, D. / Decaens, T. / Rousseaux, S. / Botte, C. / Schlattner, U. / Petosa, C. / Khochbin, S.
History
DepositionMay 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nucleoside diphosphate kinase A
B: Nucleoside diphosphate kinase A
C: Nucleoside diphosphate kinase A
D: Nucleoside diphosphate kinase A
E: Nucleoside diphosphate kinase A
F: Nucleoside diphosphate kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,97212
Polymers105,3676
Non-polymers4,6056
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, mass spectrometry, native mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21750 Å2
ΔGint-121 kcal/mol
Surface area34300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.173, 69.450, 116.296
Angle α, β, γ (deg.)90.000, 90.060, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Nucleoside diphosphate kinase A / NDK A / NDP kinase A / Metastasis inhibition factor NM23 / NDPK-A / Tumor metastatic process- ...NDK A / NDP kinase A / Metastasis inhibition factor NM23 / NDPK-A / Tumor metastatic process-associated protein / nm23-M1


Mass: 17561.199 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: NME1 hexamer in complex with CoA / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nme1, Nm23 / Plasmid: pETM-11
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P15532, nucleoside-diphosphate kinase
#2: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 36% PEG 3350, 0.2M Mg(NO3)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.6→49.13 Å / Num. obs: 26764 / % possible obs: 99.23 % / Redundancy: 3.2 % / Biso Wilson estimate: 40.72 Å2 / CC1/2: 0.945 / CC star: 0.986 / Rmerge(I) obs: 0.254 / Rpim(I) all: 0.17 / Rrim(I) all: 0.307 / Net I/σ(I): 3.37
Reflection shellResolution: 2.6→2.693 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.046 / Mean I/σ(I) obs: 0.84 / Num. unique obs: 2649 / CC1/2: 0.542 / CC star: 0.839 / Rpim(I) all: 0.684 / Rrim(I) all: 1.253 / % possible all: 98.53

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ui4

5ui4


Resolution: 2.6→49.13 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.35 / Stereochemistry target values: ML
Details: TLS was used in the first runs of refinement (1 group/chain), but not in the last runs of refinement.
RfactorNum. reflection% reflection
Rfree0.2893 1322 4.97 %
Rwork0.2725 25271 -
obs0.2733 26593 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.33 Å2 / Biso mean: 47.6645 Å2 / Biso min: 18.25 Å2
Refinement stepCycle: final / Resolution: 2.6→49.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7266 0 254 77 7597
Biso mean--70.9 41.05 -
Num. residues----912
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.70.37111090.38772821293098
2.7-2.830.36381500.30862732288299
2.83-2.980.31461470.29832782292999
2.98-3.160.31381570.30162797295499
3.16-3.410.31971710.28182770294199
3.41-3.750.29971800.269127542934100
3.75-4.290.25671440.25728512995100
4.29-5.410.24481280.243728602988100
5.41-49.130.26911360.247229043040100

+
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