[English] 日本語
Yorodumi
- PDB-5h55: Mdm12 from K. lactis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5h55
TitleMdm12 from K. lactis
ComponentsMitochondrial distribution and morphology protein 12
KeywordsLIPID BINDING PROTEIN
Function / homology
Function and homology information


ERMES complex / mitochondrial genome maintenance / lipid transport / protein insertion into mitochondrial outer membrane / lipid binding / endoplasmic reticulum membrane
Similarity search - Function
MMM1 domain / Maintenance of mitochondrial morphology protein 1 / Mitochondrial distribution and morphology protein 12 / Synaptotagmin-like mitochondrial-lipid-binding domain / Synaptotagmin-like mitochondrial lipid-binding proteins (SMP) domain profile.
Similarity search - Domain/homology
Mitochondrial distribution and morphology protein 12
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsKawano, S. / Quinbara, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science25840020 Japan
CitationJournal: J. Cell Biol. / Year: 2018
Title: Structure-function insights into direct lipid transfer between membranes by Mmm1-Mdm12 of ERMES
Authors: Kawano, S. / Tamura, Y. / Kojima, R. / Bala, S. / Asai, E. / Michel, A.H. / Kornmann, B. / Riezman, I. / Riezman, H. / Sakae, Y. / Okamoto, Y. / Endo, T.
History
DepositionNov 4, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mitochondrial distribution and morphology protein 12


Theoretical massNumber of molelcules
Total (without water)36,5751
Polymers36,5751
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11050 Å2
Unit cell
Length a, b, c (Å)137.533, 137.533, 76.602
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein Mitochondrial distribution and morphology protein 12 / Mitochondrial inheritance component MDM12


Mass: 36574.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Gene: MDM12, KLLA0C06028g / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CUC3

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 56.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M Na-malate pH 7.0, 15 - 20% PEG3400, 0.1M Tris-HCl pH8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.31→50 Å / Num. obs: 535031 / % possible obs: 99.6 % / Redundancy: 10.7 % / Net I/σ(I): 15.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→39.7 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.849 / SU B: 30.762 / SU ML: 0.477 / Cross valid method: THROUGHOUT / ESU R Free: 0.621 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32312 260 4.5 %RANDOM
Rwork0.26017 ---
obs0.26301 5467 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 77.709 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.02 Å20 Å2
2---0.03 Å20 Å2
3---0.11 Å2
Refinement stepCycle: 1 / Resolution: 3.5→39.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1596 0 0 0 1596
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191621
X-RAY DIFFRACTIONr_bond_other_d0.0010.021541
X-RAY DIFFRACTIONr_angle_refined_deg1.291.9852200
X-RAY DIFFRACTIONr_angle_other_deg0.76333534
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2755203
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.46125.69472
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.30915275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.193157
X-RAY DIFFRACTIONr_chiral_restr0.0690.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211820
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02341
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4597.973824
X-RAY DIFFRACTIONr_mcbond_other3.4527.971823
X-RAY DIFFRACTIONr_mcangle_it5.72711.9381023
X-RAY DIFFRACTIONr_mcangle_other5.72411.941024
X-RAY DIFFRACTIONr_scbond_it3.318.133797
X-RAY DIFFRACTIONr_scbond_other3.2858.127795
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.70712.11177
X-RAY DIFFRACTIONr_long_range_B_refined9.13862.6021803
X-RAY DIFFRACTIONr_long_range_B_other9.14462.5861802
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.501→3.592 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 19 -
Rwork0.32 378 -
obs--100 %

+
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