[English] 日本語
Yorodumi
- PDB-5yk7: Crystal Structure of Mdm12-Mmm1 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yk7
TitleCrystal Structure of Mdm12-Mmm1 complex
Components
  • Maintenance of mitochondrial morphology protein 1
  • Mitochondrial distribution and morphology protein 12
KeywordsLIPID TRANSPORT / Mmm1 / Mdm12 / ERMES / Phospholipid / Membrane contact site
Function / homology
Function and homology information


ERMES complex / mitochondrion inheritance / outer mitochondrial membrane protein complex / mitochondrial outer membrane translocase complex assembly / lipid transfer activity / aminophospholipid transport / peroxisome organization / protein insertion into mitochondrial outer membrane / mitochondria-associated endoplasmic reticulum membrane contact site / phospholipid transport ...ERMES complex / mitochondrion inheritance / outer mitochondrial membrane protein complex / mitochondrial outer membrane translocase complex assembly / lipid transfer activity / aminophospholipid transport / peroxisome organization / protein insertion into mitochondrial outer membrane / mitochondria-associated endoplasmic reticulum membrane contact site / phospholipid transport / : / phospholipid homeostasis / lipid transport / mitochondrion-endoplasmic reticulum membrane tethering / mitochondrion organization / mitochondrial outer membrane / lipid binding / endoplasmic reticulum membrane / mitochondrion / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Maintenance of mitochondrial morphology protein 1 / 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
PHOSPHATE ION / Maintenance of mitochondrial morphology protein 1 / Mitochondrial distribution and morphology protein 12
Similarity search - Component
Biological speciesZygosaccharomyces rouxii (yeast)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.799 Å
AuthorsJeong, H. / Park, J. / Lee, C.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Crystal structures of Mmm1 and Mdm12-Mmm1 reveal mechanistic insight into phospholipid trafficking at ER-mitochondria contact sites.
Authors: Jeong, H. / Park, J. / Jun, Y. / Lee, C.
History
DepositionOct 12, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Maintenance of mitochondrial morphology protein 1
B: Mitochondrial distribution and morphology protein 12
C: Maintenance of mitochondrial morphology protein 1
D: Mitochondrial distribution and morphology protein 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,71210
Polymers106,1424
Non-polymers5706
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10660 Å2
ΔGint-108 kcal/mol
Surface area47750 Å2
Unit cell
Length a, b, c (Å)87.560, 87.560, 436.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein Maintenance of mitochondrial morphology protein 1


Mass: 29583.342 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zygosaccharomyces rouxii (strain ATCC 2623 / CBS 732 / NBRC 1130 / NCYC 568 / NRRL Y-229) (yeast)
Strain: ATCC 2623 / CBS 732 / NBRC 1130 / NCYC 568 / NRRL Y-229
Gene: MMM1, ZYRO0B10274g / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C5DRQ1
#2: Protein Mitochondrial distribution and morphology protein 12 / Mitochondrial inheritance component MDM12


Mass: 23487.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: MDM12, YOL009C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q92328
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.73 Å3/Da / Density % sol: 74.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, HEPES, Ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.8→50 Å / Num. obs: 18459 / % possible obs: 99.8 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 27.5
Reflection shellResolution: 3.8→3.87 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GYD

5gyd


Resolution: 3.799→39.142 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 33.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2624 916 4.96 %
Rwork0.2376 --
obs0.2389 18456 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.799→39.142 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6787 0 30 0 6817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036949
X-RAY DIFFRACTIONf_angle_d0.7729411
X-RAY DIFFRACTIONf_dihedral_angle_d12.7024192
X-RAY DIFFRACTIONf_chiral_restr0.0461061
X-RAY DIFFRACTIONf_plane_restr0.0051195
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7993-3.99940.3691280.31552491X-RAY DIFFRACTION99
3.9994-4.24970.34321220.27782472X-RAY DIFFRACTION100
4.2497-4.57740.30561320.2572533X-RAY DIFFRACTION100
4.5774-5.03710.30071330.252508X-RAY DIFFRACTION100
5.0371-5.7640.31821340.25732506X-RAY DIFFRACTION100
5.764-7.25450.32771330.31562546X-RAY DIFFRACTION100
7.2545-39.14360.19181340.18892484X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
19.4962-7.73522.35575.4567-1.85690.91230.21650.0165-1.17090.7839-0.94970.4331-0.6880.28390.22182.0563-0.1147-0.16371.60911.00151.662139.01275.389444.9536
22.41020.06264.15349.3739-5.67446.52590.6402-0.83580.9390.7540.33580.77010.0051-0.418-0.94111.3950.20210.17572.06030.64581.509176.7817-26.666966.8054
36.1138-1.76431.42817.9316-2.33921.1710.05480.6415-0.3740.3803-0.25571.09150.23120.7917-0.08491.46620.1392-0.71481.47980.28491.871124.147131.152730.3434
44.66234.27751.61248.2346-2.6023.4628-0.03590.14040.0601-0.9020.5132-0.44150.84460.280.05612.43160.2536-0.41161.60120.2310.582215.318980.01428.4045
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 194 through 439)
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 238)
3X-RAY DIFFRACTION3(chain 'C' and resid 194 through 439)
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 238)

+
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