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- PDB-5yk7: Crystal Structure of Mdm12-Mmm1 complex -

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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 / : ...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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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)

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