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- PDB-5yk6: Crystal Structure of Mmm1 -

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Basic information

Entry
Database: PDB / ID: 5yk6
TitleCrystal Structure of Mmm1
ComponentsMaintenance of mitochondrial morphology protein 1
KeywordsLIPID TRANSPORT / ERMES / Phospholipid / Membrane contact site
Function / homology
Function and homology information


ERMES complex / protein insertion into mitochondrial outer membrane / : / lipid transport / lipid binding / endoplasmic reticulum membrane
Similarity search - Function
Maintenance of mitochondrial morphology protein 1 / MMM1 domain / Maintenance of mitochondrial morphology protein 1 / Synaptotagmin-like mitochondrial-lipid-binding domain / Synaptotagmin-like mitochondrial lipid-binding proteins (SMP) domain profile.
Similarity search - Domain/homology
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / Maintenance of mitochondrial morphology protein 1
Similarity search - Component
Biological speciesZygosaccharomyces rouxii (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 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 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9933
Polymers29,5831
Non-polymers1,4102
Water23413
1
A: Maintenance of mitochondrial morphology protein 1
hetero molecules

A: Maintenance of mitochondrial morphology protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9876
Polymers59,1672
Non-polymers2,8204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_557x-y,-y,-z+7/31
Buried area13300 Å2
ΔGint-98 kcal/mol
Surface area23710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.504, 125.504, 60.875
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Maintenance of mitochondrial morphology protein 1


Mass: 29583.342 Da / Num. of mol.: 1
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: Chemical ChemComp-3PH / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / PHOSPHATIDIC ACID


Mass: 704.998 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C39H77O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

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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: 4.68 Å3/Da / Density % sol: 73.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG 10000, HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 13895 / % possible obs: 99.2 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 26.8
Reflection shellResolution: 2.8→2.85 Å

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Processing

Software
NameVersionClassification
MxDCdata collection
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
PHENIX1.9_1692refinement
RefinementMethod to determine structure: SAD / Resolution: 2.8→41.081 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 24.79
RfactorNum. reflection% reflection
Rfree0.2349 703 5.06 %
Rwork0.1936 --
obs0.1957 13887 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→41.081 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1960 0 86 13 2059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082088
X-RAY DIFFRACTIONf_angle_d1.3872809
X-RAY DIFFRACTIONf_dihedral_angle_d16.729822
X-RAY DIFFRACTIONf_chiral_restr0.043302
X-RAY DIFFRACTIONf_plane_restr0.006354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7908-3.00620.31431360.25322553X-RAY DIFFRACTION98
3.0062-3.30860.26361410.22222603X-RAY DIFFRACTION99
3.3086-3.7870.25041350.19312639X-RAY DIFFRACTION100
3.787-4.77010.23351430.17782643X-RAY DIFFRACTION100
4.7701-41.08530.2111480.18742746X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 49.1436 Å / Origin y: -14.7777 Å / Origin z: 64.2078 Å
111213212223313233
T0.4545 Å2-0.0511 Å2-0.0374 Å2-0.466 Å20.0805 Å2--0.526 Å2
L1.3139 °2-1.3418 °2-0.8773 °2-6.0262 °23.5244 °2--2.2771 °2
S-0.0787 Å °-0.0604 Å °-0.0742 Å °0.1747 Å °-0.2058 Å °0.5966 Å °0.0768 Å °-0.1798 Å °0.272 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 194 through 439)

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