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- PDB-5gyd: Crystal Structure of Mdm12 -

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Basic information

Entry
Database: PDB / ID: 5gyd
TitleCrystal Structure of Mdm12
ComponentsMitochondrial distribution and morphology protein 12
KeywordsLIPID TRANSPORT / Mdm12 / ERMES complex / SMP domain
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 / mitochondria-associated endoplasmic reticulum membrane contact site / mitochondrial genome maintenance / phospholipid transport ...ERMES complex / mitochondrion inheritance / outer mitochondrial membrane protein complex / mitochondrial outer membrane translocase complex assembly / lipid transfer activity / aminophospholipid transport / peroxisome organization / mitochondria-associated endoplasmic reticulum membrane contact site / mitochondrial genome maintenance / phospholipid transport / phospholipid homeostasis / mitochondrion-endoplasmic reticulum membrane tethering / protein insertion into mitochondrial outer membrane / mitochondrion organization / mitochondrial outer membrane / lipid binding / endoplasmic reticulum membrane / mitochondrion / nucleus / plasma membrane / cytoplasm
Similarity search - Function
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
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Mitochondrial distribution and morphology protein 12
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.106 Å
AuthorsJeong, H. / Park, J. / Lee, C.
CitationJournal: EMBO Rep. / Year: 2016
Title: Crystal structure of Mdm12 reveals the architecture and dynamic organization of the ERMES complex
Authors: Jeong, H. / Park, J. / Lee, C.
History
DepositionSep 22, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 2.0Mar 20, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.mon_nstd_flag / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitochondrial distribution and morphology protein 12
B: Mitochondrial distribution and morphology protein 12
C: Mitochondrial distribution and morphology protein 12
D: Mitochondrial distribution and morphology protein 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,9719
Polymers123,2504
Non-polymers3,7205
Water00
1
A: Mitochondrial distribution and morphology protein 12
B: Mitochondrial distribution and morphology protein 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1134
Polymers61,6252
Non-polymers1,4882
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-50 kcal/mol
Surface area24670 Å2
MethodPISA
2
C: Mitochondrial distribution and morphology protein 12
D: Mitochondrial distribution and morphology protein 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8575
Polymers61,6252
Non-polymers2,2323
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-47 kcal/mol
Surface area23520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.592, 219.073, 73.097
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 30812.600 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: MDM12, YOL009C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q92328
#2: Chemical
ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE


Mass: 744.034 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C41H78NO8P / Comment: DOPE, phospholipid*YM

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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: 4.63 Å3/Da / Density % sol: 73.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: Sodium formate, ADA, DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 3.1→35 Å / Num. obs: 41953 / % possible obs: 99.6 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 19.9
Reflection shellResolution: 3.1→3.15 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data processing
AutoSolphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 3.106→32.683 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2535 2000 4.77 %
Rwork0.2137 --
obs0.2156 41909 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.106→32.683 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7200 0 185 0 7385
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077541
X-RAY DIFFRACTIONf_angle_d1.34310181
X-RAY DIFFRACTIONf_dihedral_angle_d18.62880
X-RAY DIFFRACTIONf_chiral_restr0.051167
X-RAY DIFFRACTIONf_plane_restr0.0061280
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1063-3.18390.3581380.33762747X-RAY DIFFRACTION96
3.1839-3.26990.35161410.30152809X-RAY DIFFRACTION100
3.2699-3.36610.33171400.27642792X-RAY DIFFRACTION100
3.3661-3.47460.30341430.2712872X-RAY DIFFRACTION100
3.4746-3.59860.28591400.24382803X-RAY DIFFRACTION100
3.5986-3.74250.2871430.2332833X-RAY DIFFRACTION100
3.7425-3.91260.25751420.21872854X-RAY DIFFRACTION100
3.9126-4.11850.31711430.22052839X-RAY DIFFRACTION100
4.1185-4.3760.20211420.18112844X-RAY DIFFRACTION100
4.376-4.71290.18521440.16142868X-RAY DIFFRACTION100
4.7129-5.18550.19771440.15712877X-RAY DIFFRACTION100
5.1855-5.9320.24321450.20752905X-RAY DIFFRACTION100
5.932-7.4590.25791460.24372912X-RAY DIFFRACTION99
7.459-32.68530.24531490.20092954X-RAY DIFFRACTION96
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)
13.8517-0.8685-0.84513.17080.56781.2609-0.284-0.05660.11211.24450.2050.03520.0581-0.0081-0.00860.6791-0.03150.06980.3538-0.00930.576552.397190.6667-3.1848
21.165-0.3432-0.35825.0302-0.89792.2682-0.0955-0.0608-0.08431.31830.0506-0.0380.2547-0.2476-0.0040.70060.0092-0.05770.38020.01220.412251.9761131.2981.6997
32.54790.3373-0.52871.67530.46833.65460.15710.1864-0.01390.14620.1485-0.15190.39250.40950.04040.2841-0.0198-0.11510.4541-0.12640.346445.551767.3747-19.6648
42.0254-0.52870.5434.1680.42555.06020.10780.0319-0.13120.13820.3833-0.45070.39290.62620.1660.2259-0.0342-0.11950.4639-0.20250.402735.264651.1484-56.2892
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 0 through 267)
2X-RAY DIFFRACTION2(chain 'B' and resid 0 through 266)
3X-RAY DIFFRACTION3(chain 'C' and resid 0 through 267)
4X-RAY DIFFRACTION4(chain 'D' and resid 0 through 265)

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