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- PDB-7x15: Crystal structure of MIGA2 LD targeting domain -

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Basic information

Entry
Database: PDB / ID: 7x15
TitleCrystal structure of MIGA2 LD targeting domain
ComponentsMitoguardin 2
KeywordsLIPID TRANSPORT / MIGA2 / FFAT / LD
Function / homology
Function and homology information


Synthesis of PA / mitochondrial fusion / mitochondrial outer membrane / protein heterodimerization activity / protein homodimerization activity / plasma membrane
Similarity search - Function
Mitoguardin / Mitoguardin
Similarity search - Domain/homology
FORMIC ACID / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / Mitoguardin 2
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.852 Å
AuthorsKim, H. / Lee, C.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2021M3A9G8022417 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2021R1A2C2009550 Korea, Republic Of
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis for mitoguardin-2 mediated lipid transport at ER-mitochondrial membrane contact sites.
Authors: Kim, H. / Lee, S. / Jun, Y. / Lee, C.
History
DepositionFeb 23, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mitoguardin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1843
Polymers30,4461
Non-polymers7382
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-16 kcal/mol
Surface area12970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.126, 100.126, 163.941
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Mitoguardin 2 / Protein FAM73B


Mass: 30445.709 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: miga2, fam73b, zgc:113131 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5BLE2
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-PEF / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / 3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL


Mass: 691.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H74NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.9 Å3/Da / Density % sol: 68.43 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 18% SOCKALAN cp5, 100 mM HEPES pH7.0, 300 mM ammonum formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 21478 / % possible obs: 100 % / Redundancy: 21.1 % / CC1/2: 0.997 / Net I/σ(I): 18
Reflection shellResolution: 2.85→2.9 Å / Num. unique obs: 1055 / CC1/2: 0.786

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.852→47.88 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.239 1064 4.96 %
Rwork0.1997 20368 -
obs0.2017 21432 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 158.2 Å2 / Biso mean: 44.7408 Å2 / Biso min: 6.88 Å2
Refinement stepCycle: final / Resolution: 2.852→47.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2093 0 50 10 2153
Biso mean--56.9 40.94 -
Num. residues----261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042191
X-RAY DIFFRACTIONf_angle_d0.7442941
X-RAY DIFFRACTIONf_chiral_restr0.03326
X-RAY DIFFRACTIONf_plane_restr0.005368
X-RAY DIFFRACTIONf_dihedral_angle_d15.215820
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.852-2.98140.3141340.28572533
2.9814-3.13860.32181350.27972548
3.1386-3.33520.27361360.24312546
3.3352-3.59260.27281310.21312533
3.5926-3.9540.22381340.18432551
3.954-4.52580.1791340.16942545
4.5258-5.70050.21921260.18052555
5.7005-47.880.23311340.18092557

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