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- PDB-8edv: Mitoguardin homolog (MIGA) delta TM residues 106-496 from Caenorh... -

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Basic information

Entry
Database: PDB / ID: 8edv
TitleMitoguardin homolog (MIGA) delta TM residues 106-496 from Caenorhabditis elegans bound to modelled lipid phosphatidylethanolamine
ComponentsMItoGuArdin homolog
KeywordsLIPID TRANSPORT / mitochondria / lipid droplets
Function / homologyMitoguardin / Mitoguardin / mitochondrial fusion / membrane => GO:0016020 / mitochondrion / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / MItoGuArdin homolog
Function and homology information
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsHong, Z. / Adlakha, J. / Reinisch, K.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM131715 United States
CitationJournal: J.Cell Biol. / Year: 2022
Title: Mitoguardin-2-mediated lipid transfer preserves mitochondrial morphology and lipid droplet formation.
Authors: Hong, Z. / Adlakha, J. / Wan, N. / Guinn, E. / Giska, F. / Gupta, K. / Melia, T.J. / Reinisch, K.M.
History
DepositionSep 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MItoGuArdin homolog
B: MItoGuArdin homolog
C: MItoGuArdin homolog
D: MItoGuArdin homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,4248
Polymers180,6574
Non-polymers2,7684
Water0
1
A: MItoGuArdin homolog
B: MItoGuArdin homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,7124
Polymers90,3282
Non-polymers1,3842
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-68 kcal/mol
Surface area32720 Å2
MethodPISA
2
C: MItoGuArdin homolog
D: MItoGuArdin homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,7124
Polymers90,3282
Non-polymers1,3842
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-70 kcal/mol
Surface area33120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.278, 91.278, 366.745
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 135 or resid 138 through 143...
21(chain B and (resid 135 or resid 138 through 391 or resid 401))
31(chain C and (resid 135 or resid 138 through 143...
41(chain D and (resid 135 or resid 138 through 143...
12(chain E and resid 1 through 63)
22(chain F and resid 1 through 63)
32chain G
42(chain H and resid 1 through 63)

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 135 or resid 138 through 143...A135
121(chain A and (resid 135 or resid 138 through 143...A138 - 143
131(chain A and (resid 135 or resid 138 through 143...A145 - 148
141(chain A and (resid 135 or resid 138 through 143...A151 - 359
151(chain A and (resid 135 or resid 138 through 143...A364 - 391
161(chain A and (resid 135 or resid 138 through 143...A401
211(chain B and (resid 135 or resid 138 through 391 or resid 401))B135
221(chain B and (resid 135 or resid 138 through 391 or resid 401))B138 - 391
231(chain B and (resid 135 or resid 138 through 391 or resid 401))B401
311(chain C and (resid 135 or resid 138 through 143...C135
321(chain C and (resid 135 or resid 138 through 143...C138 - 143
331(chain C and (resid 135 or resid 138 through 143...C145 - 148
341(chain C and (resid 135 or resid 138 through 143...C151 - 359
351(chain C and (resid 135 or resid 138 through 143...C364 - 391
361(chain C and (resid 135 or resid 138 through 143...C401
411(chain D and (resid 135 or resid 138 through 143...D135
421(chain D and (resid 135 or resid 138 through 143...D138 - 143
431(chain D and (resid 135 or resid 138 through 143...D145 - 148
441(chain D and (resid 135 or resid 138 through 143...D151 - 359
451(chain D and (resid 135 or resid 138 through 143...D364 - 391
461(chain D and (resid 135 or resid 138 through 143...D401
112(chain E and resid 1 through 63)E1 - 63
212(chain F and resid 1 through 63)F1 - 63
312chain GG0
412(chain H and resid 1 through 63)H1 - 63

NCS ensembles :
ID
1
2

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Components

#1: Protein
MItoGuArdin homolog / Mitoguardin 2 (MIGA2)


Mass: 45164.164 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: miga-1, CELE_K01D12.6, K01D12.6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q21096
#2: Chemical
ChemComp-PEF / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / 3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL / Phosphatidylethanolamine


Mass: 691.959 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C37H74NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
Has ligand of interestY

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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: 2.44 Å3/Da / Density % sol: 49.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 0.2 M sodium malonate pH 7.4, 22% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97911 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 3.3→48.36 Å / Num. obs: 27736 / % possible obs: 99.9 % / Redundancy: 10.2 % / CC1/2: 0.993 / Rmerge(I) obs: 0.169 / Rpim(I) all: 0.056 / Rrim(I) all: 0.179 / Net I/σ(I): 14
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.736 / Num. unique obs: 2670 / CC1/2: 0.835 / Rpim(I) all: 0.236 / Rrim(I) all: 0.774 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold2 model

Resolution: 3.3→48.35 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 32.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2956 1330 4.81 %
Rwork0.2698 26328 -
obs0.2711 27658 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 386.88 Å2 / Biso mean: 129.7132 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.3→48.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10265 0 480 0 10745
Biso mean--154.89 --
Num. residues----1272
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3156X-RAY DIFFRACTION4.217TORSIONAL
12B3156X-RAY DIFFRACTION4.217TORSIONAL
13C3156X-RAY DIFFRACTION4.217TORSIONAL
14D3156X-RAY DIFFRACTION4.217TORSIONAL
21A756X-RAY DIFFRACTION4.217TORSIONAL
22B756X-RAY DIFFRACTION4.217TORSIONAL
23C756X-RAY DIFFRACTION4.217TORSIONAL
24D756X-RAY DIFFRACTION4.217TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3-3.420.31061120.34112545265799
3.42-3.550.37481420.311325772719100
3.55-3.720.34971350.335625882723100
3.72-3.910.34761600.292725782738100
3.91-4.160.29811490.291626102759100
4.16-4.480.28441390.260625642703100
4.48-4.930.35271260.273726562782100
4.93-5.640.29271160.272926732789100
5.64-7.10.3131330.302126802813100
7.1-48.350.23511180.22552857297599
Refinement TLS params.Method: refined / Origin x: -45.7624 Å / Origin y: 42.9299 Å / Origin z: 30.3252 Å
111213212223313233
T0.7814 Å2-0.0084 Å20.0951 Å2-0.7818 Å20.0021 Å2--0.9468 Å2
L0.4596 °2-0.072 °2-0.2562 °2-0.45 °20.0565 °2--0.7833 °2
S-0.0188 Å °-0.0036 Å °0.0132 Å °-0.0041 Å °-0.0111 Å °0.0161 Å °-0.1574 Å °0.0272 Å °0.0392 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA109 - 495
2X-RAY DIFFRACTION1allA505
3X-RAY DIFFRACTION1allB109 - 495
4X-RAY DIFFRACTION1allB505
5X-RAY DIFFRACTION1allC110 - 495
6X-RAY DIFFRACTION1allC505
7X-RAY DIFFRACTION1allD109 - 495
8X-RAY DIFFRACTION1allD505

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