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- PDB-7ydo: Crystal structure of Atg44 -

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Basic information

Entry
Database: PDB / ID: 7ydo
TitleCrystal structure of Atg44
ComponentsUncharacterized protein C26A3.14c
KeywordsLIPID BINDING PROTEIN / autophagy / mitophagy
Function / homology
Function and homology information


mitochondrial membrane fission / membrane destabilizing activity / mitochondrial fission / mitophagy / mitochondrial intermembrane space / lipid binding / cytosol / cytoplasm
Similarity search - Function
Protein of unknown function DUF1748, fungi / Mitofissin
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / Mitofissin
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.58 Å
AuthorsMaruyama, T. / Noda, N.N.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR20E3 Japan
Japan Society for the Promotion of Science (JSPS)19H05707 Japan
CitationJournal: Mol.Cell / Year: 2023
Title: The mitochondrial intermembrane space protein mitofissin drives mitochondrial fission required for mitophagy.
Authors: Fukuda, T. / Furukawa, K. / Maruyama, T. / Yamashita, S.I. / Noshiro, D. / Song, C. / Ogasawara, Y. / Okuyama, K. / Alam, J.M. / Hayatsu, M. / Saigusa, T. / Inoue, K. / Ikeda, K. / Takai, A. ...Authors: Fukuda, T. / Furukawa, K. / Maruyama, T. / Yamashita, S.I. / Noshiro, D. / Song, C. / Ogasawara, Y. / Okuyama, K. / Alam, J.M. / Hayatsu, M. / Saigusa, T. / Inoue, K. / Ikeda, K. / Takai, A. / Chen, L. / Lahiri, V. / Okada, Y. / Shibata, S. / Murata, K. / Klionsky, D.J. / Noda, N.N. / Kanki, T.
History
DepositionJul 4, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1May 31, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 28, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein C26A3.14c
B: Uncharacterized protein C26A3.14c
C: Uncharacterized protein C26A3.14c
D: Uncharacterized protein C26A3.14c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7128
Polymers35,7204
Non-polymers2,9924
Water3,765209
1
A: Uncharacterized protein C26A3.14c
B: Uncharacterized protein C26A3.14c
C: Uncharacterized protein C26A3.14c
D: Uncharacterized protein C26A3.14c
hetero molecules

A: Uncharacterized protein C26A3.14c
B: Uncharacterized protein C26A3.14c
C: Uncharacterized protein C26A3.14c
D: Uncharacterized protein C26A3.14c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,42516
Polymers71,4408
Non-polymers5,9858
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554x,-y,-z-1/21
Buried area32030 Å2
ΔGint-336 kcal/mol
Surface area23250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.364, 82.364, 113.427
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Space group name HallP4w2c
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+3/4
#8: -y,-x,-z+1/4

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Components

#1: Protein
Uncharacterized protein C26A3.14c / Atg44


Mass: 8930.020 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Gene: SPAC26A3.14c / Production host: Escherichia coli (E. coli) / References: UniProt: Q10167
#2: Chemical
ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C41H82NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O
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: 2.69 Å3/Da / Density % sol: 54.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: PEG 3350, octyl-glucoside, sodium citrate

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 52606 / % possible obs: 97.1 % / Redundancy: 11.7 % / Biso Wilson estimate: 27.35 Å2 / CC1/2: 0.978 / Net I/σ(I): 5.53
Reflection shellResolution: 1.58→1.67 Å / Num. unique obs: 13704 / CC1/2: 0.543 / % possible all: 82.7

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.58→38.71 Å / SU ML: 0.2094 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.153
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2262 1995 3.79 %
Rwork0.1961 50611 -
obs0.1972 52606 96.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.35 Å2
Refinement stepCycle: LAST / Resolution: 1.58→38.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2332 0 185 209 2726
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00632573
X-RAY DIFFRACTIONf_angle_d0.8233424
X-RAY DIFFRACTIONf_chiral_restr0.0451352
X-RAY DIFFRACTIONf_plane_restr0.0042407
X-RAY DIFFRACTIONf_dihedral_angle_d30.5274481
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.620.34311030.33792649X-RAY DIFFRACTION72.46
1.62-1.660.30071260.31363208X-RAY DIFFRACTION87.41
1.66-1.710.33051410.30093550X-RAY DIFFRACTION96.83
1.71-1.770.26731420.2593642X-RAY DIFFRACTION99.32
1.77-1.830.25851460.22893689X-RAY DIFFRACTION99.95
1.83-1.90.24381450.20643674X-RAY DIFFRACTION100
1.9-1.990.23361460.19073694X-RAY DIFFRACTION99.92
1.99-2.090.22791460.2013709X-RAY DIFFRACTION99.87
2.09-2.220.20251470.17873724X-RAY DIFFRACTION99.97
2.22-2.40.18321460.17833702X-RAY DIFFRACTION99.97
2.4-2.640.25131480.19863764X-RAY DIFFRACTION100
2.64-3.020.231490.18963760X-RAY DIFFRACTION100
3.02-3.80.20651510.18343819X-RAY DIFFRACTION100
3.8-38.710.22491590.1914027X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -48.5588658242 Å / Origin y: -5.57293902343 Å / Origin z: -17.2846953183 Å
111213212223313233
T0.165905321089 Å20.018917198292 Å2-0.0156008265136 Å2-0.17673769781 Å2-0.00298713415921 Å2--0.150445585634 Å2
L1.84849141963 °2-0.206641217633 °20.598038497747 °2-0.858840703345 °20.0314548145682 °2--1.21414320687 °2
S0.0622510109727 Å °0.0820932409304 Å °-0.0801802460298 Å °0.0314744983551 Å °-0.0454678865532 Å °-0.0824903351658 Å °0.0925458020015 Å °0.109469828266 Å °-0.0149116573949 Å °
Refinement TLS groupSelection details: all

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