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- PDB-6kyl: Crystal Structure of Phosphatidic acid Transporter Ups1/Mdm35 in ... -

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Basic information

Entry
Database: PDB / ID: 6kyl
TitleCrystal Structure of Phosphatidic acid Transporter Ups1/Mdm35 in Complex with (2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate
Components
  • Mitochondrial distribution and morphology protein 35
  • Protein UPS1, mitochondrial
KeywordsTRANSPORT PROTEIN / Lipid transport
Function / homology
Function and homology information


TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / phosphatidic acid transfer activity / cardiolipin metabolic process / positive regulation of phosphatidylcholine biosynthetic process / mitochondrial respiratory chain complex assembly / phospholipid transport / phospholipid translocation / mitochondrion organization / mitochondrial intermembrane space / mitochondrial inner membrane ...TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / phosphatidic acid transfer activity / cardiolipin metabolic process / positive regulation of phosphatidylcholine biosynthetic process / mitochondrial respiratory chain complex assembly / phospholipid transport / phospholipid translocation / mitochondrion organization / mitochondrial intermembrane space / mitochondrial inner membrane / lipid binding / mitochondrion / nucleus / cytosol / cytoplasm
Similarity search - Function
PRELI/MSF1 domain / Slowmo/Ups family / PRELI-like family / PRELI/MSF1 domain profile. / Mitochondrial distribution/morphology family 35/apoptosis / Uncharacterised protein family (UPF0203) / Coiled coil-helix-coiled coil-helix (CHCH) domain profile.
Similarity search - Domain/homology
(2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate / Mitochondrial distribution and morphology protein 35 / Protein UPS1, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.55 Å
AuthorsLu, J. / Chan, K.C. / Zhai, Y. / Fan, J. / Sun, F.
CitationJournal: Commun Biol / Year: 2020
Title: Molecular mechanism of mitochondrial phosphatidate transfer by Ups1.
Authors: Lu, J. / Chan, C. / Yu, L. / Fan, J. / Sun, F. / Zhai, Y.
History
DepositionSep 19, 2019Deposition site: PDBJ / Processing site: PDBJ
SupersessionOct 2, 2019ID: 5JQO
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Sep 9, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitochondrial distribution and morphology protein 35
B: Protein UPS1, mitochondrial
C: Mitochondrial distribution and morphology protein 35
D: Protein UPS1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6966
Polymers62,9594
Non-polymers7372
Water0
1
A: Mitochondrial distribution and morphology protein 35
B: Protein UPS1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8483
Polymers31,4802
Non-polymers3681
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-8 kcal/mol
Surface area13790 Å2
MethodPISA
2
C: Mitochondrial distribution and morphology protein 35
D: Protein UPS1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8483
Polymers31,4802
Non-polymers3681
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-9 kcal/mol
Surface area14380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.140, 90.140, 81.319
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Mitochondrial distribution and morphology protein 35


Mass: 9723.954 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Gene: MDM35, YKL053C-A / Production host: Escherichia coli (E. coli) / References: UniProt: O60200
#2: Protein Protein UPS1, mitochondrial / Unprocessed MGM1 protein 1


Mass: 21755.670 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Gene: UPS1, YLR193C / Production host: Escherichia coli (E. coli) / References: UniProt: Q05776
#3: Chemical ChemComp-44E / (2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate


Mass: 368.360 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H29O8P / 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: 2.62 Å3/Da / Density % sol: 53.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1M Bis-tris Propane, 30%-32% v/v Tacsimate, pH7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9786 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jul 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 3.549→50 Å / Num. obs: 8015 / % possible obs: 100 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.022 / Rrim(I) all: 0.057 / Χ2: 1 / Net I/σ(I): 6.4
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
3.55-3.616.90.674070.8490.2730.7240.884
3.61-3.6870.5783910.8340.2360.6250.96
3.68-3.756.90.5244030.8460.2150.5670.899
3.75-3.826.80.3853900.9340.1590.4170.946
3.82-3.916.70.3424000.9450.1430.3710.915
3.91-46.40.2563910.9610.1090.2781.003
4-4.16.20.2224120.9770.0970.2430.98
4.1-4.216.50.1663900.9860.0710.1811.065
4.21-4.3370.1394030.990.0560.151.104
4.33-4.477.20.1233830.9910.050.1331.154
4.47-4.637.10.1083980.9950.0440.1171.203
4.63-4.827.10.0953970.9940.0380.1021.256
4.82-5.0470.0824140.9950.0340.0891.168
5.04-5.36.90.0814010.9960.0330.0881.091
5.3-5.636.70.0773970.9950.0320.0840.976
5.63-6.076.10.0674060.9960.030.0740.916
6.07-6.686.60.0523890.9980.0220.0570.877
6.68-7.6470.0434150.9980.0180.0470.82
7.64-9.616.80.0324000.9990.0130.0340.833
9.61-506.10.0294280.9990.0130.0320.917

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JQL

5jql


Resolution: 3.55→45.07 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.11
RfactorNum. reflection% reflection
Rfree0.3103 776 10.01 %
Rwork0.2869 --
obs0.2892 7750 96.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 90.09 Å2 / Biso mean: 34.7814 Å2 / Biso min: 21.15 Å2
Refinement stepCycle: final / Resolution: 3.55→45.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3281 0 44 0 3325
Biso mean--37.44 --
Num. residues----440
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.55-3.77120.38551120.304298782
3.7712-4.06220.30771310.30721191100
4.0622-4.47070.30361320.26541177100
4.4707-5.11690.25961310.25371194100
5.1169-6.44370.29861320.31211215100
6.4437-45.070.33161380.2919121099
Refinement TLS params.Method: refined / Origin x: -0.6368 Å / Origin y: 45.9889 Å / Origin z: -9.4485 Å
111213212223313233
T0.2932 Å2-0.371 Å2-0.0573 Å2-0.3012 Å2-0.0545 Å2--0.1446 Å2
L0.3154 °20.3655 °2-0.4426 °2-0.3172 °2-0.4436 °2--0.5652 °2
S0.0215 Å °-0.0168 Å °0.0356 Å °-0.0013 Å °0.007 Å °0.0393 Å °-0.0013 Å °-0.0105 Å °-0.0164 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA6 - 74
2X-RAY DIFFRACTION1allB0 - 166
3X-RAY DIFFRACTION1allC5 - 74
4X-RAY DIFFRACTION1allD0 - 166
5X-RAY DIFFRACTION1allE1
6X-RAY DIFFRACTION1allF2

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