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- PDB-5jql: Crystal Structure of Phosphatidic acid Transporter Ups1/Mdm35 Voi... -

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Basic information

Entry
Database: PDB / ID: 5jql
TitleCrystal Structure of Phosphatidic acid Transporter Ups1/Mdm35 Void of Bound Phospholipid from Saccharomyces Cerevisiae at 2.9 Angstroms Resolution
Components
  • (Mitochondrial distribution and morphology protein 35) x 2
  • (Protein UPS1, mitochondrial) x 3
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 / intermembrane lipid transfer / phospholipid transport / phospholipid translocation / mitochondrion organization / mitochondrial intermembrane space ...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 / intermembrane lipid transfer / phospholipid transport / phospholipid translocation / mitochondrion organization / mitochondrial intermembrane space / mitochondrial inner membrane / lipid binding / mitochondrion / nucleus / 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
Mitochondrial distribution and morphology protein 35 / Protein UPS1, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsLu, J. / Chan, K.C. / Zhai, Y. / Fan, J. / Sun, F.
Funding support China, 1items
OrganizationGrant numberCountry
China
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
DepositionMay 5, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 12, 2017Provider: 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 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Protein UPS1, mitochondrial
B: Mitochondrial distribution and morphology protein 35
C: Protein UPS1, mitochondrial
D: Mitochondrial distribution and morphology protein 35
E: Protein UPS1, mitochondrial
F: Mitochondrial distribution and morphology protein 35
G: Protein UPS1, mitochondrial
H: Mitochondrial distribution and morphology protein 35
I: Protein UPS1, mitochondrial
J: Mitochondrial distribution and morphology protein 35
K: Protein UPS1, mitochondrial
L: Mitochondrial distribution and morphology protein 35


Theoretical massNumber of molelcules
Total (without water)190,19112
Polymers190,19112
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36630 Å2
ΔGint-301 kcal/mol
Surface area67260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.311, 130.736, 84.271
Angle α, β, γ (deg.)90.000, 103.090, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Protein UPS1, mitochondrial / Unprocessed MGM1 protein 1


Mass: 21943.250 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: UPS1, YLR193C / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q05776
#2: Protein
Mitochondrial distribution and morphology protein 35


Mass: 9723.954 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: MDM35, YKL053C-A / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O60200
#3: Protein Protein UPS1, mitochondrial / Unprocessed MGM1 protein 1


Mass: 21990.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: UPS1, YLR193C / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q05776
#4: Protein Protein UPS1, mitochondrial / Unprocessed MGM1 protein 1


Mass: 22037.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: UPS1, YLR193C / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q05776
#5: Protein Mitochondrial distribution and morphology protein 35


Mass: 9770.850 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: MDM35, YKL053C-A / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O60200
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: 2.35 Å3/Da / Density % sol: 47.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 8% Tacsimate, pH5.0, 20% PEG 3350, 200mM Sodium thiocyanate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 76995 / % possible obs: 98.4 % / Redundancy: 3.6 % / Biso Wilson estimate: 70.36 Å2 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.045 / Rrim(I) all: 0.087 / Χ2: 2.797 / Net I/av σ(I): 31.707 / Net I/σ(I): 14.9 / Num. measured all: 279505
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.9-2.953.60.438197
2.95-33.60.406197.3
3-3.063.60.348198.4
3.06-3.123.60.276198.1
3.12-3.193.60.224198.3
3.19-3.273.60.182199
3.27-3.353.70.151198.5
3.35-3.443.70.133199.3
3.44-3.543.70.123199.2
3.54-3.653.70.103199.1
3.65-3.783.70.092199.1
3.78-3.943.70.087199.3
3.94-4.113.70.084199
4.11-4.333.70.076199
4.33-4.63.60.067198.9
4.6-4.963.60.062198.9
4.96-5.463.60.059198.7
5.46-6.243.50.06197.1
6.24-7.863.60.053199.6
7.86-503.50.043194

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.2data extraction
HKL-2000data scaling
PHENIX1.8_1069phasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→48.404 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.51
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2477 3845 5 %
Rwork0.2001 --
obs0.2025 76953 97.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 168.67 Å2 / Biso mean: 38.11 Å2 / Biso min: 0.13 Å2
Refinement stepCycle: final / Resolution: 2.9→48.404 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11018 0 0 0 11018
Num. residues----1432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111287
X-RAY DIFFRACTIONf_angle_d1.3115300
X-RAY DIFFRACTIONf_chiral_restr0.0771726
X-RAY DIFFRACTIONf_plane_restr0.0071928
X-RAY DIFFRACTIONf_dihedral_angle_d13.3783986
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8715-2.90790.3682980.29871945204370
2.9079-2.94610.29681400.28082681282197
2.9461-2.98650.34411590.2782794295397
2.9865-3.02910.32831340.29692654278898
3.0291-3.07430.37441290.27432714284398
3.0743-3.12240.31431490.24952755290498
3.1224-3.17360.30211360.24992729286598
3.1736-3.22830.26811490.24952797294699
3.2283-3.2870.35321440.22772713285799
3.287-3.35020.24771440.22012755289999
3.3502-3.41850.2681470.21332717286499
3.4185-3.49280.26071410.2162782292399
3.4928-3.57410.281600.212737289799
3.5741-3.66340.26521340.19042780291499
3.6634-3.76240.23311470.19592760290799
3.7624-3.87310.27091490.19492772292199
3.8731-3.99810.27181430.19452774291799
3.9981-4.14090.22861470.19632705285299
4.1409-4.30660.21541490.17662776292599
4.3066-4.50240.19161420.15852761290399
4.5024-4.73960.17491450.14762753289899
4.7396-5.03630.19641570.1562717287498
5.0363-5.42470.25951370.16692725286299
5.4247-5.96970.2271430.19592781292497
5.9697-6.83150.25031450.20682689283498
6.8315-8.5990.27741430.20812773291699
8.599-48.41120.21321340.20822569270392

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