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- PDB-4ytw: Crystal structure of Ups1-Mdm35 complex -

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Basic information

Entry
Database: PDB / ID: 4ytw
TitleCrystal structure of Ups1-Mdm35 complex
Components
  • Mitochondrial distribution and morphology protein 35
  • Protein UPS1, mitochondrial
KeywordsLIPID TRANSPORT / Phospholipid transfer / Mitochondria
Function / homology
Function and homology information


TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / cardiolipin metabolic process / phosphatidic acid transfer activity / regulation of membrane lipid distribution / positive regulation of phosphatidylcholine biosynthetic process / mitochondrial respiratory chain complex assembly / intermembrane phospholipid transfer / phospholipid transport / mitochondrion organization / mitochondrial intermembrane space ...TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / cardiolipin metabolic process / phosphatidic acid transfer activity / regulation of membrane lipid distribution / positive regulation of phosphatidylcholine biosynthetic process / mitochondrial respiratory chain complex assembly / intermembrane phospholipid transfer / phospholipid transport / 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: 1.4 Å
AuthorsWatanabe, Y. / Tamura, Y. / Kawano, S. / Endo, T.
CitationJournal: Nat Commun / Year: 2015
Title: Structural and mechanistic insights into phospholipid transfer by Ups1-Mdm35 in mitochondria.
Authors: Watanabe, Y. / Tamura, Y. / Kawano, S. / Endo, T.
History
DepositionMar 18, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Feb 5, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 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

Downloads & links

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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


Theoretical massNumber of molelcules
Total (without water)60,4684
Polymers60,4684
Non-polymers00
Water9,728540
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10570 Å2
ΔGint-90 kcal/mol
Surface area24750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.750, 71.746, 87.607
Angle α, β, γ (deg.)90.00, 95.02, 90.00
Int Tables number4
Space group name H-MP1211
DetailsChain B and D form a domain-swapped dimer because of the crystallization artifact. The chain B(1-134) and D(135-169) comprise one molecule. The chain D(1-134) and B(135-169) comprise one molecule. The biological assembly is two dimers #1 chain A and B(1-134)/D(135-169), #2 chain C and D(1-134)/B(135-169)

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Components

#1: Protein Mitochondrial distribution and morphology protein 35


Mass: 9122.262 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-81
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: MDM35, YKL053C-A / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7 / References: UniProt: O60200
#2: Protein Protein UPS1, mitochondrial / Unprocessed MGM1 protein 1


Mass: 21111.955 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: UPS1, YLR193C / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7 / References: UniProt: Q05776
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 540 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M ammonium citrate pH 7.0, 20% PEG 3350

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 103802 / % possible obs: 99.8 % / Redundancy: 7.3 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 41.6
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.824 / Mean I/σ(I) obs: 2.2 / % possible all: 99.5

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Processing

Software
NameVersionClassification
CNS1.3refinement
HKL-2000data collection
PHENIXmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.4→29.23 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 146529.97 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.236 9667 10.1 %RANDOM
Rwork0.22 ---
obs0.22 96066 92.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.7927 Å2 / ksol: 0.45 e/Å3
Displacement parametersBiso mean: 23.3 Å2
Baniso -1Baniso -2Baniso -3
1--5.02 Å20 Å2-0.2 Å2
2--9.65 Å20 Å2
3----4.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.24 Å
Refinement stepCycle: 1 / Resolution: 1.4→29.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3869 0 0 540 4409
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.241.5
X-RAY DIFFRACTIONc_mcangle_it1.962
X-RAY DIFFRACTIONc_scbond_it2.142
X-RAY DIFFRACTIONc_scangle_it3.212.5
LS refinement shellResolution: 1.4→1.49 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.351 1414 10.1 %
Rwork0.348 12619 -
obs--81.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR/protein_rep.paramCNS_TOPPAR/protein.top
X-RAY DIFFRACTION2CNS_TOPPAR/dna-rna_rep.paramCNS_TOPPAR/dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR/water_rep.paramCNS_TOPPAR/water.top
X-RAY DIFFRACTION4CNS_TOPPAR/ion.paramCNS_TOPPAR/ion.top
X-RAY DIFFRACTION5CNS_TOPPAR/carbohydrate.paramCNS_TOPPAR/carbohydrate.top

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