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- PDB-4ytx: Crystal structure of Ups1-Mdm35 complex with PA -

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Basic information

Entry
Database: PDB / ID: 4ytx
TitleCrystal structure of Ups1-Mdm35 complex with PA
Components
  • Mitochondrial distribution and morphology protein 35
  • Protein UPS1, mitochondrial
KeywordsLIPID TRANSPORT / Phospholipid transfer / Mitochondria / Phosphatidic acid
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
1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE / Mitochondrial distribution and morphology protein 35 / Protein UPS1, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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 8, 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

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
E: Mitochondrial distribution and morphology protein 35
F: Protein UPS1, mitochondrial
G: Mitochondrial distribution and morphology protein 35
H: Protein UPS1, mitochondrial
I: Mitochondrial distribution and morphology protein 35
J: Protein UPS1, mitochondrial
K: Mitochondrial distribution and morphology protein 35
L: Protein UPS1, mitochondrial
M: Mitochondrial distribution and morphology protein 35
N: Protein UPS1, mitochondrial
O: Mitochondrial distribution and morphology protein 35
P: Protein UPS1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,94518
Polymers241,87416
Non-polymers1,0712
Water0
1
A: Mitochondrial distribution and morphology protein 35
B: Protein UPS1, mitochondrial
M: Mitochondrial distribution and morphology protein 35
N: Protein UPS1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0045
Polymers60,4684
Non-polymers5361
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9590 Å2
ΔGint-59 kcal/mol
Surface area26000 Å2
MethodPISA
2
C: Mitochondrial distribution and morphology protein 35
D: Protein UPS1, mitochondrial
E: Mitochondrial distribution and morphology protein 35
F: Protein UPS1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0045
Polymers60,4684
Non-polymers5361
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10340 Å2
ΔGint-66 kcal/mol
Surface area26470 Å2
MethodPISA
3
G: Mitochondrial distribution and morphology protein 35
H: Protein UPS1, mitochondrial
O: Mitochondrial distribution and morphology protein 35
P: Protein UPS1, mitochondrial


Theoretical massNumber of molelcules
Total (without water)60,4684
Polymers60,4684
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8170 Å2
ΔGint-60 kcal/mol
Surface area25870 Å2
MethodPISA
4
I: Mitochondrial distribution and morphology protein 35
J: Protein UPS1, mitochondrial
K: Mitochondrial distribution and morphology protein 35
L: Protein UPS1, mitochondrial


Theoretical massNumber of molelcules
Total (without water)60,4684
Polymers60,4684
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8950 Å2
ΔGint-66 kcal/mol
Surface area26680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)208.642, 154.670, 99.012
Angle α, β, γ (deg.)90.00, 104.42, 90.00
Int Tables number5
Space group name H-MC121
DetailsChain B and N form a domain-swapped dimer because of the crystallization artifact. The chain B(1-134) and N(135-169) comprise one molecule. The chain N(1-134) and B(135-169) comprise one molecule. The biological assembly is two dimers #1 chain A and B(1-134)/N(135-169), #2 chain M and N(1-134)/B(135-169). The other chains (C,E,D,F), chains (I,J,K,L), chains (G,O,H,P) have the same situation with #1 and #2.

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Components

#1: Protein
Mitochondrial distribution and morphology protein 35


Mass: 9122.262 Da / Num. of mol.: 8 / Fragment: UNP RESIDUES 1-81
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 / 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.: 8 / Fragment: UNP RESIDUES 1-170
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 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7 / References: UniProt: Q05776
#3: Chemical ChemComp-PX2 / 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE


Mass: 535.671 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H52O8P

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 61.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 10% PEG 6000, 5% MPD

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 50582 / % possible obs: 100 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 19.4
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.3refinement
HKL-2000data collection
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YTW

4ytw


Resolution: 3.2→43.23 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 38390.41 / 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
Rfree0.3 4772 10 %RANDOM
Rwork0.251 ---
obs0.251 47542 94.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.9785 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 94.6 Å2
Baniso -1Baniso -2Baniso -3
1--7.37 Å20 Å2-2.97 Å2
2---13.71 Å20 Å2
3---21.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 3.2→43.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15012 0 72 0 15084
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.43
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.421.5
X-RAY DIFFRACTIONc_mcangle_it2.552
X-RAY DIFFRACTIONc_scbond_it1.662
X-RAY DIFFRACTIONc_scangle_it2.762.5
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.369 708 9.9 %
Rwork0.317 6459 -
obs--85.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6dlpa.paramdlpa.top

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