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- PDB-4xhr: Structure of a phospholipid trafficking complex, native -

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Basic information

Entry
Database: PDB / ID: 4xhr
TitleStructure of a phospholipid trafficking complex, native
Components
  • Mitochondrial distribution and morphology protein 35
  • Protein UPS1, mitochondrial
KeywordsLIPID TRANSPORT/OXIDOREDUCTASE / phospholipid / LIPID TRANSPORT-OXIDOREDUCTASE complex
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: 2.55 Å
AuthorsYu, F. / He, F. / Wang, C. / Zhang, P.
CitationJournal: Embo Rep. / Year: 2015
Title: Structural basis of intramitochondrial phosphatidic acid transport mediated by Ups1-Mdm35 complex
Authors: Yu, F. / He, F. / Yao, H. / Wang, C. / Wang, J. / Li, J. / Qi, X. / Xue, H. / Ding, J. / Zhang, P.
History
DepositionJan 6, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein UPS1, mitochondrial
N: Mitochondrial distribution and morphology protein 35
B: Protein UPS1, mitochondrial
M: Mitochondrial distribution and morphology protein 35


Theoretical massNumber of molelcules
Total (without water)62,9594
Polymers62,9594
Non-polymers00
Water68538
1
A: Protein UPS1, mitochondrial
N: Mitochondrial distribution and morphology protein 35


Theoretical massNumber of molelcules
Total (without water)31,4802
Polymers31,4802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-17 kcal/mol
Surface area12560 Å2
MethodPISA
2
B: Protein UPS1, mitochondrial
M: Mitochondrial distribution and morphology protein 35


Theoretical massNumber of molelcules
Total (without water)31,4802
Polymers31,4802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-18 kcal/mol
Surface area13090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.968, 74.868, 87.568
Angle α, β, γ (deg.)90.00, 95.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: UPS1, YLR193C / Production host: Escherichia coli (E. coli) / References: UniProt: Q05776
#2: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: MDM35, YKL053C-A / Production host: Escherichia coli (E. coli) / References: UniProt: O60200
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.23 Å3/Da / Density % sol: 44.78 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 2%(v/v) Tacsimate pH 6.0, 0.1M Bis-Tris pH 6.5, 20%(w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.7 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7 Å / Relative weight: 1
ReflectionResolution: 2.55→32.08 Å / Num. obs: 17640 / % possible obs: 97.17 % / Redundancy: 3.5 % / Net I/σ(I): 11.96
Reflection shellResolution: 2.55→3 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.116 / Mean I/σ(I) obs: 11.96 / % possible all: 97.17

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.55→32.08 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.891 / SU B: 25.837 / SU ML: 0.26 / Cross valid method: THROUGHOUT / ESU R: 1.232 / ESU R Free: 0.353 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27736 886 5.1 %RANDOM
Rwork0.2363 ---
obs0.23837 16623 96.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 78.621 Å2
Baniso -1Baniso -2Baniso -3
1--5.72 Å20 Å22.49 Å2
2--6.37 Å20 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 2.55→32.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3869 0 0 38 3907
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.150.023961
X-RAY DIFFRACTIONr_bond_other_d00.023726
X-RAY DIFFRACTIONr_angle_refined_deg1.8611.9435350
X-RAY DIFFRACTIONr_angle_other_deg3.5083.0028601
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9995476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.93623.864176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.48615708
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6791522
X-RAY DIFFRACTIONr_chiral_restr0.070.2587
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214378
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02916
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.55→2.619 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 52 -
Rwork0.314 1250 -
obs--97.38 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.24480.3320.24340.55320.35691.89540.028-0.19970.0061-0.0433-0.01690.046-0.07640.089-0.01110.1489-0.0032-0.07430.0526-0.03440.126560.4324-10.7839.2214
21.65050.1899-0.55970.93040.51822.50060.00580.323-0.336-0.07830.08430.0344-0.04040.0466-0.09010.2133-0.0026-0.07840.08-0.06870.143760.1617-14.079220.7976
31.85360.02440.04730.53270.56111.8234-0.0187-0.0128-0.02670.0155-0.0173-0.0166-0.08560.06770.0360.13350.0177-0.09590.0161-0.00050.11260.6055-42.979716.6653
44.57080.78870.08441.5161-0.2782.1093-0.04130.59350.12070.01630.08330.1612-0.18740.1155-0.0420.19330.0396-0.06580.2393-0.03060.047760.4373-40.9843-1.8287
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 170
2X-RAY DIFFRACTION2N6 - 76
3X-RAY DIFFRACTION3B1 - 170
4X-RAY DIFFRACTION4M5 - 76

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