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- PDB-6i3y: Crystal structure of the human mitochondrial PRELID1K58V-TRIAP1 c... -

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Basic information

Entry
Database: PDB / ID: 6i3y
TitleCrystal structure of the human mitochondrial PRELID1K58V-TRIAP1 complex with PS
Components
  • PRELI domain-containing protein 1, mitochondrial
  • TP53-regulated inhibitor of apoptosis 1
KeywordsLIPID TRANSPORT / Mitochondrial lipid transport / Complex / Phosphatidylserine bound / PA transport / Apoptosis
Function / homology
Function and homology information


regulation of membrane lipid distribution / phosphatidic acid transfer activity / positive regulation of phospholipid transport / positive regulation of endopeptidase activity / positive regulation of cellular respiration / intermembrane lipid transfer / phospholipid transport / positive regulation of T cell apoptotic process / phospholipid translocation / regulation of T cell differentiation ...regulation of membrane lipid distribution / phosphatidic acid transfer activity / positive regulation of phospholipid transport / positive regulation of endopeptidase activity / positive regulation of cellular respiration / intermembrane lipid transfer / phospholipid transport / positive regulation of T cell apoptotic process / phospholipid translocation / regulation of T cell differentiation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / negative regulation of release of cytochrome c from mitochondria / negative regulation of mitochondrial membrane potential / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / DNA damage response, signal transduction by p53 class mediator / Mitochondrial protein degradation / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / regulation of mitochondrial membrane potential / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / mitochondrial intermembrane space / cellular response to UV / p53 binding / apoptotic process / negative regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / nucleoplasm / nucleus / cytosol
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
Chem-P5S / TP53-regulated inhibitor of apoptosis 1 / PRELI domain-containing protein 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsMiliara, X. / Berry, J.-L. / Morgan, R.M.L. / Matthews, S.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/M019403/1 United Kingdom
CitationJournal: Nat Commun / Year: 2019
Title: Structural determinants of lipid specificity within Ups/PRELI lipid transfer proteins.
Authors: Miliara, X. / Tatsuta, T. / Berry, J.L. / Rouse, S.L. / Solak, K. / Chorev, D.S. / Wu, D. / Robinson, C.V. / Matthews, S. / Langer, T.
History
DepositionNov 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant
Revision 1.2Jan 24, 2024Group: 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
C: PRELI domain-containing protein 1, mitochondrial
F: PRELI domain-containing protein 1, mitochondrial
A: TP53-regulated inhibitor of apoptosis 1
H: TP53-regulated inhibitor of apoptosis 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2357
Polymers64,1404
Non-polymers2,0953
Water37821
1
C: PRELI domain-containing protein 1, mitochondrial
H: TP53-regulated inhibitor of apoptosis 1
hetero molecules

F: PRELI domain-containing protein 1, mitochondrial
A: TP53-regulated inhibitor of apoptosis 1
hetero molecules


  • defined by author&software
  • Evidence: mass spectrometry, Lipidomics and native mass spectrometry used to confirm substrate binding. DOPS was exchanged to 25% in the PRELIK58V sample (see supplementary materials) upon incubation ...Evidence: mass spectrometry, Lipidomics and native mass spectrometry used to confirm substrate binding. DOPS was exchanged to 25% in the PRELIK58V sample (see supplementary materials) upon incubation of 10X (6:3) DDM-DOPS.
  • 66.2 kDa, 4 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)66,2357
Polymers64,1404
Non-polymers2,0953
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z1
Buried area11690 Å2
ΔGint-112 kcal/mol
Surface area23990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.000, 126.000, 178.320
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein PRELI domain-containing protein 1, mitochondrial / 25 kDa protein of relevant evolutionary and lymphoid interest / Px19-like protein


Mass: 21551.279 Da / Num. of mol.: 2 / Mutation: K58V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRELID1, PRELI, CGI-106, SBBI12 / Plasmid: pET_Duet / Production host: Escherichia coli (E. coli) / Variant (production host): SHuffle / References: UniProt: Q9Y255
#2: Protein TP53-regulated inhibitor of apoptosis 1 / Protein 15E1.1 / WF-1 / p53-inducible cell-survival factor / p53CSV


Mass: 10518.743 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIAP1, 15E1.1, HSPC132 / Plasmid: pRSF2 / Production host: Escherichia coli (E. coli) / Variant (production host): SHuffle / References: UniProt: O43715
#3: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#4: Chemical ChemComp-P5S / O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine / phosphatidyl serine / Phosphatidylserine


Mass: 792.075 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H82NO10P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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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: 3.32 Å3/Da / Density % sol: 62.93 % / Description: large hexagonal rods
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 100 mM sodium cacodylate pH 6.5 40% PEG 300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.98→63 Å / Num. obs: 17749 / % possible obs: 100 % / Redundancy: 37.1 % / Net I/σ(I): 9.1
Reflection shellResolution: 2.98→3.03 Å / Num. unique obs: 894 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6I3V

6i3v


Resolution: 2.98→63 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.927 / SU B: 28.173 / SU ML: 0.471 / Cross valid method: THROUGHOUT / ESU R: 1.311 / ESU R Free: 0.436 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29892 874 4.9 %RANDOM
Rwork0.24376 ---
obs0.24672 16844 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 105.079 Å2
Baniso -1Baniso -2Baniso -3
1-3.88 Å21.94 Å20 Å2
2--3.88 Å20 Å2
3----12.6 Å2
Refinement stepCycle: 1 / Resolution: 2.98→63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3817 0 61 21 3899
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193981
X-RAY DIFFRACTIONr_bond_other_d0.0040.023456
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.9235410
X-RAY DIFFRACTIONr_angle_other_deg1.1637928
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5955493
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.05323.046174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.61915575
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9991524
X-RAY DIFFRACTIONr_chiral_restr0.0870.2596
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024457
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02891
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_it8.06611.2251987
X-RAY DIFFRACTIONr_mcbond_other8.06911.231985
X-RAY DIFFRACTIONr_mcangle_it12.38416.8412475
X-RAY DIFFRACTIONr_mcangle_other12.38416.8412475
X-RAY DIFFRACTIONr_scbond_it8.26711.5011994
X-RAY DIFFRACTIONr_scbond_other8.26411.4961995
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other12.71417.0622936
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.98→3.057 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.521 62 -
Rwork0.395 1214 -
obs--99.84 %

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