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- PDB-6i3v: x-ray structure of the human mitochondrial PRELID1 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 6i3v
Titlex-ray structure of the human mitochondrial PRELID1 in complex with TRIAP1
Components
  • PRELI domain-containing protein 1, mitochondrial
  • TP53-regulated inhibitor of apoptosis 1
KeywordsLIPID BINDING PROTEIN / prelid1 lipid transport mitochondrial protein
Function / homology
Function and homology information


regulation of membrane lipid distribution / positive regulation of phospholipid transport / positive regulation of endopeptidase activity / positive regulation of cellular respiration / intermembrane lipid transfer / positive regulation of T cell apoptotic process / phospholipid transport / phospholipid translocation / regulation of T cell differentiation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator ...regulation of membrane lipid distribution / positive regulation of phospholipid transport / positive regulation of endopeptidase activity / positive regulation of cellular respiration / intermembrane lipid transfer / positive regulation of T cell apoptotic process / phospholipid transport / 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 / 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
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
MYRISTIC ACID / TP53-regulated inhibitor of apoptosis 1 / PRELI domain-containing protein 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.98 Å
AuthorsBerry, J.L. / Miliara, X. / Morgan, R.M.L. / Matthews, S.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
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 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,85522
Polymers58,8694
Non-polymers98718
Water5,567309
1
B: PRELI domain-containing protein 1, mitochondrial
C: TP53-regulated inhibitor of apoptosis 1
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)59,85522
Polymers58,8694
Non-polymers98718
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z1
Buried area15220 Å2
ΔGint-220 kcal/mol
Surface area23250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.312, 127.312, 177.390
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11B-401-

HOH

21A-139-

HOH

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Components

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Protein , 2 types, 4 molecules FBAC

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


Mass: 21350.119 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRELID1, PRELI, CGI-106, SBBI12 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y255
#2: Protein TP53-regulated inhibitor of apoptosis 1 / Protein 15E1.1 / WF-1 / p53-inducible cell-survival factor / p53CSV


Mass: 8084.181 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIAP1, 15E1.1, HSPC132 / Production host: Escherichia coli (E. coli) / References: UniProt: O43715

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Non-polymers , 4 types, 327 molecules

#3: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O2
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 3.52 Å3/Da / Density % sol: 65.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM CHES/ Sodium hydroxide pH 9.5 200 mM Sodium chloride 40% (v/v) PEG 300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.98→93.642 Å / Num. obs: 59554 / % possible obs: 99 % / Redundancy: 19.7 % / Net I/σ(I): 19
Reflection shellResolution: 1.98→2.05 Å

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 1.98→93.642 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.75
RfactorNum. reflection% reflection
Rfree0.2452 2941 4.97 %
Rwork0.2052 --
obs0.2072 59216 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 154.25 Å2 / Biso mean: 47.3652 Å2 / Biso min: 18.5 Å2
Refinement stepCycle: final / Resolution: 1.98→93.642 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3964 0 48 309 4321
Biso mean--54.68 52.82 -
Num. residues----493
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0164097
X-RAY DIFFRACTIONf_angle_d1.2985536
X-RAY DIFFRACTIONf_chiral_restr0.076587
X-RAY DIFFRACTIONf_plane_restr0.007707
X-RAY DIFFRACTIONf_dihedral_angle_d15.0422438
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9795-2.0120.38071340.34472554268897
2.012-2.04670.35251480.3382609275798
2.0467-2.08390.39171410.32582612275399
2.0839-2.1240.35381240.31822624274899
2.124-2.16730.34241320.2912618275099
2.1673-2.21450.31981260.28622640276699
2.2145-2.2660.33891380.26862646278499
2.266-2.32260.35141440.255226532797100
2.3226-2.38550.28861510.242826282779100
2.3855-2.45560.27521300.22626702800100
2.4556-2.53490.26991310.21392652278399
2.5349-2.62550.2751530.205126612814100
2.6255-2.73070.21691530.202226572810100
2.7307-2.85490.29091260.206826862812100
2.8549-3.00550.25141480.203526922840100
3.0055-3.19380.24731360.195327102846100
3.1938-3.44040.20971560.181726952851100
3.4404-3.78660.21861510.170627202871100
3.7866-4.33450.181210.164627712892100
4.3345-5.4610.17121490.154228002949100
5.461-93.74650.25961490.211629773126100
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)
17.98110.18824.39715.692-0.00552.4320.2216-0.41530.29040.1933-0.56240.10260.4202-0.28190.15590.2848-0.01830.05320.47740.05320.3288-32.105655.0437-17.5044
22.8483-1.4089-3.05631.01271.66483.3560.08020.2726-0.0886-0.267-0.20160.18610.0317-0.74350.10440.282-0.0086-0.04050.40790.01790.2853-29.188651.8826-28.7524
32.2048-0.09070.15293.13020.49392.1656-0.14670.018-0.2233-0.35540.2995-0.29360.06720.2069-0.14310.2178-0.02770.02540.3136-0.01130.2251-12.844148.5915-33.5309
41.0774-0.6751-0.94831.05290.11891.7139-0.0354-0.19530.12360.00050.1434-0.1451-0.10690.1322-0.09250.2135-0.0353-0.01420.3349-0.02080.2795-14.906354.3037-21.176
51.37290.88040.58453.75233.17622.65350.05670.0484-0.0624-0.3895-0.14740.2874-0.1189-0.91780.21310.28-0.0216-0.02830.44460.01690.2677-28.329548.9683-28.7069
61.7213-0.2646-0.57122.10011.29471.68680.1243-0.48550.10390.3330.0862-0.1547-0.05630.7538-0.29290.2492-0.0861-00.3776-0.02480.2551-21.145765.50422.6296
72.30940.34680.05082.57411.70062.21980.3007-0.2616-0.04880.2011-0.095-0.4704-0.22740.9547-0.08440.2506-0.1321-0.07470.42650.01480.342-38.218159.0151-17.329
81.85910.0379-0.30261.2747-0.6673.16090.010.34570.1345-0.12520.29540.27820.0366-0.6673-0.26040.1888-0.0637-0.0130.40630.07690.2995-51.774258.6762-21.9058
91.9166-0.29321.14181.4028-0.25632.0253-0.0493-0.21940.03250.14540.0590.064-0.15640.01650.06570.241-0.01070.00580.2608-0.01730.2346-41.198948.941726.6342
108.10680.26290.13517.70380.17726.30590.09450.82250.6364-0.85630.3298-0.5062-0.32270.5862-0.25730.3481-0.12440.10490.5173-0.01750.459-2.921657.5939-33.383
118.90734.70643.03115.28711.61185.20410.08370.2819-0.5984-0.57740.093-0.81910.23640.6129-0.22130.35150.03660.1130.4395-0.0890.4283-5.087843.3871-39.1202
121.9153-0.0531-0.58274.12182.27596.84970.11950.0019-0.5265-0.22890.1448-0.95050.16671.1889-0.17080.27770.10480.04230.6954-0.18380.62013.987146.1325-28.2424
131.3751-0.462.3925.71881.47167.49910.3421-0.872-0.34090.3928-0.0809-0.08550.66840.2908-0.20010.27370.0633-0.00530.44990.00980.351-7.528846.5543-17.2921
146.9331-0.8006-1.09636.941.27895.24470.12311.2115-0.4792-0.88070.09750.52260.2012-0.95340.04160.5206-0.2472-0.12921.08950.08380.5998-65.2850.8597-27.5769
151.1691-0.04420.22791.4378-0.2971.16540.32140.4702-0.1007-0.4098-0.19120.57190.2276-0.7367-0.80570.291-0.102-0.26861.33690.36790.6866-66.744160.3223-32.9636
163.22652.9543-0.3332.7069-0.34680.37430.25080.55971.10430.11030.50851.1735-0.7034-1.2828-0.68140.61520.14630.06091.09240.46140.7803-61.385373.0631-37.6717
172.9421-0.2817-0.09230.71560.30490.5740.04540.57520.692-0.1657-0.00940.3351-0.1338-0.4921-0.29690.23740.07980.12691.29130.46961.0018-71.903761.2921-21.8482
183.8773.7948-5.17693.7789-5.17017.11380.3782-0.11910.40120.5173-0.10110.217-0.6594-0.1565-0.3130.39590.07970.14620.59850.11730.6198-59.618265.0513-12.0133
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'F' and (resid 4 through 14 )F4 - 14
2X-RAY DIFFRACTION2chain 'F' and (resid 15 through 26 )F15 - 26
3X-RAY DIFFRACTION3chain 'F' and (resid 27 through 61 )F27 - 61
4X-RAY DIFFRACTION4chain 'F' and (resid 62 through 128 )F62 - 128
5X-RAY DIFFRACTION5chain 'F' and (resid 129 through 147 )F129 - 147
6X-RAY DIFFRACTION6chain 'F' and (resid 148 through 185 )F148 - 185
7X-RAY DIFFRACTION7chain 'B' and (resid 12 through 23 )B12 - 23
8X-RAY DIFFRACTION8chain 'B' and (resid 24 through 147 )B24 - 147
9X-RAY DIFFRACTION9chain 'B' and (resid 148 through 184 )B148 - 184
10X-RAY DIFFRACTION10chain 'A' and (resid 12 through 18 )A12 - 18
11X-RAY DIFFRACTION11chain 'A' and (resid 19 through 50 )A19 - 50
12X-RAY DIFFRACTION12chain 'A' and (resid 51 through 67 )A51 - 67
13X-RAY DIFFRACTION13chain 'A' and (resid 68 through 80 )A68 - 80
14X-RAY DIFFRACTION14chain 'C' and (resid 12 through 18 )C12 - 18
15X-RAY DIFFRACTION15chain 'C' and (resid 19 through 38 )C19 - 38
16X-RAY DIFFRACTION16chain 'C' and (resid 39 through 50 )C39 - 50
17X-RAY DIFFRACTION17chain 'C' and (resid 51 through 68 )C51 - 68
18X-RAY DIFFRACTION18chain 'C' and (resid 69 through 80 )C69 - 80

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