- PDB-6i3y: Crystal structure of the human mitochondrial PRELID1K58V-TRIAP1 c... -
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Basic information
Entry
Database: PDB / ID: 6i3y
Title
Crystal structure of the human mitochondrial PRELID1K58V-TRIAP1 complex with PS
Components
PRELI domain-containing protein 1, mitochondrial
TP53-regulated inhibitor of apoptosis 1
Keywords
LIPID 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 cellular respiration / positive regulation of endopeptidase activity / 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 cellular respiration / positive regulation of endopeptidase activity / 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 / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / negative regulation of mitochondrial membrane potential / 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
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.
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
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.29892
874
4.9 %
RANDOM
Rwork
0.24376
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-
-
obs
0.24672
16844
99.84 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parameters
Biso mean: 105.079 Å2
Baniso -1
Baniso -2
Baniso -3
1-
3.88 Å2
1.94 Å2
0 Å2
2-
-
3.88 Å2
0 Å2
3-
-
-
-12.6 Å2
Refinement step
Cycle: 1 / Resolution: 2.98→63 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3817
0
61
21
3899
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.011
0.019
3981
X-RAY DIFFRACTION
r_bond_other_d
0.004
0.02
3456
X-RAY DIFFRACTION
r_angle_refined_deg
1.527
1.923
5410
X-RAY DIFFRACTION
r_angle_other_deg
1.16
3
7928
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.595
5
493
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.053
23.046
174
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
20.619
15
575
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
21.999
15
24
X-RAY DIFFRACTION
r_chiral_restr
0.087
0.2
596
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
4457
X-RAY DIFFRACTION
r_gen_planes_other
0.003
0.02
891
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
8.066
11.225
1987
X-RAY DIFFRACTION
r_mcbond_other
8.069
11.23
1985
X-RAY DIFFRACTION
r_mcangle_it
12.384
16.841
2475
X-RAY DIFFRACTION
r_mcangle_other
12.384
16.841
2475
X-RAY DIFFRACTION
r_scbond_it
8.267
11.501
1994
X-RAY DIFFRACTION
r_scbond_other
8.264
11.496
1995
X-RAY DIFFRACTION
r_scangle_it
X-RAY DIFFRACTION
r_scangle_other
12.714
17.062
2936
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.98→3.057 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.521
62
-
Rwork
0.395
1214
-
obs
-
-
99.84 %
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