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- PDB-8ag0: Crystal structure of mutant PRELID3a-TRIAP1 complex - R53E -

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Basic information

Entry
Database: PDB / ID: 8ag0
TitleCrystal structure of mutant PRELID3a-TRIAP1 complex - R53E
Components
  • Maltose/maltodextrin-binding periplasmic protein,TP53-regulated inhibitor of apoptosis 1
  • PRELI domain containing protein 3A
KeywordsLIPID TRANSPORT / Complex / phospholipid transport / mitochondria
Function / homology
Function and homology information


regulation of membrane lipid distribution / phosphatidic acid transfer activity / positive regulation of phospholipid transport / intermembrane lipid transfer / phospholipid transport / phospholipid translocation / 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 / detection of maltose stimulus / maltose transport complex ...regulation of membrane lipid distribution / phosphatidic acid transfer activity / positive regulation of phospholipid transport / intermembrane lipid transfer / phospholipid transport / phospholipid translocation / 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 / detection of maltose stimulus / maltose transport complex / maltose binding / carbohydrate transport / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / maltose transport / maltodextrin transmembrane transport / DNA damage response, signal transduction by p53 class mediator / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / Mitochondrial protein degradation / ATP-binding cassette (ABC) transporter complex / : / cell chemotaxis / mitochondrial intermembrane space / cellular response to UV / p53 binding / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / negative regulation of apoptotic process / apoptotic process / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / nucleoplasm / membrane / 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) / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. ...PRELI/MSF1 domain / Slowmo/Ups family / PRELI-like family / PRELI/MSF1 domain profile. / Mitochondrial distribution/morphology family 35/apoptosis / Uncharacterised protein family (UPF0203) / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
TP53-regulated inhibitor of apoptosis 1 / Maltose/maltodextrin-binding periplasmic protein / PRELI domain containing protein 3A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMilara, X. / Perez-Dorado, J.I. / Matthews, S.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/M019403/1 United Kingdom
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2022
Title: An intermolecular hydrogen bonded network in the PRELID-TRIAP protein family plays a role in lipid sensing.
Authors: Miliara, X. / Tatsuta, T. / Eiyama, A. / Langer, T. / Rouse, S.L. / Matthews, S.
History
DepositionJul 18, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PRELI domain containing protein 3A
B: Maltose/maltodextrin-binding periplasmic protein,TP53-regulated inhibitor of apoptosis 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2443
Polymers69,9012
Non-polymers3421
Water88349
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.300, 66.815, 82.140
Angle α, β, γ (deg.)90.000, 96.460, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein PRELI domain containing protein 3A / Protein slowmo homolog 1


Mass: 20961.900 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRELID3A, C18orf43, SLMO1 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q96N28
#2: Protein Maltose/maltodextrin-binding periplasmic protein,TP53-regulated inhibitor of apoptosis 1 / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / Protein 15E1.1 / WF-1 / p53- ...MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / Protein 15E1.1 / WF-1 / p53-inducible cell-survival factor / p53CSV


Mass: 48939.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: K12 / Gene: malE, b4034, JW3994, TRIAP1, 15E1.1, HSPC132 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9, UniProt: O43715
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.6 Å3/Da / Density % sol: 52.73 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: Sodium acetate pH 4.6, 8% (w/v) PEG 4000

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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: PSI PILATUS 6M / Detector: PIXEL / Date: May 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.7→45.41 Å / Num. obs: 18444 / % possible obs: 99.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 55.12 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 8.1
Reflection shellResolution: 2.7→2.83 Å / Rmerge(I) obs: 0.62 / Num. unique obs: 2445

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZXV

4zxv


Resolution: 2.7→45.41 Å / SU ML: 0.4932 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.4144
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3036 964 5.23 %
Rwork0.2135 17452 -
obs0.2184 18416 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.09 Å2
Refinement stepCycle: LAST / Resolution: 2.7→45.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4523 0 23 49 4595
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00824652
X-RAY DIFFRACTIONf_angle_d1.06646334
X-RAY DIFFRACTIONf_chiral_restr0.0588715
X-RAY DIFFRACTIONf_plane_restr0.0085813
X-RAY DIFFRACTIONf_dihedral_angle_d7.7641640
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.840.42361260.33152487X-RAY DIFFRACTION99.09
2.84-3.020.36171360.29662477X-RAY DIFFRACTION98.75
3.02-3.250.3651410.26272456X-RAY DIFFRACTION98.75
3.25-3.580.35151310.2462473X-RAY DIFFRACTION98.86
3.58-4.10.30531430.19782487X-RAY DIFFRACTION98.65
4.1-5.160.23041490.16612515X-RAY DIFFRACTION99.48
5.16-45.410.28931380.192557X-RAY DIFFRACTION99.04
Refinement TLS params.Method: refined / Origin x: -9.68885940322 Å / Origin y: 15.6777461761 Å / Origin z: -46.5987700059 Å
111213212223313233
T0.299391905172 Å2-0.0796625277538 Å2-0.021948613208 Å2-0.264584160853 Å2-0.0391607459029 Å2--0.483643859432 Å2
L1.21598789284 °2-0.353631539075 °20.0788655295472 °2-0.845979247917 °2-0.498780773811 °2--2.24501821445 °2
S0.0429306078544 Å °0.0359271021135 Å °-0.0624637413474 Å °-0.150423564649 Å °-0.030660780078 Å °0.0511374740123 Å °0.103114094781 Å °-0.290096972609 Å °-0.00773904667112 Å °
Refinement TLS groupSelection details: all

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