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- PDB-6i4y: X-ray structure of the human mitochondrial PRELID3b-TRIAP1 complex -

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Basic information

Entry
Database: PDB / ID: 6i4y
TitleX-ray structure of the human mitochondrial PRELID3b-TRIAP1 complex
Components
  • Maltose transport system, substrate-binding protein,TP53-regulated inhibitor of apoptosis 1
  • PRELI domain containing protein 3B
KeywordsLIPID TRANSPORT / Mitochondrial lipid transport / Complex / Phospholipid transporter / Apoptosis / Phosphatidylserine / PS transport
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 / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / mitotic G1 DNA damage checkpoint signaling / Mitochondrial protein degradation / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / DNA damage response, signal transduction by p53 class mediator / mitochondrial intermembrane space / p53 binding / cellular response to UV / outer membrane-bounded periplasmic space / periplasmic space / apoptotic process / DNA damage response / negative regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / nucleoplasm / nucleus / membrane
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 / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. ...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 / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
alpha-maltose / Maltodextrin-binding protein / TP53-regulated inhibitor of apoptosis 1 / Maltose/maltodextrin-binding periplasmic protein / PRELI domain containing protein 3B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 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 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose transport system, substrate-binding protein,TP53-regulated inhibitor of apoptosis 1
B: PRELI domain containing protein 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4324
Polymers72,0672
Non-polymers3652
Water27015
1
A: Maltose transport system, substrate-binding protein,TP53-regulated inhibitor of apoptosis 1
B: PRELI domain containing protein 3B
hetero molecules

A: Maltose transport system, substrate-binding protein,TP53-regulated inhibitor of apoptosis 1
B: PRELI domain containing protein 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,8648
Polymers144,1334
Non-polymers7314
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
Buried area10830 Å2
ΔGint-92 kcal/mol
Surface area49200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.020, 133.000, 146.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Maltose transport system, substrate-binding protein,TP53-regulated inhibitor of apoptosis 1 / 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.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Gene: malE, NCTC8450_00456, NCTC9775_03059, TRIAP1, 15E1.1, HSPC132
Production host: Escherichia coli (E. coli) / Variant (production host): SHuffle
References: UniProt: A0A376KDN7, UniProt: O43715, UniProt: P0AEX9*PLUS
#2: Protein PRELI domain containing protein 3B / Protein slowmo homolog 2


Mass: 23127.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRELID3B, C20orf45, SLMO2, CGI-107 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y3B1
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.39 Å3/Da / Density % sol: 63.71 % / Description: multi plate ellipsoid shape
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: Tacsimate (60% v/v) pH 7

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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: Jul 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.91→76.23 Å / Num. obs: 20182 / % possible obs: 99.6 % / Redundancy: 7.3 % / Net I/σ(I): 15.8
Reflection shellResolution: 2.91→3.014 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XZV

4xzv


Resolution: 2.91→76.23 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.903 / SU B: 25.368 / SU ML: 0.431 / Cross valid method: THROUGHOUT / ESU R: 1.404 / ESU R Free: 0.429 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29635 972 4.8 %RANDOM
Rwork0.20983 ---
obs0.21394 19209 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 85.688 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å20 Å2
2--8.88 Å20 Å2
3----8.21 Å2
Refinement stepCycle: 1 / Resolution: 2.91→76.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4485 0 24 15 4524
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194632
X-RAY DIFFRACTIONr_bond_other_d0.0030.024055
X-RAY DIFFRACTIONr_angle_refined_deg1.4681.9496341
X-RAY DIFFRACTIONr_angle_other_deg1.09639399
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.195602
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.26825.469192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.70415660
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5891511
X-RAY DIFFRACTIONr_chiral_restr0.0810.2724
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215269
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02898
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_it5.5188.9532416
X-RAY DIFFRACTIONr_mcbond_other5.5038.9522415
X-RAY DIFFRACTIONr_mcangle_it8.56313.4223016
X-RAY DIFFRACTIONr_mcangle_other8.56413.4243017
X-RAY DIFFRACTIONr_scbond_it5.049.0052216
X-RAY DIFFRACTIONr_scbond_other5.0399.0052216
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.03213.4153326
X-RAY DIFFRACTIONr_long_range_B_refined13.01513.41519175
X-RAY DIFFRACTIONr_long_range_B_other13.00713.41519160
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.91→2.986 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.448 82 -
Rwork0.383 1374 -
obs--99.18 %

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