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- PDB-4xzs: Crystal Structure of TRIAP1-MBP fusion -

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Basic information

Entry
Database: PDB / ID: 4xzs
TitleCrystal Structure of TRIAP1-MBP fusion
ComponentsMaltose-binding periplasmic protein,TP53-regulated inhibitor of apoptosis 1
KeywordsAPOPTOSIS / lipid / cX9cX motif / cancer / mitochondria / chaperone
Function / homology
Function and homology information


regulation of membrane lipid distribution / 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 / detection of maltose stimulus / negative regulation of release of cytochrome c from mitochondria / maltose transport complex / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release ...regulation of membrane lipid distribution / 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 / detection of maltose stimulus / negative regulation of release of cytochrome c from mitochondria / 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 / DNA damage response, signal transduction by p53 class mediator / cell chemotaxis / mitochondrial intermembrane space / cellular response to UV / p53 binding / 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
Mitochondrial distribution/morphology family 35/apoptosis / Uncharacterised protein family (UPF0203) / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / 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 / TP53-regulated inhibitor of apoptosis 1 / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsMiliara, X. / Garnett, J.A. / Abid-Ali, F. / Perez-Dorado, I. / Matthews, S.J.
CitationJournal: Embo Rep. / Year: 2015
Title: Structural insight into the TRIAP1/PRELI-like domain family of mitochondrial phospholipid transfer complexes.
Authors: Miliara, X. / Garnett, J.A. / Tatsuta, T. / Abid Ali, F. / Baldie, H. / Perez-Dorado, I. / Simpson, P. / Yague, E. / Langer, T. / Matthews, S.
History
DepositionFeb 4, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / 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 / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
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-binding periplasmic protein,TP53-regulated inhibitor of apoptosis 1
B: Maltose-binding periplasmic protein,TP53-regulated inhibitor of apoptosis 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,5634
Polymers97,8792
Non-polymers6852
Water4,792266
1
A: Maltose-binding periplasmic protein,TP53-regulated inhibitor of apoptosis 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2822
Polymers48,9391
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Maltose-binding periplasmic protein,TP53-regulated inhibitor of apoptosis 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2822
Polymers48,9391
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.390, 56.010, 100.280
Angle α, β, γ (deg.)90.00, 106.35, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 1 - 419 / Label seq-ID: 2 - 420

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Maltose-binding periplasmic protein,TP53-regulated inhibitor of apoptosis 1 / MBP / MMBP / Maltodextrin-binding protein / Protein 15E1.1 / WF-1 / p53-inducible cell-survival ...MBP / MMBP / Maltodextrin-binding protein / Protein 15E1.1 / WF-1 / p53-inducible cell-survival factor / p53CSV


Mass: 48939.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria), (gene. exp.) Homo sapiens (human)
Gene: malE, b4034, JW3994, TRIAP1, 15E1.1, HSPC132 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9, UniProt: O43715
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 100 mM sodium acetate, 25% (w/v) PEG 4000, 18% (w/v) MPD, 200 mM ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97949 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.12→48.41 Å / Num. obs: 45307 / % possible obs: 98.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 35.5 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 9.3
Reflection shellResolution: 2.12→2.18 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 2.2 / % possible all: 94

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1hsj

1hsj


Resolution: 2.12→48.41 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / Cross valid method: THROUGHOUT / ESU R: 0.278 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24163 2246 5 %RANDOM
Rwork0.19585 ---
obs0.19813 43048 98.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.257 Å2
Baniso -1Baniso -2Baniso -3
1-1.56 Å20 Å2-2.01 Å2
2---1.01 Å20 Å2
3---0.54 Å2
Refinement stepCycle: 1 / Resolution: 2.12→48.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6446 0 46 266 6758
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.026696
X-RAY DIFFRACTIONr_bond_other_d00.026238
X-RAY DIFFRACTIONr_angle_refined_deg1.471.9619120
X-RAY DIFFRACTIONr_angle_other_deg3.863314392
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6645851
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.06725.705298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.037151061
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4021516
X-RAY DIFFRACTIONr_chiral_restr0.0840.2998
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217696
X-RAY DIFFRACTIONr_gen_planes_other0.010.021476
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_it1.3973.0663377
X-RAY DIFFRACTIONr_mcbond_other1.3973.0653376
X-RAY DIFFRACTIONr_mcangle_it2.2494.5914222
X-RAY DIFFRACTIONr_mcangle_other2.2494.5924223
X-RAY DIFFRACTIONr_scbond_it2.1643.3243319
X-RAY DIFFRACTIONr_scbond_other2.1643.3253320
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5684.8614894
X-RAY DIFFRACTIONr_long_range_B_refined5.02325.0017873
X-RAY DIFFRACTIONr_long_range_B_other4.99324.9687819
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2582 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.12→2.175 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 157 -
Rwork0.332 3010 -
obs--93.67 %
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)
10.32770.02620.13240.9762-0.33020.9939-0.01310.00180.02850.0652-0.0179-0.0569-0.06310.01310.03090.09620.0139-0.0210.0425-0.00140.0089-41.230.42522.291
20.3025-0.06390.12181.0197-0.39420.7914-0.01290.03020.01540.0514-0.021-0.0032-0.00180.03550.0340.14550.0165-0.05150.0632-0.01140.0219-2.9030.51522.874
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 421
2X-RAY DIFFRACTION2B1 - 420

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