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- PDB-4xzv: Crystal Structure of SLMO1-TRIAP1 Complex -

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Basic information

Entry
Database: PDB / ID: 4xzv
TitleCrystal Structure of SLMO1-TRIAP1 Complex
Components
  • Maltose-binding periplasmic protein,TP53-regulated inhibitor of apoptosis 1
  • Protein slowmo homolog 1
KeywordsAPOPTOSIS / lipid transport / mitochondria / complex
Function / homology
Function and homology information


regulation of membrane lipid distribution / phosphatidic acid transfer activity / positive regulation of phospholipid transport / phospholipid transport / phospholipid translocation / detection of maltose stimulus / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / maltose transport complex / negative regulation of release of cytochrome c from mitochondria / maltose binding ...regulation of membrane lipid distribution / phosphatidic acid transfer activity / positive regulation of phospholipid transport / phospholipid transport / phospholipid translocation / detection of maltose stimulus / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / maltose transport complex / negative regulation of release of cytochrome c from mitochondria / maltose binding / maltose transport / maltodextrin transmembrane transport / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / carbohydrate transport / carbohydrate transmembrane transporter activity / DNA damage response, signal transduction by p53 class mediator / Mitochondrial protein degradation / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / 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 / membrane / 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. / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / 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) / 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 / PRELI domain containing protein 3A
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.58 Å
AuthorsMiliara, X. / Garnett, J.A. / 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 5, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / 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 / _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

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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: Protein slowmo homolog 1
C: Maltose-binding periplasmic protein,TP53-regulated inhibitor of apoptosis 1
D: Protein slowmo homolog 1
E: Maltose-binding periplasmic protein,TP53-regulated inhibitor of apoptosis 1
F: Protein slowmo homolog 1
G: Maltose-binding periplasmic protein,TP53-regulated inhibitor of apoptosis 1
H: Protein slowmo homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)281,08612
Polymers279,7178
Non-polymers1,3694
Water0
1
A: Maltose-binding periplasmic protein,TP53-regulated inhibitor of apoptosis 1
B: Protein slowmo homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2723
Polymers69,9292
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-4 kcal/mol
Surface area24270 Å2
MethodPISA
2
C: Maltose-binding periplasmic protein,TP53-regulated inhibitor of apoptosis 1
D: Protein slowmo homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2723
Polymers69,9292
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-3 kcal/mol
Surface area24270 Å2
MethodPISA
3
E: Maltose-binding periplasmic protein,TP53-regulated inhibitor of apoptosis 1
F: Protein slowmo homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2723
Polymers69,9292
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-4 kcal/mol
Surface area24430 Å2
MethodPISA
4
G: Maltose-binding periplasmic protein,TP53-regulated inhibitor of apoptosis 1
H: Protein slowmo homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2723
Polymers69,9292
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-2 kcal/mol
Surface area24150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.620, 80.680, 98.020
Angle α, β, γ (deg.)87.25, 85.62, 89.92
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13A
23G
14B
24D
15B
25F
16B
26H
17C
27E
18C
28G
19D
29F
110D
210H
111E
211G
112F
212H

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSGLUGLUAA1 - 4252 - 426
21LYSLYSGLUGLUCC1 - 4252 - 426
12GLUGLULYSLYSAA4 - 4245 - 425
22GLUGLULYSLYSEE4 - 4245 - 425
13LYSLYSGLUGLUAA1 - 4232 - 424
23LYSLYSGLUGLUGG1 - 4232 - 424
14METMETSERSERBB1 - 16715 - 181
24METMETSERSERDD1 - 16715 - 181
15METMETSERSERBB1 - 16715 - 181
25METMETSERSERFF1 - 16715 - 181
16METMETSERSERBB1 - 16715 - 181
26METMETSERSERHH1 - 16715 - 181
17GLUGLULYSLYSCC4 - 4245 - 425
27GLUGLULYSLYSEE4 - 4245 - 425
18LYSLYSGLUGLUCC1 - 4232 - 424
28LYSLYSGLUGLUGG1 - 4232 - 424
19METMETSERSERDD1 - 16715 - 181
29METMETSERSERFF1 - 16715 - 181
110METMETSERSERDD1 - 16715 - 181
210METMETSERSERHH1 - 16715 - 181
111GLUGLUGLUGLUEE4 - 4235 - 424
211GLUGLUGLUGLUGG4 - 4235 - 424
112METMETSERSERFF1 - 16715 - 181
212METMETSERSERHH1 - 16715 - 181

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

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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.: 4
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: Protein
Protein slowmo homolog 1


Mass: 20989.980 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLMO1, C18orf43 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96N28
#3: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 100 mM sodium formate, 12% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98 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: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.58→97.62 Å / Num. obs: 28326 / % possible obs: 98.9 % / Redundancy: 3.5 % / Rsym value: 0.108 / Net I/σ(I): 11.6
Reflection shellResolution: 3.58→3.67 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 2.7 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XZS

4xzs


Resolution: 3.58→97.62 Å / Cor.coef. Fo:Fc: 0.869 / Cor.coef. Fo:Fc free: 0.812 / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30927 1499 5.3 %RANDOM
Rwork0.27342 ---
obs0.27528 26826 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.48 Å2-1.88 Å2-3.17 Å2
2--0.03 Å20.34 Å2
3----5.87 Å2
Refinement stepCycle: LAST / Resolution: 3.58→97.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17156 0 92 0 17248
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0217637
X-RAY DIFFRACTIONr_bond_other_d00.0216691
X-RAY DIFFRACTIONr_angle_refined_deg1.6631.95823966
X-RAY DIFFRACTIONr_angle_other_deg3.589338447
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.91252189
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.91225.213752
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.251152903
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.141560
X-RAY DIFFRACTIONr_chiral_restr0.0810.22705
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02119789
X-RAY DIFFRACTIONr_gen_planes_other0.0070.023831
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_it2.94510.7488843
X-RAY DIFFRACTIONr_mcbond_other2.94510.7478842
X-RAY DIFFRACTIONr_mcangle_it5.06116.09911003
X-RAY DIFFRACTIONr_mcangle_other5.06116.111004
X-RAY DIFFRACTIONr_scbond_it3.10610.9148794
X-RAY DIFFRACTIONr_scbond_other3.10610.9148794
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.28216.24412964
X-RAY DIFFRACTIONr_long_range_B_refined9.88274834
X-RAY DIFFRACTIONr_long_range_B_other9.88274828
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A26430.07
12C26430.07
21A26200.07
22E26200.07
31A26160.06
32G26160.06
41B7530.18
42D7530.18
51B7620.14
52F7620.14
61B7110.14
62H7110.14
71C26330.05
72E26330.05
81C26320.05
82G26320.05
91D7730.16
92F7730.16
101D7080.17
102H7080.17
111E26110.04
112G26110.04
121F7200.14
122H7200.14
LS refinement shellResolution: 3.58→3.673 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 92 -
Rwork0.34 2015 -
obs--98.73 %
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)
13.9646-1.05530.48282.17630.25385.47120.14090.29070.0539-0.2672-0.0565-0.21080.15250.4058-0.08450.04580.0410.09360.10980.21050.7348-155.758-30.339-53.379
28.50962.28653.317311.3835-0.49839.17550.37940.2667-0.42740.386-0.07420.2630.5429-0.2079-0.30530.05640.02740.05460.51770.16250.7178-181.684-26.914-50.405
33.3833-1.33840.9746.06310.23757.96110.090.20870.2784-0.409-0.24490.8771-0.5329-0.4180.15480.35690.2411-0.02970.6282-0.05551.0201-191.01-13.183-59.545
43.40140.43730.21362.33650.09665.9045-0.067-0.0532-0.06660.26670.2944-0.4075-0.52330.4703-0.22740.11110.01770.03090.11550.09760.8748-116.31-35.438-10.051
511.2731-1.8928-0.15218.7671-0.6486.4910.2406-0.11630.2266-1.00950.1673-0.5879-0.2503-0.5835-0.4080.17390.12170.11250.4280.30140.7522-142.102-38.426-13.794
66.05881.1087-0.5375.7538-1.19517.55580.0948-0.6304-0.59830.32850.25230.48130.5517-0.4695-0.34710.3931-0.0447-0.01260.80270.34260.8764-152.191-51.534-4.4
74.85360.9140.60292.6413-0.53045.05280.79210.3799-0.3644-0.1174-0.04-0.04650.935-0.0938-0.75221.08650.1621-0.28980.10810.17730.9213-131.361-5.483-9.74
88.1125-0.76061.40948.73541.86977.19660.41640.4426-0.5576-1.3342-0.0907-0.62551.1027-0.0313-0.32570.99660.2834-0.00340.65310.02961.251-105.051-2.736-9.195
93.0882.36941.36555.181-0.02545.22680.46020.12820.2016-0.1771-0.1732-0.25250.51950.6304-0.28710.80540.11150.09080.849-0.01371.4932-96.78311.4510.991
103.61360.1331-0.41054.3458-0.02043.40330.08610.4590.15160.25110.2940.48260.1064-0.2988-0.38020.41170.07180.04370.36090.21571.1651-169.52820.994-52.805
117.51035.17410.31869.80636.1687.90460.24370.123-0.14980.74120.4059-0.2706-0.98580.1816-0.64961.14280.13530.1950.7305-0.16371.3777-143.36817.6-53.301
123.4343-0.6028-0.54713.98680.56995.5438-0.43890.5846-0.7301-0.50411.027-1.02790.011-0.0478-0.58820.72130.0910.08191.1347-0.4221.7878-135.3123.528-63.517
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 370
2X-RAY DIFFRACTION2A371 - 425
3X-RAY DIFFRACTION3B1 - 167
4X-RAY DIFFRACTION4C1 - 370
5X-RAY DIFFRACTION5C371 - 425
6X-RAY DIFFRACTION6D1 - 167
7X-RAY DIFFRACTION7E4 - 370
8X-RAY DIFFRACTION8E371 - 425
9X-RAY DIFFRACTION9F1 - 167
10X-RAY DIFFRACTION10G1 - 370
11X-RAY DIFFRACTION11G371 - 424
12X-RAY DIFFRACTION12H1 - 167

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