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- PDB-5d9g: Crystal structure of TIPRL, TOR signaling pathway regulator-like,... -

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Basic information

Entry
Database: PDB / ID: 5d9g
TitleCrystal structure of TIPRL, TOR signaling pathway regulator-like, in complex with peptide
Components
  • TIP41-like protein
  • oligo peptide
KeywordsPROTEIN BINDING / protein binding TIP41-like family PP2A
Function / homology
Function and homology information


regulation of phosphoprotein phosphatase activity / negative regulation of phosphoprotein phosphatase activity / TOR signaling / DNA damage checkpoint signaling / cytosol
Similarity search - Function
TIP41-like protein / TIP41-like family
Similarity search - Domain/homology
NICKEL (II) ION / PHOSPHATE ION / TIP41-like protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / SAD / Resolution: 2.15 Å
AuthorsScorsato, V. / Sandy, J. / Brandao-Neto, J. / Pereira, H.M. / Smetana, J.H.C. / Aparicio, R.
Funding support Brazil, 3items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2011/03054-9 Brazil
Sao Paulo Research Foundation (FAPESP)2014/12445-0 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)474402/2013-4 Brazil
CitationJournal: Sci Rep / Year: 2016
Title: Crystal structure of the human Tip41 orthologue, TIPRL, reveals a novel fold and a binding site for the PP2Ac C-terminus.
Authors: Scorsato, V. / Lima, T.B. / Righetto, G.L. / Zanchin, N.I. / Brandao-Neto, J. / Sandy, J. / Pereira, H.D. / Ferrari, A.J. / Gozzo, F.C. / Smetana, J.H. / Aparicio, R.
History
DepositionAug 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Data collection / Derived calculations
Category: diffrn_source / pdbx_audit_support / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TIP41-like protein
B: TIP41-like protein
C: oligo peptide
D: oligo peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6329
Polymers59,3134
Non-polymers3205
Water4,197233
1
A: TIP41-like protein
C: oligo peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8455
Polymers29,6562
Non-polymers1893
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-32 kcal/mol
Surface area12590 Å2
MethodPISA
2
B: TIP41-like protein
D: oligo peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7874
Polymers29,6562
Non-polymers1302
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-21 kcal/mol
Surface area13130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.307, 145.307, 95.950
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
DetailsTHE BIOLOGICAL UNIT HAS BEEN DETERMINED BY SAXS AND GEL FILTRATION

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein TIP41-like protein / Putative MAPK-activating protein PM10 / Type 2A-interacting protein / TIP


Mass: 28843.502 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TIPRL / Production host: Escherichia coli (E. coli) / References: UniProt: O75663
#2: Protein/peptide oligo peptide


Mass: 812.866 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 4 types, 238 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O

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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: 4.95 Å3/Da / Density % sol: 75.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 100mM SPG buffer, pH 5.5. 1.5M NaCl, TIPRL 90mg/mL / PH range: 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.99219 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99219 Å / Relative weight: 1
ReflectionResolution: 2.15→95.95 Å / Num. obs: 62695 / % possible obs: 100 % / Redundancy: 15.2 % / Biso Wilson estimate: 44.69 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.031 / Net I/σ(I): 12.1 / Num. measured all: 952365 / Scaling rejects: 241
Reflection shell

Diffraction-ID: 1 / Rejects: 0 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all
2.15-2.2515.11.5742.312566583010.760.413
7.13-95.9514.80.09527.62679718050.9930.025

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.5.1data scaling
SHELXphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MAD / Resolution: 2.15→52.616 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1985 2520 4.03 %Random selection
Rwork0.1824 59995 --
obs0.1832 62515 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 163.94 Å2 / Biso mean: 58.5944 Å2 / Biso min: 29.84 Å2
Refinement stepCycle: final / Resolution: 2.15→52.616 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4001 0 13 233 4247
Biso mean--107.41 58.32 -
Num. residues----502
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034184
X-RAY DIFFRACTIONf_angle_d0.6915677
X-RAY DIFFRACTIONf_chiral_restr0.026630
X-RAY DIFFRACTIONf_plane_restr0.003723
X-RAY DIFFRACTIONf_dihedral_angle_d12.9771558
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.19140.37871570.3513277343499
2.1914-2.23610.35051550.311233063461100
2.2361-2.28470.33771740.300432633437100
2.2847-2.33790.34131670.28373271343899
2.3379-2.39630.33021400.288632983438100
2.3963-2.4611100000000.26513469100
2.4611-2.5335100000000.24573454100
2.5335-2.6153100000000.2483461100
2.6153-2.70880.24391260.230433533479100
2.7088-2.81720.25731720.228632933465100
2.8172-2.94540.25161870.222132753462100
2.9454-3.10070.24571820.214133313513100
3.1007-3.29490.22371790.192132913470100
3.2949-3.54930.19951790.161233153494100
3.5493-3.90640.2011540.144133083462100
3.9064-4.47140.1131570.125933393496100
4.4714-5.63240.15721980.127533193517100
5.6324-52.63160.17241930.166933723565100
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)
16.4264-0.1926-0.12984.5578-0.61392.2274-0.10040.7576-0.3901-0.2155-0.02550.29890.12350.09240.13620.3117-0.0865-0.05220.402-0.08280.2761-27.467763.3485-5.3033
24.3508-1.45750.99482.3213-0.29681.3651-0.13130.2025-0.0289-0.0214-0.03530.0144-0.07370.0120.14650.3195-0.06540.00290.2867-0.03620.2802-20.852465.8964.8147
34.2031-2.08272.94163.3346-2.89135.797-0.1957-0.02490.14640.09730.06410.2209-0.1156-0.11630.15760.3626-0.06480.01450.2648-0.08050.4082-24.10272.095913.319
42.23231.00820.09876.82681.85951.45960.1788-0.41750.04380.6208-0.1937-0.33670.1570.04080.01170.4244-0.0371-0.00220.49820.01960.309-46.91145.0853.5864
57.11411.44840.9870.3498-0.17382.1059-0.0632-0.70780.06740.5536-0.1015-0.31780.17360.13720.1980.58690.0008-0.00110.33880.05050.5061-50.635125.7272-1.0705
61.14530.29130.08214.40641.06851.42230.005-0.18960.1625-0.0832-0.03750.1944-0.0819-0.1960.01720.2817-0.05040.01120.4320.02180.3642-53.31650.5837-6.3714
72.1216-0.6979-1.53683.66333.22097.26270.024-0.09710.2291-0.0222-0.0970.3936-0.014-0.50320.10510.2219-0.0566-0.00410.3810.03860.4585-59.139250.3517-12.3688
85.2797-4.7007-4.94118.10680.30559.04450.3903-1.60970.21060.3783-0.07280.7523-0.8789-0.631-0.30680.6929-0.01320.10220.8746-0.03430.8464-37.103369.780114.6558
94.4792.85212.76363.5937-0.07273.5766-0.56341.19420.9506-0.83410.43910.1566-0.12730.13440.02780.5602-0.0199-0.05980.7261-0.0240.6071-50.689462.6129-13.5428
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 75 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 76 through 197 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 198 through 256 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 11 through 85 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 86 through 105 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 106 through 197 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 198 through 256 )B0
8X-RAY DIFFRACTION8chain 'C' and (resid 11 through 14 )C0
9X-RAY DIFFRACTION9chain 'D' and (resid 9 through 14 )D0

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