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- PDB-4psi: PIH1D1/phospho-Tel2 complex -

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Basic information

Entry
Database: PDB / ID: 4psi
TitlePIH1D1/phospho-Tel2 complex
Components
  • PIH1 domain-containing protein 1
  • Telomere length regulation protein TEL2 homolog
KeywordsPROTEIN BINDING / alpha / beta / Phospho-binding / Tel2 / phsophorylation
Function / homology
Function and homology information


positive regulation of DNA damage checkpoint / TTT Hsp90 cochaperone complex / TORC1 complex assembly / snoRNA localization / positive regulation of glucose mediated signaling pathway / pre-snoRNP complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / R2TP complex / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / RPAP3/R2TP/prefoldin-like complex ...positive regulation of DNA damage checkpoint / TTT Hsp90 cochaperone complex / TORC1 complex assembly / snoRNA localization / positive regulation of glucose mediated signaling pathway / pre-snoRNP complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / R2TP complex / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / RPAP3/R2TP/prefoldin-like complex / box C/D snoRNP assembly / telomeric DNA binding / telomere maintenance via telomerase / positive regulation of TORC1 signaling / epithelial cell differentiation / histone reader activity / phosphoprotein binding / Hsp90 protein binding / positive regulation of protein serine/threonine kinase activity / rRNA processing / histone binding / ATPase binding / chromosome, telomeric region / molecular adaptor activity / nuclear body / protein stabilization / chromatin remodeling / ribonucleoprotein complex / protein-containing complex binding / nucleolus / protein kinase binding / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Telomere length regulation protein, conserved domain / TEL2, C-terminal domain superfamily / Telomere length regulation protein / PIH1D1/2/3, CS-like domain / PIH1 CS-like domain / PIH1, N-terminal / PIH1 N-terminal domain / Armadillo-type fold
Similarity search - Domain/homology
PIH1 domain-containing protein 1 / Telomere length regulation protein TEL2 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 Å
AuthorsSmerdon, S.J. / Boulton, S.J. / Stach, L. / Flower, T.G. / Horejsi, Z.
CitationJournal: Cell Rep / Year: 2014
Title: Phosphorylation-Dependent PIH1D1 Interactions Define Substrate Specificity of the R2TP Cochaperone Complex.
Authors: Horejsi, Z. / Stach, L. / Flower, T.G. / Joshi, D. / Flynn, H. / Skehel, J.M. / O'Reilly, N.J. / Ogrodowicz, R.W. / Smerdon, S.J. / Boulton, S.J.
History
DepositionMar 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PIH1 domain-containing protein 1
B: PIH1 domain-containing protein 1
D: Telomere length regulation protein TEL2 homolog
E: Telomere length regulation protein TEL2 homolog


Theoretical massNumber of molelcules
Total (without water)34,1824
Polymers34,1824
Non-polymers00
Water59433
1
A: PIH1 domain-containing protein 1
D: Telomere length regulation protein TEL2 homolog


Theoretical massNumber of molelcules
Total (without water)17,0912
Polymers17,0912
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-6 kcal/mol
Surface area8090 Å2
MethodPISA
2
B: PIH1 domain-containing protein 1
E: Telomere length regulation protein TEL2 homolog


Theoretical massNumber of molelcules
Total (without water)17,0912
Polymers17,0912
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-5 kcal/mol
Surface area7750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.600, 81.840, 83.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PIH1 domain-containing protein 1 / Nucleolar protein 17 homolog


Mass: 15740.846 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIH1D1, NOP17 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NWS0
#2: Protein/peptide Telomere length regulation protein TEL2 homolog


Mass: 1350.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: phospho-peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9Y4R8
#3: Water ChemComp-HOH / water / Protein clk-2 homolog / hCLK2


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.49 Å3/Da / Density % sol: 50.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Crystals grew from a 8 mg/ml solution of complex in 20 mM Tris pH 8.0, 150 mM NaCl, 0.5 mM TCEP equilibrated well solution containing 32 % w/v PEG4000, 100 mM sodium acetate, 100 mM Tris pH ...Details: Crystals grew from a 8 mg/ml solution of complex in 20 mM Tris pH 8.0, 150 mM NaCl, 0.5 mM TCEP equilibrated well solution containing 32 % w/v PEG4000, 100 mM sodium acetate, 100 mM Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 1, 2013
RadiationMonochromator: 0.98 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.45→30 Å / Num. all: 13120 / Num. obs: 13117 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2
Reflection shellResolution: 2.45→2.55 Å / % possible all: 99.2

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 2.45→29.843 Å / SU ML: 0.34 / σ(F): 0.35 / Phase error: 35.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2684 1216 5.05 %random
Rwork0.2399 ---
all0.243 ---
obs0.2413 -99.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→29.843 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2109 0 0 33 2142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032156
X-RAY DIFFRACTIONf_angle_d0.8022918
X-RAY DIFFRACTIONf_dihedral_angle_d13.328809
X-RAY DIFFRACTIONf_chiral_restr0.058309
X-RAY DIFFRACTIONf_plane_restr0.003388
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.54810.36441420.39382521X-RAY DIFFRACTION98
2.5481-2.66390.36571330.34652499X-RAY DIFFRACTION99
2.6639-2.80430.3851660.30832512X-RAY DIFFRACTION99
2.8043-2.97980.30431280.29552541X-RAY DIFFRACTION99
2.9798-3.20970.28821220.25582557X-RAY DIFFRACTION99
3.2097-3.53220.25291490.23012557X-RAY DIFFRACTION99
3.5322-4.04230.25331260.21122545X-RAY DIFFRACTION99
4.0423-5.08870.2031460.18622546X-RAY DIFFRACTION100
5.0887-29.84550.24981040.22332572X-RAY DIFFRACTION99
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)
17.6493-0.44050.15528.133-3.31284.8360.03140.1026-0.2527-0.53980.09220.4953-0.3211-0.591-0.18960.80250.00940.11380.33190.08091.304911.114862.68841.397
23.5248-0.76140.61568.5764-2.58392.56720.1113-0.23660.4150.4738-0.1193-0.1947-0.29830.05490.04150.6096-0.04070.01130.343-0.12280.738316.949259.83326.1389
35.2154-1.2267-0.95578.7127-2.28153.897-0.0231-0.61410.19990.6707-0.4491-1.0319-0.12830.42610.17460.7365-0.0477-0.03760.44960.00170.882921.409253.285510.0755
44.7478-0.80620.98874.94062.2941.8542-0.4423-0.1469-0.11990.09150.64080.05170.09680.0605-0.14210.59720.072-0.10960.35530.06161.122119.426618.2582.5127
51.6252-0.9668-0.4865.01121.78232.56310.11680.061-0.36080.2087-0.20580.4014-0.0115-0.0216-0.01210.5345-0.07930.0410.37920.0390.65713.305622.40515.3968
60.1473-0.7256-0.48454.21371.54330.9450.3771-0.551-0.13211.0125-0.2147-0.7810.4954-0.116-0.08570.8666-0.0517-0.13640.518-0.02650.802920.316615.74424.6234
71.2011-0.07750.44154.65311.57641.02670.1151-0.1836-0.50310.543-0.12470.71530.3066-0.17010.04080.6202-0.0266-0.03150.35510.010.8512.574723.01136.8887
82.6175-0.5170.72854.44781.23012.84060.1067-0.3806-0.48140.4073-0.34060.1110.2273-0.42780.09450.8062-0.05250.03060.51210.03181.07979.501928.423710.3289
93.00642.87841.16693.59270.85128.86090.51780.7270.3903-0.6029-0.0024-1.0573-0.59650.4032-0.09680.62380.0511-0.11090.85380.10841.424129.701648.27787.012
106.69440.42375.08922.0581.4989.10530.17520.5345-0.141-0.39210.02320.003-0.2745-0.03-0.3210.7368-0.04780.16190.6103-0.12111.24171.181633.55666.621
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 37 through 51 )
2X-RAY DIFFRACTION2chain 'A' and (resid 52 through 154 )
3X-RAY DIFFRACTION3chain 'A' and (resid 155 through 174 )
4X-RAY DIFFRACTION4chain 'B' and (resid 37 through 51 )
5X-RAY DIFFRACTION5chain 'B' and (resid 52 through 82 )
6X-RAY DIFFRACTION6chain 'B' and (resid 83 through 105 )
7X-RAY DIFFRACTION7chain 'B' and (resid 106 through 154 )
8X-RAY DIFFRACTION8chain 'B' and (resid 155 through 174 )
9X-RAY DIFFRACTION9chain 'D' and (resid 26 through 36 )
10X-RAY DIFFRACTION10chain 'E' and (resid 27 through 36 )

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