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- PDB-4psf: PIH1D1 N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 4psf
TitlePIH1D1 N-terminal domain
ComponentsPIH1 domain-containing protein 1
KeywordsPROTEIN BINDING / alpha / beta / Phospho-binding / Tel2 / Phosphorylation
Function / homology
Function and homology information


TORC1 complex assembly / snoRNA localization / positive regulation of glucose mediated signaling pathway / R2TP complex / pre-snoRNP complex / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / RPAP3/R2TP/prefoldin-like complex / box C/D snoRNP assembly / positive regulation of TORC1 signaling ...TORC1 complex assembly / snoRNA localization / positive regulation of glucose mediated signaling pathway / R2TP complex / pre-snoRNP complex / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / RPAP3/R2TP/prefoldin-like complex / box C/D snoRNP assembly / positive regulation of TORC1 signaling / epithelial cell differentiation / histone reader activity / phosphoprotein binding / positive regulation of protein serine/threonine kinase activity / rRNA processing / ATPase binding / histone binding / protein stabilization / chromatin remodeling / ribonucleoprotein complex / nucleolus / protein kinase binding / nucleus / cytoplasm
Similarity search - Function
PIH1D1/2/3, CS-like domain / PIH1 CS-like domain / PIH1, N-terminal / PIH1 N-terminal domain
Similarity search - Domain/homology
PIH1 domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.578 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
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)30,9192
Polymers30,9192
Non-polymers00
Water5,170287
1
A: PIH1 domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)15,4591
Polymers15,4591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PIH1 domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)15,4591
Polymers15,4591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.620, 60.620, 169.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 15459.477 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.53 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2% PEG 400 (v/v), 20% methoxy PEG 5000, 0.1 M imidazole pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 5, 2013
RadiationMonochromator: 0.92 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.578→35 Å / Num. all: 44722 / Num. obs: 44722 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2
Reflection shellResolution: 1.58→1.66 Å / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.578→34.798 Å / SU ML: 0.13 / σ(F): 1.34 / Phase error: 17.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1923 2167 4.85 %random
Rwork0.1749 ---
all0.178 44637 --
obs0.1757 44637 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.578→34.798 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2104 0 0 287 2391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052154
X-RAY DIFFRACTIONf_angle_d0.962913
X-RAY DIFFRACTIONf_dihedral_angle_d13.544827
X-RAY DIFFRACTIONf_chiral_restr0.036307
X-RAY DIFFRACTIONf_plane_restr0.005395
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.578-1.61470.2241560.20372777X-RAY DIFFRACTION100
1.6147-1.65510.23821460.1952778X-RAY DIFFRACTION100
1.6551-1.69980.20391210.18542782X-RAY DIFFRACTION100
1.6998-1.74990.21041480.17912768X-RAY DIFFRACTION100
1.7499-1.80630.17851520.18652771X-RAY DIFFRACTION100
1.8063-1.87090.18351380.18532800X-RAY DIFFRACTION100
1.8709-1.94580.20041390.17872805X-RAY DIFFRACTION100
1.9458-2.03430.18981560.17292782X-RAY DIFFRACTION100
2.0343-2.14160.19351550.17092802X-RAY DIFFRACTION100
2.1416-2.27570.19091520.16522802X-RAY DIFFRACTION100
2.2757-2.45140.20781340.1822849X-RAY DIFFRACTION100
2.4514-2.6980.20451380.18162857X-RAY DIFFRACTION100
2.698-3.08820.19031330.18382890X-RAY DIFFRACTION100
3.0882-3.890.18761510.1632909X-RAY DIFFRACTION100
3.89-34.80660.17641480.16833098X-RAY DIFFRACTION100
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)
15.69770.0918-1.32081.66670.40751.29860.0447-0.02250.1917-0.04680.01670.10860.0307-0.1655-0.06420.09540.0018-0.0050.1404-0.00030.0656-10.73310.47913.6496
22.28320.6275-0.69931.9661-0.74812.7841-0.0317-0.2522-0.28050.1771-0.0777-0.08750.21740.12760.09730.10780.01080.0030.1401-0.00430.1124-8.01575.184916.4828
32.02190.4514-0.83352.0403-0.13791.9406-0.0381-0.2221-0.11270.0938-0.0141-0.14430.0550.08680.03450.08770.00930.00180.1423-0.0180.1026-4.57177.655315.3736
43.77390.5844-0.58869.6147-0.98782.8756-0.16020.3918-0.3374-0.41330.0266-0.3830.468-0.2424-0.31160.1028-0.043-0.00060.1757-0.01790.120133.7647-0.849114.8836
55.4163-1.73052.97752.5615-0.85222.68810.0053-0.0768-0.1315-0.062-0.01260.2442-0.0142-0.1374-0.02380.09880.00310.01560.129-0.00610.12818.5614-0.621713.6567
65.6981-3.6932-2.66373.63893.373.5197-0.2799-0.51640.17010.68740.4526-0.37590.09780.2614-0.19190.23890.0414-0.01940.21460.02240.209234.95653.56926.8071
79.4657-2.6730.95652.0509-0.21525.28960.0848-0.2407-0.0224-0.35570.2049-0.7035-0.2132-0.1501-0.39210.35420.04430.05480.3453-0.07810.284125.355915.922631.4334
81.57330.5770.8840.99770.48992.5192-0.0667-0.01560.12560.0946-0.0410.06890.0079-0.0620.1070.12110.01870.01910.12710.01960.151524.78831.341917.2161
91.9298-0.0705-0.70932.32490.58722.2691-0.1114-0.02180.20270.03-0.03140.2496-0.2646-0.2360.13960.11440.0041-0.01160.1627-0.00270.203722.86657.535918.5235
101.65580.65961.873.64710.07532.24420.11330.69930.6315-0.57120.180.3571-0.4462-0.6974-0.36820.26460.021-0.04990.24240.0540.268418.74410.30727.6144
112.68450.86230.03294.4169-1.02714.1902-0.1259-0.4059-0.34280.2060.0610.9260.2213-0.54550.06370.125-0.0190.01220.2510.02330.233814.3167-3.030117.1995
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 29 )
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 85 )
3X-RAY DIFFRACTION3chain 'A' and (resid 86 through 141 )
4X-RAY DIFFRACTION4chain 'B' and (resid 10 through 21 )
5X-RAY DIFFRACTION5chain 'B' and (resid 22 through 42 )
6X-RAY DIFFRACTION6chain 'B' and (resid 43 through 52 )
7X-RAY DIFFRACTION7chain 'B' and (resid 53 through 61 )
8X-RAY DIFFRACTION8chain 'B' and (resid 62 through 104 )
9X-RAY DIFFRACTION9chain 'B' and (resid 105 through 124 )
10X-RAY DIFFRACTION10chain 'B' and (resid 125 through 129 )
11X-RAY DIFFRACTION11chain 'B' and (resid 130 through 142 )

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