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- PDB-4cse: PIH N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 4cse
TitlePIH N-terminal domain
Components
  • PIH1 DOMAIN-CONTAINING PROTEIN 1
  • TELOMERE LENGTH REGULATION PROTEIN TEL2 HOMOLOG
KeywordsCHAPERONE / MOLECULAR CHAPERONES / MULTIPROTEIN COMPLEXES / PHOSPHORYLATION
Function / homology
Function and homology information


protein-containing complex stabilizing activity / : / TTT Hsp90 cochaperone complex / TORC1 complex assembly / positive regulation of TORC2 signaling / snoRNA localization / positive regulation of glucose mediated signaling pathway / pre-snoRNP complex / R2TP complex / TORC2 complex ...protein-containing complex stabilizing activity / : / TTT Hsp90 cochaperone complex / TORC1 complex assembly / positive regulation of TORC2 signaling / snoRNA localization / positive regulation of glucose mediated signaling pathway / pre-snoRNP complex / R2TP complex / TORC2 complex / TORC1 complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / RPAP3/R2TP/prefoldin-like complex / regulation of TOR signaling / box C/D snoRNP assembly / telomeric DNA binding / telomere maintenance via telomerase / positive regulation of TORC1 signaling / epithelial cell differentiation / histone reader activity / nuclear periphery / phosphoprotein binding / Hsp90 protein binding / kinase binding / 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
Similarity search - Domain/homology
PIH1 domain-containing protein 1 / Telomere length regulation protein TEL2 homolog
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsMorgan, R.M. / Roe, S.M.
CitationJournal: Structure / Year: 2014
Title: Structural Basis for Phosphorylation-Dependent Recruitment of Tel2 to Hsp90 by Pih1.
Authors: Pal, M. / Morgan, M. / Phelps, S.E. / Roe, S.M. / Parry-Morris, S. / Downs, J.A. / Polier, S. / Pearl, L.H. / Prodromou, C.
History
DepositionMar 7, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

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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
C: TELOMERE LENGTH REGULATION PROTEIN TEL2 HOMOLOG
D: TELOMERE LENGTH REGULATION PROTEIN TEL2 HOMOLOG


Theoretical massNumber of molelcules
Total (without water)32,2264
Polymers32,2264
Non-polymers00
Water27015
1
B: PIH1 DOMAIN-CONTAINING PROTEIN 1
D: TELOMERE LENGTH REGULATION PROTEIN TEL2 HOMOLOG


Theoretical massNumber of molelcules
Total (without water)16,1132
Polymers16,1132
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint-1.7 kcal/mol
Surface area6010 Å2
MethodPISA
2
A: PIH1 DOMAIN-CONTAINING PROTEIN 1
C: TELOMERE LENGTH REGULATION PROTEIN TEL2 HOMOLOG


Theoretical massNumber of molelcules
Total (without water)16,1132
Polymers16,1132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-4.8 kcal/mol
Surface area6700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.220, 67.730, 104.020
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 / PIH1D1


Mass: 14976.923 Da / Num. of mol.: 2 / Fragment: RESIDUES 47-179
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9CQJ2
#2: Protein/peptide TELOMERE LENGTH REGULATION PROTEIN TEL2 HOMOLOG


Mass: 1135.972 Da / Num. of mol.: 2 / Fragment: RESIDUES 498-506 / Source method: obtained synthetically / Source: (synth.) MUS MUSCULUS (house mouse) / References: UniProt: Q9DC40
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.76 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal growpH: 7
Details: 0.15M SODIUM POTASSIUM PHOSPHATE, 20% PEG 3350, 0.1M BIS-TRIS PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.3→56.76 Å / Num. obs: 5693 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 11.7 % / Biso Wilson estimate: 66.3 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 12.8
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 4.7 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CKT

4ckt


Resolution: 3.3→56.759 Å / SU ML: 0.48 / σ(F): 1.36 / Phase error: 30.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3055 258 4.6 %
Rwork0.2135 --
obs0.2176 5662 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→56.759 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1778 0 0 15 1793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011818
X-RAY DIFFRACTIONf_angle_d1.2982468
X-RAY DIFFRACTIONf_dihedral_angle_d15.096654
X-RAY DIFFRACTIONf_chiral_restr0.08269
X-RAY DIFFRACTIONf_plane_restr0.01324
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3001-4.15760.33511360.21782642X-RAY DIFFRACTION100
4.1576-56.76690.28561220.21092762X-RAY DIFFRACTION99

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