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- PDB-4ckt: PIH1 N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 4ckt
TitlePIH1 N-terminal domain
Components
  • PIH1 DOMAIN-CONTAINING PROTEIN 1
  • TELOMERE LENGTH REGULATION PROTEIN TEL2 HOMOLOG
KeywordsCHAPERONE/PEPTIDE / CHAPERONE-PEPTIDE COMPLEX / CHAPERONE / MULTIPROTEIN COMPLEXES / PHOSPHORYLATION / R2TP
Function / homology
Function and homology information


protein-containing complex stabilizing activity / TORC1 complex assembly / snoRNA localization / positive regulation of glucose mediated signaling pathway / TTT Hsp90 cochaperone complex / pre-snoRNP complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / R2TP complex / RPAP3/R2TP/prefoldin-like complex / box C/D snoRNP assembly ...protein-containing complex stabilizing activity / TORC1 complex assembly / snoRNA localization / positive regulation of glucose mediated signaling pathway / TTT Hsp90 cochaperone complex / pre-snoRNP complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / R2TP complex / RPAP3/R2TP/prefoldin-like complex / box C/D snoRNP assembly / epithelial cell differentiation / positive regulation of TORC1 signaling / histone reader activity / phosphoprotein binding / Hsp90 protein binding / kinase binding / ATPase binding / molecular adaptor activity / histone binding / chromosome, telomeric region / protein stabilization / nuclear body / chromatin remodeling / protein-containing complex binding / protein kinase binding / nucleolus / nucleus / membrane / cytosol / cytoplasm
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 / SAD / Resolution: 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
DepositionJan 8, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Database references
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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

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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)47,4734
Polymers47,4734
Non-polymers00
Water543
1
B: PIH1 DOMAIN-CONTAINING PROTEIN 1
D: TELOMERE LENGTH REGULATION PROTEIN TEL2 HOMOLOG


Theoretical massNumber of molelcules
Total (without water)23,7362
Polymers23,7362
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690 Å2
ΔGint-4.2 kcal/mol
Surface area8090 Å2
MethodPISA
2
A: PIH1 DOMAIN-CONTAINING PROTEIN 1
C: TELOMERE LENGTH REGULATION PROTEIN TEL2 HOMOLOG


Theoretical massNumber of molelcules
Total (without water)23,7362
Polymers23,7362
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-7.1 kcal/mol
Surface area7610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.020, 62.150, 114.290
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: 22600.400 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-200
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: 1135.973 Da / Num. of mol.: 2 / Fragment: RESIDUES 489-496 / 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.: 3 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.88 Å3/Da / Density % sol: 34.59 % / Description: NONE
Crystal growpH: 7 / Details: pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.06→61.67 Å / Num. obs: 68364 / % possible obs: 90.1 % / Observed criterion σ(I): 0 / Redundancy: 10.8 % / Biso Wilson estimate: 62.28 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 15.4
Reflection shellResolution: 3.06→3.14 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.5 / % possible all: 56.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
xia2data reduction
xia2data scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 3→54.599 Å / SU ML: 0.41 / σ(F): 1.91 / Phase error: 28.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2814 634 4.7 %
Rwork0.224 --
obs0.2267 13607 98.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→54.599 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 0 3 2052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112091
X-RAY DIFFRACTIONf_angle_d1.8382844
X-RAY DIFFRACTIONf_dihedral_angle_d16.724745
X-RAY DIFFRACTIONf_chiral_restr0.104317
X-RAY DIFFRACTIONf_plane_restr0.007376
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0002-3.23180.33411420.31262580X-RAY DIFFRACTION99
3.2318-3.5570.32061280.28092627X-RAY DIFFRACTION100
3.557-4.07150.2891170.21332625X-RAY DIFFRACTION100
4.0715-5.12910.20821050.18222612X-RAY DIFFRACTION99
5.1291-54.60830.29051420.2132529X-RAY DIFFRACTION97

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