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- PDB-4cv4: PIH N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 4cv4
TitlePIH N-terminal domain
ComponentsPIH1 DOMAIN-CONTAINING PROTEIN 1
KeywordsCHAPERONE / PHOSPHORYLATION
Function / homology
Function and homology information


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 / RPAP3/R2TP/prefoldin-like complex / box C/D snoRNP assembly / positive regulation of TORC1 signaling / epithelial cell differentiation ...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 / RPAP3/R2TP/prefoldin-like complex / box C/D snoRNP assembly / positive regulation of TORC1 signaling / epithelial cell differentiation / histone reader activity / phosphoprotein binding / rRNA processing / histone binding / ATPase binding / 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 speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.902 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 23, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1May 28, 2014Group: Atomic model
Revision 1.2Jun 25, 2014Group: Database references
Revision 1.3Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 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 / pdbx_struct_conn_angle / struct_conn / struct_site
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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PIH1 DOMAIN-CONTAINING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4206
Polymers14,9771
Non-polymers4435
Water3,207178
1
A: PIH1 DOMAIN-CONTAINING PROTEIN 1
hetero molecules

A: PIH1 DOMAIN-CONTAINING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,84012
Polymers29,9542
Non-polymers88610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area3650 Å2
ΔGint-138.7 kcal/mol
Surface area12980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.860, 50.140, 35.180
Angle α, β, γ (deg.)90.00, 103.21, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2046-

HOH

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Components

#1: Protein PIH1 DOMAIN-CONTAINING PROTEIN 1 / NUCLEOLAR PROTEIN 17 HOMOLOG / PIH1D1


Mass: 14976.923 Da / Num. of mol.: 1 / 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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 1.87 Å3/Da / Density % sol: 34.42 % / Description: NONE
Crystal growpH: 7
Details: 0.02M MAGNESIUM CHLORIDE HEXAHYDRATE, 0.002M COBALT (2) CHLORIDE, 0.05M HEPES PH 7.5, 2M AMMONIUM SULFATE, 0.001M SPERMINE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187
DetectorType: SATURN / Detector: CCD / Date: Mar 1, 2013 / Details: VARIMAX-HF MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.9→34.25 Å / Num. obs: 8928 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 10.63 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 22.7
Reflection shellResolution: 1.9→2.16 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 14.9 / % possible all: 96.4

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Processing

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

4ckt


Resolution: 1.902→34.249 Å / SU ML: 0.13 / σ(F): 1.35 / Phase error: 15.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1585 425 4.8 %
Rwork0.1187 --
obs0.1207 8925 94.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.7 Å2
Refinement stepCycle: LAST / Resolution: 1.902→34.249 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1011 0 21 178 1210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151088
X-RAY DIFFRACTIONf_angle_d1.2551489
X-RAY DIFFRACTIONf_dihedral_angle_d12.584406
X-RAY DIFFRACTIONf_chiral_restr0.07163
X-RAY DIFFRACTIONf_plane_restr0.006191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9021-2.17720.18551240.11572629X-RAY DIFFRACTION88
2.1772-2.74290.16731460.11952886X-RAY DIFFRACTION98
2.7429-34.25460.1441550.11952985X-RAY DIFFRACTION99

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