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- PDB-4xhl: Structure of S. cerevisiae Hrr25 1-394 (K38R mutant) -

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Basic information

Entry
Database: PDB / ID: 4xhl
TitleStructure of S. cerevisiae Hrr25 1-394 (K38R mutant)
ComponentsCasein kinase I homolog HRR25
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / casein kinase / monopolin / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


regulation of vesicle fusion with Golgi apparatus / regulation of protein localization by the Cvt pathway / monopolin complex / positive regulation of clathrin-dependent endocytosis / spindle attachment to meiosis I kinetochore / meiotic chromosome segregation / regulation of ER to Golgi vesicle-mediated transport / COPII-mediated vesicle transport / tRNA wobble uridine modification / cellular bud tip ...regulation of vesicle fusion with Golgi apparatus / regulation of protein localization by the Cvt pathway / monopolin complex / positive regulation of clathrin-dependent endocytosis / spindle attachment to meiosis I kinetochore / meiotic chromosome segregation / regulation of ER to Golgi vesicle-mediated transport / COPII-mediated vesicle transport / tRNA wobble uridine modification / cellular bud tip / cellular bud neck / regulation of autophagosome assembly / pexophagy / spindle pole body / preribosome, small subunit precursor / chromosome, centromeric region / regulation of DNA repair / ribosomal large subunit biogenesis / P-body / endocytosis / regulation of protein localization / ribosomal small subunit biogenesis / protein tyrosine kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / nucleolus / Golgi apparatus / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-CKI / Casein kinase I homolog HRR25
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsYe, Q. / Corbett, K.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM104141 United States
CitationJournal: Embo J. / Year: 2016
Title: Structure of the Saccharomyces cerevisiae Hrr25:Mam1 monopolin subcomplex reveals a novel kinase regulator.
Authors: Ye, Q. / Ur, S.N. / Su, T.Y. / Corbett, K.D.
History
DepositionJan 5, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Casein kinase I homolog HRR25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8939
Polymers45,9351
Non-polymers9588
Water1267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.497, 137.497, 94.639
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Casein kinase I homolog HRR25


Mass: 45934.566 Da / Num. of mol.: 1 / Fragment: UNP residues 1-394 / Mutation: K38R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HRR25 / Production host: Escherichia coli (E. coli)
References: UniProt: P29295, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-CKI / N-(2-AMINOETHYL)-5-CHLOROISOQUINOLINE-8-SULFONAMIDE


Mass: 285.750 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12ClN3O2S
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.81 Å3/Da / Density % sol: 56.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 11
Details: 0.1 M CAPS pH 11, 0.2 M lithium sulfate, and 1.5-1.6 M ammonium sulfate
PH range: 11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 15, 2012
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.01→119.08 Å / Num. obs: 10857 / % possible obs: 99.5 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 16.8
Reflection shellResolution: 3.01→3.17 Å / Redundancy: 10.7 % / Rmerge(I) obs: 1.252 / Mean I/σ(I) obs: 2 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XH0

4xh0


Resolution: 3.01→119.08 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2847 526 4.85 %
Rwork0.267 --
obs0.2679 10856 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.01→119.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2751 0 53 7 2811
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022866
X-RAY DIFFRACTIONf_angle_d0.5993854
X-RAY DIFFRACTIONf_dihedral_angle_d12.4591073
X-RAY DIFFRACTIONf_chiral_restr0.025393
X-RAY DIFFRACTIONf_plane_restr0.002480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0088-3.31160.36851350.33432510X-RAY DIFFRACTION99
3.3116-3.79080.32721260.28522553X-RAY DIFFRACTION99
3.7908-4.77610.30181250.24382570X-RAY DIFFRACTION99
4.7761-119.16920.24391400.26262697X-RAY DIFFRACTION98
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)
11.7919-0.6732-0.08081.1882-0.49810.5818-0.25470.0009-0.236-0.07780.25910.6042-0.1269-0.9970.01740.64240.01980.10241.2413-0.13340.590818.776232.74154.9996
22.9418-0.54490.02872.36930.28672.15090.3414-0.07480.4043-0.5677-0.1307-0.61720.14360.1765-0.02840.7613-0.03760.43690.5326-0.13640.852644.858927.841-1.2907
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 85 )
2X-RAY DIFFRACTION2chain 'A' and (resid 86 through 371 )

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