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- PDB-5cyz: Structure of S. cerevisiae Hrr25:Mam1 complex, form 1 -

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Basic information

Entry
Database: PDB / ID: 5cyz
TitleStructure of S. cerevisiae Hrr25:Mam1 complex, form 1
Components
  • Casein kinase I homolog HRR25
  • Monopolin complex subunit MAM1
KeywordsTRANSFERASE / casein kinase / monopolin
Function / homology
Function and homology information


meiotic sister chromatid cohesion involved in meiosis I / 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 / regulation of ER to Golgi vesicle-mediated transport / meiotic chromosome segregation / homologous chromosome segregation / tRNA wobble uridine modification ...meiotic sister chromatid cohesion involved in meiosis I / 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 / regulation of ER to Golgi vesicle-mediated transport / meiotic chromosome segregation / homologous chromosome segregation / tRNA wobble uridine modification / cellular bud tip / regulation of autophagosome assembly / pexophagy / cellular bud neck / spindle pole body / preribosome, small subunit precursor / Major pathway of rRNA processing in the nucleolus and cytosol / chromosome, centromeric region / ribosomal large subunit biogenesis / ribosomal small subunit biogenesis / kinetochore / endocytosis / regulation of protein localization / protein tyrosine kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / nucleolus / Golgi apparatus / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Monopolin complex, subunit Mam1 / Monopolin complex protein MAM1 / 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
Casein kinase I homolog HRR25 / Monopolin complex subunit MAM1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.841 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
DepositionJul 31, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2016Group: Database references
Revision 1.2Sep 20, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Casein kinase I homolog HRR25
C: Monopolin complex subunit MAM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4073
Polymers59,3422
Non-polymers651
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-26 kcal/mol
Surface area21610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.190, 83.986, 67.424
Angle α, β, γ (deg.)90.00, 108.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Casein kinase I homolog HRR25


Mass: 46438.375 Da / Num. of mol.: 1 / Mutation: K38R, N-terminal Ala from tag
Source method: isolated from a genetically manipulated source
Details: surface LYS residues methylated (MLY)
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: HRR25, YPL204W / Production host: Escherichia coli (E. coli)
References: UniProt: P29295, non-specific serine/threonine protein kinase
#2: Protein Monopolin complex subunit MAM1 / / Monopolar microtubule attachment during meiosis 1 protein 1


Mass: 12903.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: surface LYS residues methylated (MLY)
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: MAM1, YER106W / Production host: Escherichia coli (E. coli) / References: UniProt: P40065
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.9
Details: 0.1M CHES pH8.9, 5% Tacsimate, 25 mM YCl3, 19% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.84→48.2 Å / Num. obs: 48597 / % possible obs: 99 % / Redundancy: 6.1 % / Rsym value: 0.152 / Net I/σ(I): 17
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 1.4 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XHL

4xhl


Resolution: 1.841→48.2 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1921 2465 5.07 %
Rwork0.1632 --
obs0.1647 48572 97.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.841→48.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3954 0 1 353 4308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074048
X-RAY DIFFRACTIONf_angle_d1.0165450
X-RAY DIFFRACTIONf_dihedral_angle_d13.6311541
X-RAY DIFFRACTIONf_chiral_restr0.044564
X-RAY DIFFRACTIONf_plane_restr0.004689
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8412-1.87660.29391120.25432053X-RAY DIFFRACTION78
1.8766-1.91490.28521280.23612544X-RAY DIFFRACTION98
1.9149-1.95650.2831280.21792605X-RAY DIFFRACTION99
1.9565-2.00210.26221340.20152598X-RAY DIFFRACTION99
2.0021-2.05210.21941360.19622552X-RAY DIFFRACTION98
2.0521-2.10760.23851600.18582570X-RAY DIFFRACTION99
2.1076-2.16960.2211540.17132577X-RAY DIFFRACTION100
2.1696-2.23970.21821460.16722575X-RAY DIFFRACTION99
2.2397-2.31970.18571360.16122611X-RAY DIFFRACTION99
2.3197-2.41260.19521150.15662585X-RAY DIFFRACTION99
2.4126-2.52240.16891190.15972604X-RAY DIFFRACTION99
2.5224-2.65530.21981420.16362560X-RAY DIFFRACTION98
2.6553-2.82170.19241650.17052607X-RAY DIFFRACTION100
2.8217-3.03950.19761500.16222598X-RAY DIFFRACTION100
3.0395-3.34530.21941500.16192601X-RAY DIFFRACTION99
3.3453-3.82930.14561290.13752583X-RAY DIFFRACTION98
3.8293-4.82370.14121190.13282639X-RAY DIFFRACTION99
4.8237-48.20.18171420.17242645X-RAY DIFFRACTION99
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)
12.10380.5351-0.11571.55030.12450.8033-0.00410.1741-0.2665-0.06140.0191-0.13390.02740.09990.01750.21280.00650.00970.2078-0.04490.2332125.9131-11.641125.0164
21.65770.20140.13771.46820.48461.0117-0.0255-0.3374-0.1210.2447-0.05050.08320.0508-0.07290.03250.19250.0240.01860.21460.02920.1504111.8996-4.6853145.0362
32.2391-0.348-0.29131.53360.00461.5135-0.0632-0.67610.53650.4881-0.0201-0.4884-0.45920.3595-0.0850.4568-0.0272-0.0860.462-0.14830.376123.364917.0531154.4656
42.1744-0.6363-0.24272.24550.57811.1176-0.06140.07690.0414-0.04560.1314-0.344-0.07270.1927-0.02660.1663-0.0336-0.01340.1870.00140.2474134.95584.6626129.7811
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resi 1:83
2X-RAY DIFFRACTION2chain A and resi 84:305
3X-RAY DIFFRACTION3chain A and resi 306:388
4X-RAY DIFFRACTION4chain C

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