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- PDB-5ktb: Structure of a complex between S. cerevisiae Csm1 and Mam1 -

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Basic information

Entry
Database: PDB / ID: 5ktb
TitleStructure of a complex between S. cerevisiae Csm1 and Mam1
Components
  • Monopolin complex subunit CSM1
  • Monopolin complex subunit MAM1
KeywordsREPLICATION / monopolin
Function / homology
Function and homology information


meiotic sister chromatid cohesion involved in meiosis I / monopolin complex / spindle attachment to meiosis I kinetochore / protein localization to nucleolar rDNA repeats / meiotic chromosome segregation / meiotic sister chromatid cohesion, centromeric / rDNA chromatin condensation / homologous chromosome segregation / kinetochore / nuclear envelope ...meiotic sister chromatid cohesion involved in meiosis I / monopolin complex / spindle attachment to meiosis I kinetochore / protein localization to nucleolar rDNA repeats / meiotic chromosome segregation / meiotic sister chromatid cohesion, centromeric / rDNA chromatin condensation / homologous chromosome segregation / kinetochore / nuclear envelope / nucleolus / identical protein binding / nucleus
Similarity search - Function
Monopolin complex, subunit Mam1 / Monopolin complex protein MAM1 / Aspartate Aminotransferase, domain 1 - #80 / Monopolin complex subunit Csm1/Pcs1, C-terminal / Csm1/Pcs1, C-terminal domain superfamily / Monopolin complex subunit Csm1/Pcs1 / Csm1 N-terminal domain / Chromosome segregation protein Csm1/Pcs1 / Csm1 N-terminal domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 ...Monopolin complex, subunit Mam1 / Monopolin complex protein MAM1 / Aspartate Aminotransferase, domain 1 - #80 / Monopolin complex subunit Csm1/Pcs1, C-terminal / Csm1/Pcs1, C-terminal domain superfamily / Monopolin complex subunit Csm1/Pcs1 / Csm1 N-terminal domain / Chromosome segregation protein Csm1/Pcs1 / Csm1 N-terminal domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 / Aspartate Aminotransferase, domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Monopolin complex subunit CSM1 / Monopolin complex subunit MAM1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsCorbett, K.D. / Harrison, S.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Cell Rep / Year: 2012
Title: Molecular architecture of the yeast monopolin complex.
Authors: Corbett, K.D. / Harrison, S.C.
History
DepositionJul 11, 2016Deposition site: RCSB / Processing site: RCSB
SupersessionJul 20, 2016ID: 4EMC
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Author supporting evidence / Data collection / Derived calculations
Category: pdbx_audit_support / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 4, 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

Downloads & links

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Assembly

Deposited unit
A: Monopolin complex subunit CSM1
B: Monopolin complex subunit CSM1
C: Monopolin complex subunit MAM1


Theoretical massNumber of molelcules
Total (without water)51,5953
Polymers51,5953
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7580 Å2
ΔGint-68 kcal/mol
Surface area21240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.851, 101.851, 225.077
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Monopolin complex subunit CSM1 / / Chromosome segregation in meiosis protein 1


Mass: 21776.379 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CSM1, SPO86, YCR086W, YCR86W / Production host: Escherichia coli (E. coli) / References: UniProt: P25651
#2: Protein Monopolin complex subunit MAM1 / / Monopolar microtubule attachment during meiosis 1 protein 1


Mass: 8042.377 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MAM1, YER106W / Production host: Escherichia coli (E. coli) / References: UniProt: P40065

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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: 6.53 Å3/Da / Density % sol: 81.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES, pH 7.5, 100 mM magnesium chloride, 6% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 21, 2011
RadiationMonochromator: cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. obs: 26073 / % possible obs: 98.6 % / Redundancy: 2.3 % / Biso Wilson estimate: 93.4 Å2 / Rmerge(I) obs: 0.125 / Rsym value: 0.091 / Net I/σ(I): 5.5
Reflection shellResolution: 3.05→3.22 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.991 / Mean I/σ(I) obs: 1.4 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3N4X

3n4x


Resolution: 3.05→24.92 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.13
RfactorNum. reflection% reflection
Rfree0.2406 1312 5.04 %
Rwork0.2132 --
obs0.2146 26017 98.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.05→24.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2834 0 0 0 2834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092876
X-RAY DIFFRACTIONf_angle_d1.1583883
X-RAY DIFFRACTIONf_dihedral_angle_d15.0671761
X-RAY DIFFRACTIONf_chiral_restr0.058450
X-RAY DIFFRACTIONf_plane_restr0.007494
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0501-3.1720.35991460.35822701X-RAY DIFFRACTION99
3.172-3.31610.34371410.31112725X-RAY DIFFRACTION99
3.3161-3.49050.31721490.27182718X-RAY DIFFRACTION99
3.4905-3.70850.29831490.25372736X-RAY DIFFRACTION99
3.7085-3.99380.24811500.20122759X-RAY DIFFRACTION99
3.9938-4.39370.18911500.17362763X-RAY DIFFRACTION99
4.3937-5.0250.18261700.16282740X-RAY DIFFRACTION99
5.025-6.31380.26071450.22382783X-RAY DIFFRACTION98
6.3138-24.92040.2231120.19882780X-RAY DIFFRACTION93
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)
10.4599-0.09220.7915-0.0191-0.34692.1066-0.13780.2950.04170.40180.2923-0.03960.36590.0843-0.10641.12440.6009-0.25750.80840.01540.6206-66.837125.325122.2876
20.4245-0.53030.69190.8243-1.2231.4669-0.17760.50830.11450.41360.1175-0.1470.19760.0402-0.12621.02890.5386-0.19440.9161-0.04140.6269-59.406619.192612.164
30.4195-0.0553-0.29710.3597-0.4070.76070.25430.27360.2425-0.9212-0.16620.1491-0.0770.14290.16431.41970.5987-0.25880.9823-0.13730.7629-48.15686.306321.7697
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C

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