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- PDB-3n4x: Structure of Csm1 full-length -

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Basic information

Entry
Database: PDB / ID: 3n4x
TitleStructure of Csm1 full-length
ComponentsMonopolin complex subunit CSM1
KeywordsREPLICATION / meiosis / rDNA
Function / homology
Function and homology information


microtubule site clamp / chromosome, centromeric core domain / monopolin complex / meiotic sister chromatid segregation / spindle attachment to meiosis I kinetochore / protein localization to nucleolar rDNA repeats / meiotic chromosome segregation / rDNA chromatin condensation / meiotic sister chromatid cohesion, centromeric / homologous chromosome segregation ...microtubule site clamp / chromosome, centromeric core domain / monopolin complex / meiotic sister chromatid segregation / spindle attachment to meiosis I kinetochore / protein localization to nucleolar rDNA repeats / meiotic chromosome segregation / rDNA chromatin condensation / meiotic sister chromatid cohesion, centromeric / homologous chromosome segregation / attachment of mitotic spindle microtubules to kinetochore / mitotic spindle / nuclear envelope / nucleolus / identical protein binding
Similarity search - Function
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 ...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
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.408 Å
AuthorsCorbett, K.D. / Harrison, S.C.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2010
Title: The Monopolin Complex Crosslinks Kinetochore Components to Regulate Chromosome-Microtubule Attachments.
Authors: Corbett, K.D. / Yip, C.K. / Ee, L.S. / Walz, T. / Amon, A. / Harrison, S.C.
History
DepositionMay 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 CSM1
D: Monopolin complex subunit CSM1


Theoretical massNumber of molelcules
Total (without water)87,1064
Polymers87,1064
Non-polymers00
Water00
1
A: Monopolin complex subunit CSM1
B: Monopolin complex subunit CSM1


Theoretical massNumber of molelcules
Total (without water)43,5532
Polymers43,5532
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-48 kcal/mol
Surface area19290 Å2
MethodPISA
2
C: Monopolin complex subunit CSM1
D: Monopolin complex subunit CSM1


Theoretical massNumber of molelcules
Total (without water)43,5532
Polymers43,5532
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-46 kcal/mol
Surface area20130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.269, 105.269, 234.792
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
32
42
13
23
33
43
14
24
34
44
15
25
35
45
16
26
36
46
17
27
37
47

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND RESID 17:25 AND (BACKBONE OR NAME CB)
211CHAIN B AND RESID 17:25 AND (BACKBONE OR NAME CB)
311CHAIN C AND RESID 17:25 AND (BACKBONE OR NAME CB)
411CHAIN D AND RESID 17:25 AND (BACKBONE OR NAME CB)
112CHAIN A AND RESID 26:35 AND (BACKBONE OR NAME CB)
212CHAIN B AND RESID 26:35 AND (BACKBONE OR NAME CB)
312CHAIN C AND RESID 26:35 AND (BACKBONE OR NAME CB)
412CHAIN D AND RESID 26:35 AND (BACKBONE OR NAME CB)
113CHAIN A AND RESID 36:45 AND (BACKBONE OR NAME CB)
213CHAIN B AND RESID 36:45 AND (BACKBONE OR NAME CB)
313CHAIN C AND RESID 36:45 AND (BACKBONE OR NAME CB)
413CHAIN D AND RESID 36:45 AND (BACKBONE OR NAME CB)
114CHAIN A AND RESID 46:55 AND (BACKBONE OR NAME CB)
214CHAIN B AND RESID 46:55 AND (BACKBONE OR NAME CB)
314CHAIN C AND RESID 46:55 AND (BACKBONE OR NAME CB)
414CHAIN D AND RESID 46:55 AND (BACKBONE OR NAME CB)
115CHAIN A AND RESID 56:65 AND (BACKBONE OR NAME CB)
215CHAIN B AND RESID 56:65 AND (BACKBONE OR NAME CB)
315CHAIN C AND RESID 56:65 AND (BACKBONE OR NAME CB)
415CHAIN D AND RESID 56:65 AND (BACKBONE OR NAME CB)
116CHAIN A AND RESID 66:75 AND (BACKBONE OR NAME CB)
216CHAIN B AND RESID 66:75 AND (BACKBONE OR NAME CB)
316CHAIN C AND RESID 66:75 AND (BACKBONE OR NAME CB)
416CHAIN D AND RESID 66:75 AND (BACKBONE OR NAME CB)
117CHAIN A AND RESID 76:180 AND (BACKBONE OR NAME CB)
217CHAIN B AND RESID 76:180 AND (BACKBONE OR NAME CB)
317CHAIN C AND RESID 76:180 AND (BACKBONE OR NAME CB)
417CHAIN D AND RESID 76:180 AND (BACKBONE OR NAME CB)

NCS ensembles :
ID
1
2
3
4
5
6
7

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Components

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


Mass: 21776.379 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CSM1, SPO86, YCR086W, YCR86W / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 pLysS / References: UniProt: P25651

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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: 4.31 Å3/Da / Density % sol: 71.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 150 mM lithium chloride, 12% PEG 2000, 4% 1,4-butanediol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 15, 2008 / Details: mirrors
RadiationMonochromator: side-bounce cryogenically cooled 220 silicon monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. all: 16731 / Num. obs: 16731 / % possible obs: 78.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 125.7 Å2 / Rsym value: 0.116 / Net I/σ(I): 10.5
Reflection shellResolution: 3.4→3.5 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2 / Num. unique all: 248 / Rsym value: 0.517 / % possible all: 14

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ENTRY ID 3N4R

3n4r


Resolution: 3.408→35.04 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2816 824 4.93 %random
Rwork0.2376 ---
obs0.2398 16707 78.56 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 88.053 Å2 / ksol: 0.281 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.408→35.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4949 0 0 0 4949
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115021
X-RAY DIFFRACTIONf_angle_d1.3666777
X-RAY DIFFRACTIONf_dihedral_angle_d17.3951841
X-RAY DIFFRACTIONf_chiral_restr0.087791
X-RAY DIFFRACTIONf_plane_restr0.006851
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A35X-RAY DIFFRACTIONPOSITIONAL
12B35X-RAY DIFFRACTIONPOSITIONAL0.1
13C40X-RAY DIFFRACTIONPOSITIONAL0.103
14D40X-RAY DIFFRACTIONPOSITIONAL0.119
21A50X-RAY DIFFRACTIONPOSITIONAL
22B50X-RAY DIFFRACTIONPOSITIONAL0.068
23C50X-RAY DIFFRACTIONPOSITIONAL0.072
24D50X-RAY DIFFRACTIONPOSITIONAL0.068
31A50X-RAY DIFFRACTIONPOSITIONAL
32B50X-RAY DIFFRACTIONPOSITIONAL0.065
33C50X-RAY DIFFRACTIONPOSITIONAL0.064
34D50X-RAY DIFFRACTIONPOSITIONAL0.066
41A50X-RAY DIFFRACTIONPOSITIONAL
42B50X-RAY DIFFRACTIONPOSITIONAL0.063
43C50X-RAY DIFFRACTIONPOSITIONAL0.065
44D50X-RAY DIFFRACTIONPOSITIONAL0.074
51A50X-RAY DIFFRACTIONPOSITIONAL
52B50X-RAY DIFFRACTIONPOSITIONAL0.074
53C50X-RAY DIFFRACTIONPOSITIONAL0.059
54D50X-RAY DIFFRACTIONPOSITIONAL0.065
61A50X-RAY DIFFRACTIONPOSITIONAL
62B50X-RAY DIFFRACTIONPOSITIONAL0.064
63C50X-RAY DIFFRACTIONPOSITIONAL0.068
64D50X-RAY DIFFRACTIONPOSITIONAL0.067
71A428X-RAY DIFFRACTIONPOSITIONAL
72B428X-RAY DIFFRACTIONPOSITIONAL0.074
73C447X-RAY DIFFRACTIONPOSITIONAL0.08
74D427X-RAY DIFFRACTIONPOSITIONAL0.064
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.408-3.62180.4034270.3788658X-RAY DIFFRACTION20
3.6218-3.90120.3664990.31011715X-RAY DIFFRACTION52
3.9012-4.29310.33421660.24573313X-RAY DIFFRACTION100
4.2931-4.91290.24562050.18943304X-RAY DIFFRACTION100
4.9129-6.18420.30561740.22723400X-RAY DIFFRACTION100
6.1842-35.0420.25041530.2323493X-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)
10.802-1.1940.7259-0.59570.0578-0.80070.1020.07560.07750.4718-0.2620.0280.25980.53950.07380.91170.55310.02180.55130.06670.3549-51.74898.467928.0328
2-0.4924-1.837-1.85920.974-0.5591.3329-0.5931-0.1672-0.31970.36080.73610.01720.672-0.1424-0.0480.9840.6951-0.03460.67160.11020.4956-66.937821.457638.9013
31.47230.81841.31752.06911.1619-0.06340.2249-0.24430.06010.2331-0.31350.09940.0613-0.08720.05810.61080.0860.08960.4955-0.01080.2769-57.26559.7003-0.4575
41.3756-0.3063-1.24241.5709-0.00280.9602-0.53420.74810.2208-0.66970.084-0.2489-0.2860.02380.26570.8545-0.4011-0.13361.15340.23940.7775-47.229128.071-9.4271
5-0.4740.3151-0.63560.507-0.433-0.0415-1.7835-0.5001-0.83710.7422.15760.8886-0.6731.3908-0.110.2047-0.262-0.06951.47620.28640.7794-87.124844.009-35.0853
61.81540.915-1.05790.30380.77330.135-0.23470.8994-0.0345-0.09540.7199-0.0841-0.56150.3161-0.22851.1503-0.2984-0.05261.29750.10950.952-20.468950.549269.3957
71.4888-0.0984-0.68250.90880.74670.2562-1.11331.56950.25250.08590.57590.1751-1.43120.740.1785-0.54030.61170.15160.265-0.08620.5029-73.913231.1772-3.1645
8-1.16490.23040.1321-0.198-0.32910.32740.21560.123-0.70710.15780.166-0.2339-0.18130.09750.07760.6656-0.10920.08891.6941-0.12950.8692-38.996433.767932.8712
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESI 69:180
2X-RAY DIFFRACTION2CHAIN B AND RESI 69:180
3X-RAY DIFFRACTION3CHAIN C AND RESI 69:180
4X-RAY DIFFRACTION4CHAIN D AND RESI 69:180
5X-RAY DIFFRACTION5(CHAIN A OR CHAIN B) AND RESI 16:36
6X-RAY DIFFRACTION6(CHAIN C OR CHAIN D) AND RESI 3:36
7X-RAY DIFFRACTION7(CHAIN A OR CHAIN B) AND RESI 37:68
8X-RAY DIFFRACTION8(CHAIN C OR CHAIN D) AND RESI 37:68

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