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- PDB-4geq: Crystal structure of the Spc24-Spc25/Cnn1 binding interface -

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Basic information

Entry
Database: PDB / ID: 4geq
TitleCrystal structure of the Spc24-Spc25/Cnn1 binding interface
Components
  • Kinetochore protein SPC24
  • Kinetochore protein SPC25
  • Kinetochore-associated protein CNN1
KeywordsCELL CYCLE / protein-protein complex / Ndc80-binding motif / RWD domain / kinetochore components / nucleus
Function / homology
Function and homology information


centromere clustering / negative regulation of kinetochore assembly / Ndc80 complex / sister chromatid biorientation / centromeric DNA binding / chromosome segregation / kinetochore / cell division / protein-containing complex binding / identical protein binding / nucleus
Similarity search - Function
Double Stranded RNA Binding Domain - #430 / Chromosome segregation protein Spc25 / Spc24, Fungi, globular domain superfamily / Kinetochore-Ndc80 subunit Spc24 / Spc24 subunit of Ndc80 / Copper Amine Oxidase; Chain A, domain 1 / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Kinetochore protein SPC25 / Inner kinetochore subunit CNN1 / Kinetochore protein SPC24
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsMalvezzi, F. / Litos, G. / Schleiffer, A. / Heuck, A. / Clausen, T. / Westermann, S.
CitationJournal: Embo J. / Year: 2013
Title: A structural basis for kinetochore recruitment of the Ndc80 complex via two distinct centromere receptors.
Authors: Malvezzi, F. / Litos, G. / Schleiffer, A. / Heuck, A. / Mechtler, K. / Clausen, T. / Westermann, S.
History
DepositionAug 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Jul 1, 2015Group: Data collection
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Sep 13, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Kinetochore protein SPC25
B: Kinetochore protein SPC24
C: Kinetochore protein SPC25
D: Kinetochore protein SPC24
E: Kinetochore-associated protein CNN1
F: Kinetochore-associated protein CNN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4658
Polymers41,2816
Non-polymers1842
Water2,702150
1
A: Kinetochore protein SPC25
B: Kinetochore protein SPC24
F: Kinetochore-associated protein CNN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7334
Polymers20,6403
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-35 kcal/mol
Surface area8670 Å2
MethodPISA
2
C: Kinetochore protein SPC25
D: Kinetochore protein SPC24
E: Kinetochore-associated protein CNN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7334
Polymers20,6403
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-36 kcal/mol
Surface area8530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.142, 61.848, 139.056
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Kinetochore protein SPC25 /


Mass: 9889.295 Da / Num. of mol.: 2 / Fragment: Spc25p C-terminal domain, residues 133-221
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: SPC25, YER018C / Plasmid: pETduett-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P40014
#2: Protein Kinetochore protein SPC24 /


Mass: 7903.027 Da / Num. of mol.: 2 / Fragment: Spc24p C-terminal domain, residues 155-213
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: SPC24, YM9718.16C, YMR117C / Plasmid: pETduett-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q04477
#3: Protein/peptide Kinetochore-associated protein CNN1 / Co-purified with NNF1 protein 1


Mass: 2848.133 Da / Num. of mol.: 2 / Fragment: Cnn1p N-terminal motif, residues 60-84 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P43618
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 1.78 Å3/Da / Density % sol: 30.83 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 15% PEG6000, 5% glycerol; Drop volume: 0.2ul; Protein proportion: 50%; Protein concentration: 6 mg/ml, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.127 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 2, 2011
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 2→61.85 Å / Num. all: 20020 / Num. obs: 19858 / % possible obs: 96.9 % / Observed criterion σ(I): 3 / Redundancy: 4.6 % / Biso Wilson estimate: 24.44 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 8.5
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 2.5 / % possible all: 87.1

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
PHENIXrefinement
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FTX

2ftx


Resolution: 2.01→37.09 Å / Cor.coef. Fo:Fc: 0.9472 / Cor.coef. Fo:Fc free: 0.9174 / SU R Cruickshank DPI: 0.236 / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: Engh & Huber, buster common-compounds v 1.0
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1004 5.09 %RANDOM
Rwork0.2067 ---
all0.2092 19706 --
obs0.2092 19706 96.68 %-
Displacement parametersBiso mean: 37.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.0799 Å20 Å20 Å2
2---1.4656 Å20 Å2
3---1.3857 Å2
Refine analyzeLuzzati coordinate error obs: 0.325 Å
Refinement stepCycle: LAST / Resolution: 2.01→37.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2582 0 12 150 2744
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONf_dihedral_angle_d1232SINUSOIDAL2
X-RAY DIFFRACTIONf_trig_c_planes79HARMONIC2
X-RAY DIFFRACTIONf_gen_planes377HARMONIC5
X-RAY DIFFRACTIONf_it2638HARMONIC20
X-RAY DIFFRACTIONf_nbd
X-RAY DIFFRACTIONf_improper_torsion
X-RAY DIFFRACTIONf_pseud_angle
X-RAY DIFFRACTIONf_chiral_improper_torsion339SEMIHARMONIC5
X-RAY DIFFRACTIONf_sum_occupancies
X-RAY DIFFRACTIONf_utility_distance
X-RAY DIFFRACTIONf_utility_angle
X-RAY DIFFRACTIONf_utility_torsion
X-RAY DIFFRACTIONf_ideal_dist_contact3194SEMIHARMONIC4
X-RAY DIFFRACTIONf_bond_d2638HARMONIC20.01
X-RAY DIFFRACTIONf_angle_deg3581HARMONIC20.97
X-RAY DIFFRACTIONf_omega_torsion2.68
X-RAY DIFFRACTIONf_other_torsion2.95
LS refinement shellResolution: 2.01→2.12 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2625 144 5.51 %
Rwork0.211 2470 -
all0.2139 2614 -
obs-2614 96.68 %
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)
10.64150.31350.09140.80830.76415.56260.00150.01920.08030.00790.01680.0925-0.2206-0.0581-0.0183-0.15160.0391-0.00540.16940.0037-0.1202-0.64221.498125.1567
24.5631-0.4195-1.03320.29730.44284.40120.08580.07110.1853-0.30050.0052-0.113-0.3276-0.0791-0.091-0.14620.0214-0.01950.2466-0.001-0.2233.015-0.77758.0268
31.08080.36010.41971.11961.15595.0982-0.0283-0.0778-0.0597-0.08950.0357-0.0233-0.0819-0.126-0.0074-0.11410.0065-0.01130.14720.0506-0.1423-0.527332.027319.9359
46.0575-0.0644-0.1771.2220.01675.56190.20630.0370.0483-0.1834-0.0815-0.1497-0.25260.1371-0.1249-0.1423-0.0044-0.00190.18110.0021-0.22953.227929.76323.3668
55.7356-1.2451-0.27550.67222.91591.7170.0340.0142-0.1105-0.06340.06220.0697-0.1752-0.0105-0.0962-0.30470.0313-0.02280.30480.0224-0.2694-13.784633.820417.7835
64.4838-2.69520.75270.61332.74482.378-0.01360.0820.0485-0.0259-0.01080.1199-0.216-0.1270.0244-0.30370.081-0.01210.3045-0.0359-0.3033-13.44763.720222.3201
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|133 - A|221 }A133 - 221
2X-RAY DIFFRACTION2{ B|155 - B|213 }B155 - 213
3X-RAY DIFFRACTION3{ C|132 - C|221 }C132 - 221
4X-RAY DIFFRACTION4{ D|155 - D|213 }D155 - 213
5X-RAY DIFFRACTION5{ E|62 - E|79 }E62 - 79
6X-RAY DIFFRACTION6{ F|61 - F|79 }F61 - 79

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