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- PDB-3vz9: Crystal structure of the chicken Spc24-Spc25 globular domain -

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Basic information

Entry
Database: PDB / ID: 3vz9
TitleCrystal structure of the chicken Spc24-Spc25 globular domain
Components
  • Spc24 protein
  • Uncharacterized protein
KeywordsCELL CYCLE / RWD domain / kinetochore component / chromosome segregation / Ndc80 complex
Function / homology
Function and homology information


Mitotic Prometaphase / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Resolution of Sister Chromatid Cohesion / EML4 and NUDC in mitotic spindle formation / RHO GTPases Activate Formins / Separation of Sister Chromatids / kinetochore => GO:0000776 / Ndc80 complex / chromosome segregation / cell cycle ...Mitotic Prometaphase / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Resolution of Sister Chromatid Cohesion / EML4 and NUDC in mitotic spindle formation / RHO GTPases Activate Formins / Separation of Sister Chromatids / kinetochore => GO:0000776 / Ndc80 complex / chromosome segregation / cell cycle / cell division / nucleus
Similarity search - Function
Chromosome segregation protein Spc25 / Chromosome segregation protein Spc25, C-terminal / Kinetochore protein Spc25 / Chromosome segregation protein Spc25 / Kinetochore-Ndc80 subunit Spc24 / Spc24 subunit of Ndc80 / Copper Amine Oxidase; Chain A, domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Kinetochore protein SPC25 / Kinetochore protein Spc24
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.03 Å
AuthorsNishino, T. / Fukagawa, T.
CitationJournal: Embo J. / Year: 2013
Title: CENP-T provides a structural platform for outer kinetochore assembly
Authors: Nishino, T. / Rago, F. / Hori, T. / Tomii, K. / Cheeseman, I.M. / Fukagawa, T.
History
DepositionOct 9, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Uncharacterized protein
D: Spc24 protein


Theoretical massNumber of molelcules
Total (without water)20,9952
Polymers20,9952
Non-polymers00
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-22 kcal/mol
Surface area9560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.321, 58.137, 58.479
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 Uncharacterized protein / Spc25 protein


Mass: 12491.179 Da / Num. of mol.: 1 / Fragment: RWD domain, globular domain, UNP residues 131-234
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: SPC25 / Production host: Escherichia coli (E. coli) / References: UniProt: E1C4Y2
#2: Protein Spc24 protein


Mass: 8503.399 Da / Num. of mol.: 1 / Fragment: RWD domain, globular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Escherichia coli (E. coli) / References: UniProt: R4GRT3*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR CHAIN D DOES NOT CURRENTLY EXIST.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 35.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.12M Monosaccharides, 0.1M MES-Imidazol, 30% PEG20K/P550MME, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 28, 2011 / Details: mirror
RadiationMonochromator: SI 111 DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.03→50 Å / Num. all: 79724 / Num. obs: 79657 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 9.9 Å2 / Rsym value: 0.043 / Net I/σ(I): 49
Reflection shellResolution: 1.03→1.05 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 5 / Num. unique all: 4048 / Rsym value: 0.305 / % possible all: 99.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ve7

2ve7


Resolution: 1.03→41.229 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8846 / SU ML: 0.21 / σ(F): 1.34 / Phase error: 18.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2066 2000 2.51 %
Rwork0.1929 --
obs0.1932 79657 99.17 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.031 Å2 / ksol: 0.361 e/Å3
Displacement parametersBiso max: 53.16 Å2 / Biso mean: 16.2841 Å2 / Biso min: 6.33 Å2
Baniso -1Baniso -2Baniso -3
1-1.0151 Å2-0 Å2-0 Å2
2---0.7806 Å20 Å2
3----0.2345 Å2
Refinement stepCycle: LAST / Resolution: 1.03→41.229 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1366 0 0 251 1617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061402
X-RAY DIFFRACTIONf_angle_d1.0921895
X-RAY DIFFRACTIONf_chiral_restr0.077200
X-RAY DIFFRACTIONf_plane_restr0.006243
X-RAY DIFFRACTIONf_dihedral_angle_d13.015525
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.0301-1.05590.24381430.25235465560899
1.0559-1.08440.24991390.231955065645100
1.0844-1.11630.20361420.207355315673100
1.1163-1.15240.20141440.201855225666100
1.1524-1.19360.22961460.199155725718100
1.1936-1.24140.1971380.19555265664100
1.2414-1.29790.18481430.192855525695100
1.2979-1.36630.17861460.191455615707100
1.3663-1.45190.21321410.19555715712100
1.4519-1.5640.20231440.178955925736100
1.564-1.72140.22811430.19225526566999
1.7214-1.97050.23471460.18785519566598
1.9705-2.48260.17971380.18025614575299
2.4826-41.26250.20591470.19515600574795
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)
12.5866-0.6313-0.63973.2464-0.83165.905-0.04320.63740.0018-0.66410.1193-0.0991-0.10140.1661-0.03190.162-0.04110.0080.2003-0.02420.0974-7.5007-18.956-8.0825
23.38830.1658-0.39956.4411-0.36553.49530.00550.11660.4776-0.1371-0.0550.0689-0.53020.04440.00670.1068-0.0106-0.01380.06850.0120.1067-9.042-5.19393.3485
32.68940.7867-0.78542.94470.50631.284-0.0059-0.2353-0.35870.511-0.13380.82310.2074-0.27470.03170.0916-0.01790.06580.10340.00060.1759-16.8384-18.382712.867
44.40444.419-5.25714.6115-5.44746.43410.00980.11080.27150.07150.09280.2179-0.1228-0.0191-0.13990.0827-0.0070.0020.0913-0.00080.0851-6.7384-5.04379.3744
57.14733.7538-2.80794.3708-0.73241.91630.15380.12060.6637-0.07420.05180.2042-0.1584-0.0087-0.2240.09270.00060.0010.07650.01740.092-0.12790.86929.1491
64.94260.1417-1.24761.25790.59231.04760.0664-0.2307-0.08880.146-0.10890.04560.0383-0.01510.05110.1002-0.02610.00670.0872-0.00910.05432.4716-6.369616.0369
73.72811.0382-1.40582.1637-0.93542.65070.0641-0.391-0.14920.185-0.06840.12610.0306-0.03280.01940.0635-0.01940.0030.08750.01260.0588-5.8279-14.725916.7315
83.7923-2.0433-0.09457.7577-0.76373.15930.1560.43990.3146-0.4072-0.0928-0.0072-0.2877-0.2399-0.05910.08380.01040.01050.12590.01870.0738-0.6668-13.9077-0.9282
97.0023.85634.74142.35392.933.6526-0.11460.3309-0.1242-0.23840.1841-0.0257-0.04220.2371-0.07990.0928-0.0068-0.0130.0801-0.00380.0771-3.4097-27.6203-3.9007
106.5008-3.8041-2.46129.18871.88050.9612-0.1242-1.4905-0.05661.00330.1738-0.59380.13590.87320.00720.1452-0.0271-0.00070.3680.030.14289.6869-25.49043.7468
110.0990.41320.05423.26540.28382.0356-0.00780.083-0.08530.01880.07560.16690.2092-0.052-0.06420.07830.0067-0.00290.06760.01420.078-5.2358-26.82127.9304
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN B AND (RESSEQ 131:149)B131 - 149
2X-RAY DIFFRACTION2CHAIN B AND (RESSEQ 150:165)B150 - 165
3X-RAY DIFFRACTION3CHAIN B AND (RESSEQ 166:176)B166 - 176
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 177:183)B177 - 183
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 184:195)B184 - 195
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 196:213)B196 - 213
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 214:233)B214 - 233
8X-RAY DIFFRACTION8CHAIN D AND (RESSEQ 136:145)D136 - 145
9X-RAY DIFFRACTION9CHAIN D AND (RESSEQ 146:162)D146 - 162
10X-RAY DIFFRACTION10CHAIN D AND (RESSEQ 163:168)D163 - 168
11X-RAY DIFFRACTION11CHAIN D AND (RESSEQ 169:195)D169 - 195

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