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- PDB-5tcs: Crystal structure of a Dwarf Ndc80 Tetramer -

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Basic information

Entry
Database: PDB / ID: 5tcs
TitleCrystal structure of a Dwarf Ndc80 Tetramer
Components(Kinetochore protein ...) x 4
KeywordsREPLICATION / RWD / CH / coiled-coil / tetramer / Ndc80 / Kinetochore
Function / homology
Function and homology information


centromere clustering / Ndc80 complex / mitotic sister chromatid biorientation / kinetochore organization / sister chromatid biorientation / meiotic chromosome segregation / outer kinetochore / attachment of mitotic spindle microtubules to kinetochore / condensed chromosome, centromeric region / protein localization to kinetochore ...centromere clustering / Ndc80 complex / mitotic sister chromatid biorientation / kinetochore organization / sister chromatid biorientation / meiotic chromosome segregation / outer kinetochore / attachment of mitotic spindle microtubules to kinetochore / condensed chromosome, centromeric region / protein localization to kinetochore / spindle pole body / mitotic spindle organization / spindle microtubule / chromosome segregation / kinetochore / cell division / protein-containing complex binding / identical protein binding / nucleus
Similarity search - Function
Ncd80 complex, Ncd80 subunit / Chromosome segregation protein Spc25 / Spc24, Fungi, globular domain superfamily / Kinetochore protein Nuf2, N-terminal / Nuf2, N-terminal domain superfamily / Nuf2 family / Kinetochore protein Ndc80 / Ndc80 domain superfamily / Domain of unknown function DUF5595 / : ...Ncd80 complex, Ncd80 subunit / Chromosome segregation protein Spc25 / Spc24, Fungi, globular domain superfamily / Kinetochore protein Nuf2, N-terminal / Nuf2, N-terminal domain superfamily / Nuf2 family / Kinetochore protein Ndc80 / Ndc80 domain superfamily / Domain of unknown function DUF5595 / : / HEC/Ndc80p family / Domain of unknown function (DUF5595) / Kinetochore-Ndc80 subunit Spc24 / Spc24 subunit of Ndc80 / Copper Amine Oxidase; Chain A, domain 1 / Actin-binding Protein, T-fimbrin; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Kinetochore protein NUF2 / Kinetochore protein SPC25 / Kinetochore protein NDC80 / Kinetochore protein SPC24
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8313 Å
AuthorsValverde, R. / Harrison, S.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Cell Rep / Year: 2016
Title: Conserved Tetramer Junction in the Kinetochore Ndc80 Complex.
Authors: Valverde, R. / Ingram, J. / Harrison, S.C.
History
DepositionSep 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2016Group: Database references
Revision 1.2Aug 9, 2017Group: Database references / Category: pdbx_related_exp_data_set
Revision 2.0Nov 20, 2019Group: Atomic model / Author supporting evidence / Category: atom_site / pdbx_audit_support
Item: _atom_site.occupancy / _pdbx_audit_support.funding_organization
Revision 2.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Kinetochore protein NDC80
B: Kinetochore protein NUF2
C: Kinetochore protein SPC24
D: Kinetochore protein SPC25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7015
Polymers83,6774
Non-polymers241
Water70339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14680 Å2
ΔGint-141 kcal/mol
Surface area39910 Å2
Unit cell
Length a, b, c (Å)169.381, 186.593, 122.039
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-703-

HOH

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Components

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Kinetochore protein ... , 4 types, 4 molecules ABCD

#1: Protein Kinetochore protein NDC80 / 80 kDa spindle component protein / Nuclear division cycle protein 80 / Two-hybrid interaction with ...80 kDa spindle component protein / Nuclear division cycle protein 80 / Two-hybrid interaction with DMC1 protein 3


Mass: 33276.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: NDC80, HEC1, TID3, YIL144W / Production host: Escherichia coli (E. coli) / References: UniProt: P40460
#2: Protein Kinetochore protein NUF2


Mass: 25415.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: NUF2, YOL069W / Production host: Escherichia coli (E. coli) / References: UniProt: P33895
#3: Protein Kinetochore protein SPC24


Mass: 11975.247 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SPC24, YMR117C, YM9718.16C / Production host: Escherichia coli (E. coli) / References: UniProt: Q04477
#4: Protein Kinetochore protein SPC25


Mass: 13010.204 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SPC25, YER018C / Production host: Escherichia coli (E. coli) / References: UniProt: P40014

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Non-polymers , 2 types, 40 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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

Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6 / Details: 1.2 magnesium sulfate, 0.1 M ME pH 6.0 / PH range: 6.0 - 6.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.83→49.5 Å / Num. obs: 45973 / % possible obs: 100 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.8
Reflection shellResolution: 2.83→2.93 Å / Redundancy: 8.2 % / Rmerge(I) obs: 1.44 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8313→41.75 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 41.75 / Phase error: 27.57
RfactorNum. reflection% reflection
Rfree0.2664 2334 5.08 %
Rwork0.2386 --
obs0.24 45968 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8313→41.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5668 0 1 39 5708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035762
X-RAY DIFFRACTIONf_angle_d0.5747767
X-RAY DIFFRACTIONf_dihedral_angle_d13.0653538
X-RAY DIFFRACTIONf_chiral_restr0.037868
X-RAY DIFFRACTIONf_plane_restr0.0051010
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8313-2.88910.35521160.34012262X-RAY DIFFRACTION89
2.8891-2.95190.34751500.32492541X-RAY DIFFRACTION100
2.9519-3.02050.28821450.29882561X-RAY DIFFRACTION100
3.0205-3.09610.34391360.29952543X-RAY DIFFRACTION100
3.0961-3.17980.34291220.3012564X-RAY DIFFRACTION100
3.1798-3.27330.28851280.28742572X-RAY DIFFRACTION100
3.2733-3.3790.29291540.26952557X-RAY DIFFRACTION100
3.379-3.49970.27661290.25472586X-RAY DIFFRACTION100
3.4997-3.63980.26141370.2512541X-RAY DIFFRACTION100
3.6398-3.80540.29361320.24632597X-RAY DIFFRACTION100
3.8054-4.00590.29881460.23492555X-RAY DIFFRACTION100
4.0059-4.25680.25651480.21512568X-RAY DIFFRACTION100
4.2568-4.58520.23611540.20562582X-RAY DIFFRACTION100
4.5852-5.04620.21531220.19012610X-RAY DIFFRACTION100
5.0462-5.77550.29751430.23282607X-RAY DIFFRACTION100
5.7755-7.27280.28451330.25882644X-RAY DIFFRACTION100
7.2728-49.51520.19881390.20732744X-RAY DIFFRACTION100
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)
16.2376-1.66160.12579.6685-5.60586.49960.06870.4095-0.2557-0.5034-0.3108-0.8642-0.53810.90820.18740.6798-0.27070.10430.6994-0.02540.5603103.9576-62.7145-7.4532
24.54615.15240.14739.49342.39049.9436-0.2074-0.3806-0.68110.0138-0.7262-1.25411.00361.14990.88170.6897-0.30440.61411.1010.06961.1359108.5484-67.3749-13.692
31.74470.6399-0.93742.1799-0.82574.1114-0.2604-00.1693-0.23110.2632-0.1592-0.55620.2188-0.0330.4566-0.0456-0.02830.40550.02460.390685.1032-68.05265.4585
40.4576-0.67140.04090.3765-0.0039-0.3151-0.8416-0.8286-0.00520.88780.9420.29910.5110.7331-0.10310.81760.35150.13340.7861-0.15240.812655.7868-45.351258.1821
56.4271-2.37811.09226.0384-4.17034.91420.28970.58380.4107-0.19610.37080.322-0.5428-0.5066-0.63180.9236-0.0614-0.01820.61220.06460.626663.551-85.1863-12.3375
67.9728-1.9178-0.88616.37511.22935.5055-0.3850.29160.063-0.57030.02260.8047-0.4543-0.60480.28580.3947-0.0584-0.07910.35550.07430.394162.8443-78.74962.453
75.2593-0.6788-3.89375.0774-2.48644.664-0.38191.8590.4656-1.1691-0.47020.1397-0.90631.2082-0.74111.119-0.2533-0.56850.63810.3649-0.299966.1358-70.3498-7.1594
88.39263.5448-0.08697.09360.90485.8755-0.1557-0.28111.2807-0.3138-0.27350.0933-0.6533-0.04020.50120.48440.0783-0.09720.34980.02240.709674.4575-66.58399.109
91.9242-1.4171-1.54831.0921.27331.71220.0233-2.03721.04160.41140.2940.1304-1.64660.42230.06381.3575-0.16860.13171.0753-0.10180.934491.6109-49.93778.124
105.492.8969-1.55286.0581-1.64443.4102-0.34940.3368-0.1799-0.34860.19-0.4299-0.3848-0.01720.09570.31420.0108-0.05390.2210.03750.30975.9686-75.58483.9435
112.0205-4.688-3.81016.52935.09953.07070.2425-0.09620.127-0.87090.04050.0383-0.51840.1142-0.25650.73120.3764-0.09750.9335-0.21360.843454.1263-48.87447.0862
123.3064-2.6296-3.84192.79983.47544.71121.1824-1.2024-1.26430.7476-0.80940.52730.8643-0.1789-0.27411.10420.1033-0.02130.96120.07990.882349.3722-51.169664.5166
138.6457-5.5062-1.91293.97522.28723.5961-0.1718-0.161-1.8691-0.2505-0.50242.8870.51470.10330.78710.79350.30850.07340.8815-0.06441.050840.9679-37.607659.9925
144.3462-2.3336-1.00467.22886.04738.08110.00450.05240.5067-0.770.1008-0.0201-0.89540.4576-0.18570.6310.1529-0.07710.6402-0.17840.73534.3456-5.121370.4603
150.2965-0.28520.31372.9385-0.23820.3337-0.3154-0.44220.96220.1390.0286-2.32310.08340.35770.20331.0721-0.41520.11051.6438-0.45422.065348.47836.356482.3193
162.0714-2.77783.23288.6765-1.6476.4817-0.1470.01370.30180.0063-0.3576-1.0984-0.80910.33130.28642.0201-0.29550.44911.58410.03362.064650.189920.257683.8039
178.10322.1595-0.52334.53390.39772.0011-0.5419-0.64911.22540.45920.3341-0.6125-0.87991.39810.31941.4244-0.0658-0.71671.8507-0.32452.277550.69812.367192.0492
181.8227-1.7380.82943.80080.92221.7156-0.72440.05950.24710.32910.6356-2.1518-0.15971.24320.13751.4567-0.3663-0.40772.1823-0.54491.88743.898411.30594.2396
198.2772-6.9932-4.30687.14533.07292.7514-0.3851-0.75650.5006-0.50930.5919-0.7988-0.07541.1314-0.28280.57590.19520.02651.1193-0.21241.011353.5332-24.423662.6898
200.08090.60450.49414.53583.33274.1245-0.057-0.4554-0.09770.60930.3343-0.9712-0.14470.7502-0.13930.9169-0.0189-0.22760.8336-0.12590.832137.21770.629883.9564
211.25081.0626-2.34560.965-2.18584.97641.0551-0.85333.91410.6221-0.39451.5483-2.5005-1.1301-0.4711.03630.0050.21640.6911-0.13441.233815.966811.210884.6248
227.862-0.41550.19336.15663.75445.75670.1375-0.21010.7022-0.00220.248-0.4966-0.3995-0.0087-0.33451.2841-0.15510.24660.7826-0.23490.77126.082918.107790.5731
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 115 through 148 )
2X-RAY DIFFRACTION2chain 'A' and (resid 149 through 158 )
3X-RAY DIFFRACTION3chain 'A' and (resid 159 through 298 )
4X-RAY DIFFRACTION4chain 'A' and (resid 299 through 682 )
5X-RAY DIFFRACTION5chain 'B' and (resid -13 through 5 )
6X-RAY DIFFRACTION6chain 'B' and (resid 6 through 32 )
7X-RAY DIFFRACTION7chain 'B' and (resid 33 through 39 )
8X-RAY DIFFRACTION8chain 'B' and (resid 40 through 65 )
9X-RAY DIFFRACTION9chain 'B' and (resid 66 through 81 )
10X-RAY DIFFRACTION10chain 'B' and (resid 82 through 137 )
11X-RAY DIFFRACTION11chain 'B' and (resid 138 through 451 )
12X-RAY DIFFRACTION12chain 'C' and (resid 4 through 10 )
13X-RAY DIFFRACTION13chain 'C' and (resid 11 through 23 )
14X-RAY DIFFRACTION14chain 'C' and (resid 24 through 167 )
15X-RAY DIFFRACTION15chain 'C' and (resid 168 through 181 )
16X-RAY DIFFRACTION16chain 'C' and (resid 182 through 189 )
17X-RAY DIFFRACTION17chain 'C' and (resid 190 through 199 )
18X-RAY DIFFRACTION18chain 'C' and (resid 200 through 213 )
19X-RAY DIFFRACTION19chain 'D' and (resid 2 through 24 )
20X-RAY DIFFRACTION20chain 'D' and (resid 25 through 151 )
21X-RAY DIFFRACTION21chain 'D' and (resid 152 through 158 )
22X-RAY DIFFRACTION22chain 'D' and (resid 159 through 221 )

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