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- PDB-8v10: Structure of a Saccharomyces cerevisiae Mps1 peptide bound to dwa... -

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Basic information

Entry
Database: PDB / ID: 8v10
TitleStructure of a Saccharomyces cerevisiae Mps1 peptide bound to dwarf Ndc80 Complex
Components
  • Kinetochore protein NDC80
  • Kinetochore protein SPC24
  • Kinetochore protein SPC25
  • Mps1/NUF2 chimera protein
KeywordsCELL CYCLE / tension sensing / Ndc80 / kinetochore
Function / homology
Function and homology information


centromere clustering / spindle pole body duplication / Ndc80 complex / mitotic sister chromatid biorientation / kinetochore organization / sister chromatid biorientation / meiotic chromosome segregation / meiotic spindle assembly checkpoint signaling / kinetochore binding / regulation of attachment of spindle microtubules to kinetochore ...centromere clustering / spindle pole body duplication / Ndc80 complex / mitotic sister chromatid biorientation / kinetochore organization / sister chromatid biorientation / meiotic chromosome segregation / meiotic spindle assembly checkpoint signaling / kinetochore binding / regulation of attachment of spindle microtubules to kinetochore / mitogen-activated protein kinase kinase / condensed chromosome, centromeric region / attachment of mitotic spindle microtubules to kinetochore / spindle pole body / protein localization to kinetochore / mitotic spindle assembly checkpoint signaling / MAP kinase kinase activity / spindle assembly / protein serine/threonine/tyrosine kinase activity / mitotic spindle organization / chromosome segregation / spindle microtubule / kinetochore / microtubule binding / protein tyrosine kinase activity / protein kinase activity / phosphorylation / cell division / protein serine kinase activity / protein serine/threonine kinase activity / protein-containing complex binding / ATP binding / identical protein binding / nucleus
Similarity search - Function
Serine/threonine-protein kinase Mps1 / 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) ...Serine/threonine-protein kinase Mps1 / 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 / Protein kinase Mps1 family / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
NICKEL (II) ION / Kinetochore protein NUF2 / Kinetochore protein SPC25 / Kinetochore protein NDC80 / Serine/threonine-protein kinase MPS1 / Kinetochore protein SPC24
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 Å
AuthorsZahm, J.A. / Harrison, S.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Curr.Biol. / Year: 2024
Title: A communication hub for phosphoregulation of kinetochore-microtubule attachment.
Authors: Zahm, J.A. / Harrison, S.C.
History
DepositionNov 19, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jun 12, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kinetochore protein NDC80
B: Mps1/NUF2 chimera protein
C: Kinetochore protein SPC24
D: Kinetochore protein SPC25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,3955
Polymers85,3364
Non-polymers591
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15730 Å2
ΔGint-150 kcal/mol
Surface area38010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.657, 168.295, 230.214
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Kinetochore protein NDC80


Mass: 33256.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NDC80, HEC1, TID3, YIL144W / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P40460
#2: Protein Mps1/NUF2 chimera protein


Mass: 27375.189 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MPS1, RPK1, YDL028C, D2785, NUF2, YOL069W / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P54199, UniProt: P33895, mitogen-activated protein kinase kinase
#3: Protein Kinetochore protein SPC24


Mass: 11881.458 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SPC24, YMR117C, YM9718.16C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q04477
#4: Protein Kinetochore protein SPC25


Mass: 12822.623 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SPC25, YER018C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P40014
#5: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
Has ligand of interestN

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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: 4.03 Å3/Da / Density % sol: 69.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 13% polyethylene glycol 8000, 1M sodium chloride 100 mM PIPES pH 6.1

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Data collection

DiffractionMean temperature: 77.36 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 2.0.1 / Wavelength: 1.0309 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0309 Å / Relative weight: 1
ReflectionResolution: 3.02→115.11 Å / Num. obs: 18187 / % possible obs: 64.98 % / Redundancy: 6.1 % / Biso Wilson estimate: 67.66 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.068 / Rrim(I) all: 0.181 / Net I/σ(I): 5.3
Reflection shellResolution: 3.02→3.398 Å / Rmerge(I) obs: 0.853 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 909 / CC1/2: 0.683 / Rpim(I) all: 0.637 / Rrim(I) all: 0.181

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.02→115.11 Å / SU ML: 0.3592 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.5023
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2707 900 5 %
Rwork0.2381 17102 -
obs0.2399 18002 64.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 89.22 Å2
Refinement stepCycle: LAST / Resolution: 3.02→115.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5724 0 1 0 5725
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00115818
X-RAY DIFFRACTIONf_angle_d0.34897840
X-RAY DIFFRACTIONf_chiral_restr0.033876
X-RAY DIFFRACTIONf_plane_restr0.00181019
X-RAY DIFFRACTIONf_dihedral_angle_d4.2623755
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.02-3.210.2209100.3725183X-RAY DIFFRACTION4.23
3.21-3.460.3359520.3352997X-RAY DIFFRACTION22.66
3.46-3.810.35941410.28442688X-RAY DIFFRACTION60.88
3.81-4.360.28272200.23394172X-RAY DIFFRACTION94.59
4.36-5.490.24152340.21884442X-RAY DIFFRACTION99.81
5.5-115.110.25412430.23264620X-RAY DIFFRACTION99.63
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)
11.351764976570.1749160357910.09309589251872.71051867898-0.3221050187841.034734152480.03599326685880.2825040458730.355568976415-0.6660812249660.198536545645-0.230763187308-0.1910424123440.149428757647-0.07302300229551.176838983550.254737440333-0.01674328085810.4035128731990.03818527413180.94825624065134.5225511237-20.364189195486.6720089617
22.37876895218-0.3878557164332.438799685792.31028369122-1.768058569073.55487416544-0.04040009944750.591127559772-0.0583626193717-0.570068166103-0.351638115445-0.247363965467-0.03930508004490.9104915521510.3115567903630.9238751715760.291126345532-0.08302813933790.3701110610090.05485432483460.34741152066417.242482485114.130328975680.0284825449
30.470451668803-0.113046576130.05467605399910.543762642697-0.3455213099890.87870523814-0.346005688470.319002408820.2943548152410.1284652241550.05860556121650.0933322465579-0.1566685833240.244367762899-0.4761289441880.0635225842228-0.132485723985-0.2484805234810.2683707592960.1741893031390.3115458558997.8147185919136.051927389240.6187233345
40.851421388355-0.0006278938618920.2358983502222.3656037412-0.1411685948171.404976880240.124611492963-0.196455883645-0.382640744134-0.02639437996070.005500664706830.2844811605710.334227326501-0.307119927253-0.05070324608311.102905205250.158076690826-0.05690585056860.4714098780860.1983654434960.965884104026.53363292708-0.22786030283591.5980250386
51.44124313851-1.113640877270.2710593088473.179043556650.06830981182210.4028987733690.3462477512320.149456721379-0.434234053508-0.449152784547-0.126524413293-0.107569684660.1255349734280.1527190693980.1404868164291.029184554960.405540039937-0.1518470685040.4578266892590.24088114360.650108141818.6382351963-5.2002572406787.7493274105
60.547753552978-0.02579609344370.1150165414070.565213653722-0.08234724547311.25426314602-0.2822499825130.1999432096650.07673081957680.05338785881620.151390011257-0.04276163114250.137601398215-0.0718409071478-0.1441537190140.171279119701-0.09825397991440.01258211356540.100440786940.07032571444170.1859885607362.263476182427.721764672844.8097668904
70.4873586027380.0274302573666-0.2076300024250.163557740352-0.2448171932571.10898800847-0.08699009617510.4398973275220.196913757263-0.0152886817159-0.008697852750510.1432316864630.011565644587-0.191689502722-0.04436557502060.0858721450847-0.273899289116-0.0284395327120.5076640560140.1816090240440.350589991-8.305912897739.91753991049.35738580399
83.744157984590.271399374319-0.8823884779512.64519739215-0.5877331754620.4858251230240.248460886633-0.383379845984-0.284994975027-0.0184692358494-0.0684192336415-0.4481598714460.01076707220010.375891403147-0.1656309923470.635818169675-0.1773197498810.130091064371.816617396690.2828601039041.368098863268.0372114582744.1533930498-20.6060791089
93.82468299568-0.111553704414-0.5464691484193.29168624882-1.659323427456.64846718303-0.164514991281-0.0516842563794-0.241291347971-0.103985111897-0.138638304219-0.1250840168380.6604759082830.2928746395890.2799125626540.325339774589-0.1624935507670.1133911431280.5966084084520.12044154330.2387296537644.6916489470632.164308482717.2373860915
102.41097646951-0.06569616182520.4190337205060.460797762783-0.4914935758011.81667725030.04232724480950.006665153651030.07058808902880.143855070846-0.0899077286818-0.107571247787-0.3336383324960.4404306463220.2476824485290.424703916427-0.250039548558-0.06459656855551.174830912810.4862317295040.446144321585-7.6539515531951.3091492197-19.3153029047
114.23741905941-1.58584542961-1.484371239355.38445260105-1.583654835042.13725662032-0.152554972080.220565883903-0.0175962105659-0.348862978486-0.0462255928975-0.185374222246-0.2963226547290.2095377964870.144691433420.642308570331-0.305295861118-0.1977452631221.393719030940.4739975204770.656095766709-13.595895379152.6193655828-33.1669435364
123.57794746306-1.246479124641.439812278951.549719469-0.5627417428382.851334235620.3736011909490.300772370353-0.11145271894-0.487538137977-0.212835981790.5281696595710.05636090525790.386420876904-0.1538911974080.636245825666-0.0845938824689-0.07357676525782.168003841640.3080051485750.908372039512-5.5532851114250.2192618589-37.009705658
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 113 through 247 )AA113 - 2471 - 135
22chain 'A' and (resid 248 through 297 )AA248 - 297136 - 185
33chain 'A' and (resid 298 through 682 )AA298 - 682186 - 268
44chain 'B' and (resid 151 through 1064 )BB151 - 10641 - 84
55chain 'B' and (resid 1065 through 1140 )BB1065 - 114085 - 160
66chain 'B' and (resid 1141 through 1451 )BB1141 - 1451161 - 218
77chain 'C' and (resid 6 through 55 )CC6 - 551 - 50
88chain 'C' and (resid 56 through 98 )CC56 - 9851 - 93
99chain 'D' and (resid 1 through 26 )DD1 - 261 - 26
1010chain 'D' and (resid 27 through 62 )DD27 - 6227 - 62
1111chain 'D' and (resid 63 through 83 )DD63 - 8363 - 83
1212chain 'D' and (resid 84 through 115 )DD84 - 11584 - 115

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