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- PDB-7kdf: Structure of Stu2 Bound to dwarf Ndc80c -

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Basic information

Entry
Database: PDB / ID: 7kdf
TitleStructure of Stu2 Bound to dwarf Ndc80c
Components
  • NDC80 isoform 1,NDC80 isoform 1
  • NUF2 isoform 1,NUF2 isoform 1
  • SPC25 isoform 1,SPC25 isoform 1
  • STU2
  • Spc24
KeywordsCELL CYCLE / Stu2 / tension sensing / Ndc80 / kinetochore
Function / homology
Function and homology information


kinetochore => GO:0000776 / centromere clustering / microtubule plus end polymerase / Ndc80 complex / cell cycle / mitotic sister chromatid biorientation / kinetochore organization / establishment or maintenance of microtubule cytoskeleton polarity / sister chromatid biorientation / repair of mitotic kinetochore microtubule attachment defect ...kinetochore => GO:0000776 / centromere clustering / microtubule plus end polymerase / Ndc80 complex / cell cycle / mitotic sister chromatid biorientation / kinetochore organization / establishment or maintenance of microtubule cytoskeleton polarity / sister chromatid biorientation / repair of mitotic kinetochore microtubule attachment defect / meiotic chromosome segregation / outer kinetochore / attachment of mitotic spindle microtubules to kinetochore / condensed chromosome, centromeric region / microtubule nucleation / protein localization to kinetochore / microtubule plus-end binding / spindle pole body / microtubule polymerization / mitotic spindle organization / spindle microtubule / chromosome segregation / kinetochore / spindle pole / cell cortex / microtubule binding / cell division / protein-containing complex binding / identical protein binding / nucleus
Similarity search - Function
Ncd80 complex, Nuf2 subunit / Ncd80 complex, Ncd80 subunit / : / Stu2, C-terminal segment / Spc24, Fungi, globular domain superfamily / Kinetochore protein Nuf2, N-terminal / Nuf2, N-terminal domain superfamily / Nuf2 family / Kinetochore protein Ndc80 / Ndc80 domain superfamily ...Ncd80 complex, Nuf2 subunit / Ncd80 complex, Ncd80 subunit / : / Stu2, C-terminal segment / 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 / XMAP215 family / : / XMAP215/Dis1/CLASP, TOG domain / TOG domain / TOG / Actin-binding Protein, T-fimbrin; domain 1 / HEAT repeat profile. / HEAT, type 2 / Armadillo-like helical / Armadillo-type fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
STU2 isoform 1 / SPC25 isoform 1 / NDC80 isoform 1 / Kinetochore protein NUF2 / Kinetochore protein NUF2 / Kinetochore protein SPC25 / Kinetochore protein NDC80 / Protein STU2 / Kinetochore protein SPC24
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å
AuthorsZahm, J.A. / Stewart, M.G. / Miller, M.P. / Harrison, S.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
Citation
Journal: Elife / Year: 2021
Title: Structural basis of Stu2 recruitment to yeast kinetochores.
Authors: Zahm, J.A. / Stewart, M.G. / Carrier, J.S. / Harrison, S.C. / Miller, M.P.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Adams, P.D.
History
DepositionOct 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 24, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NDC80 isoform 1,NDC80 isoform 1
B: NUF2 isoform 1,NUF2 isoform 1
C: Spc24
D: SPC25 isoform 1,SPC25 isoform 1
E: STU2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,17511
Polymers86,5985
Non-polymers5766
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, Pulldown experiments confirmed that the interaction occurs in solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17650 Å2
ΔGint-229 kcal/mol
Surface area41730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.886, 183.175, 124.317
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
Components on special symmetry positions
IDModelComponents
11B-502-

SO4

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein NDC80 isoform 1,NDC80 isoform 1


Mass: 33041.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NDC80, GI526_G0001489 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A6A5Q2M2, UniProt: P40460*PLUS
#2: Protein NUF2 isoform 1,NUF2 isoform 1


Mass: 25040.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NUF2, GI526_G0005257 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A6A5Q3C2, UniProt: P33895*PLUS
#3: 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)
Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q04477*PLUS
#4: Protein SPC25 isoform 1,SPC25 isoform 1


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, GI526_G0001792 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A6A5PX14, UniProt: P40014*PLUS

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Protein/peptide , 1 types, 1 molecules E

#5: Protein/peptide STU2 / Y55_G0035590.mRNA.1.CDS.1


Mass: 3812.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PTU3, UniProt: P46675*PLUS

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Non-polymers , 2 types, 101 molecules

#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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

CrystalDensity Matthews: 4.94 Å3/Da / Density % sol: 75.08 %
Crystal growTemperature: 288.15 K / Method: vapor diffusion, hanging drop / pH: 7.3 / Details: 1.3 M Ammonium Sulfate 0.1 M Hepes pH 7.3

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.72→44.06 Å / Num. obs: 52106 / % possible obs: 99.03 % / Redundancy: 13.4 % / Biso Wilson estimate: 63.7 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1071 / Rpim(I) all: 0.03047 / Rrim(I) all: 0.1114 / Net I/σ(I): 18.4
Reflection shellResolution: 2.72→2.817 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.9043 / Num. unique obs: 62919 / CC1/2: 0.829 / CC star: 0.952 / Rpim(I) all: 0.03047 / Rrim(I) all: 0.9395 / % possible all: 91.15

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XSCALEdata scaling
PHENIXphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TCS

5tcs


Resolution: 2.72→42.72 Å / SU ML: 0.3439 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.9868
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2417 3882 3.87 %
Rwork0.1976 96468 -
obs0.1993 52103 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 88.87 Å2
Refinement stepCycle: LAST / Resolution: 2.72→42.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5856 0 30 95 5981
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00455988
X-RAY DIFFRACTIONf_angle_d0.73378072
X-RAY DIFFRACTIONf_chiral_restr0.0481901
X-RAY DIFFRACTIONf_plane_restr0.00471043
X-RAY DIFFRACTIONf_dihedral_angle_d12.3263775
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.72-2.750.3402810.29882245X-RAY DIFFRACTION64.54
2.75-2.780.27491840.27563440X-RAY DIFFRACTION99.89
2.78-2.820.28371340.26843503X-RAY DIFFRACTION100
2.82-2.860.30841380.25953466X-RAY DIFFRACTION99.97
2.86-2.90.28411240.26633562X-RAY DIFFRACTION100
2.9-2.940.29221430.28133459X-RAY DIFFRACTION100
2.94-2.990.34981390.26033530X-RAY DIFFRACTION99.97
2.99-3.040.26481420.24593474X-RAY DIFFRACTION99.94
3.04-3.090.23551270.24283500X-RAY DIFFRACTION99.92
3.09-3.150.25231500.23233458X-RAY DIFFRACTION100
3.15-3.210.28391360.23013535X-RAY DIFFRACTION99.97
3.21-3.270.31751450.23353445X-RAY DIFFRACTION99.81
3.27-3.340.28341450.22983469X-RAY DIFFRACTION99.94
3.34-3.420.24941280.22463469X-RAY DIFFRACTION100
3.42-3.510.2991680.21533479X-RAY DIFFRACTION99.97
3.51-3.60.22911170.20243562X-RAY DIFFRACTION99.97
3.6-3.710.21721740.18893447X-RAY DIFFRACTION100
3.71-3.830.2291240.18333510X-RAY DIFFRACTION99.97
3.83-3.960.19811530.18173478X-RAY DIFFRACTION99.97
3.96-4.120.23741320.16643499X-RAY DIFFRACTION100
4.12-4.310.19931520.16453503X-RAY DIFFRACTION99.95
4.31-4.540.17621360.17143465X-RAY DIFFRACTION99.7
4.54-4.820.20841550.16473476X-RAY DIFFRACTION99.84
4.82-5.190.20031130.16233527X-RAY DIFFRACTION99.97
5.19-5.710.25421350.21093484X-RAY DIFFRACTION100
5.71-6.540.26521420.22033506X-RAY DIFFRACTION100
6.54-8.230.31291230.21153496X-RAY DIFFRACTION100
8.23-44.060.21821420.1563481X-RAY DIFFRACTION99.56
Refinement TLS params.Method: refined / Origin x: -22.7267285986 Å / Origin y: -43.5708296011 Å / Origin z: -24.3484578945 Å
111213212223313233
T0.545825823506 Å20.0648460395688 Å2-0.0355027835481 Å2-0.5784368939 Å2-0.0631253503745 Å2--0.532251529512 Å2
L0.492137350313 °2-0.436911092293 °2-0.545626809601 °2-0.745365156365 °20.588040000098 °2--0.726601084739 °2
S-0.0495236786863 Å °-0.227628151116 Å °0.179668995389 Å °-0.0746571154109 Å °0.154699250998 Å °0.016910438894 Å °-0.233360459841 Å °0.217338020121 Å °0.00387306042912 Å °
Refinement TLS groupSelection details: all

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