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- PDB-8v11: Structure of a Saccharomyces cerevisiae Ipl1 peptide Bound to dwa... -

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Basic information

Entry
Database: PDB / ID: 8v11
TitleStructure of a Saccharomyces cerevisiae Ipl1 peptide Bound to dwarf Ndc80 complex
Components
  • Ipl1/Nuf2 chimera protein
  • Kinetochore protein NDC80
  • Kinetochore protein SPC24
  • Kinetochore protein SPC25
KeywordsCELL CYCLE / Stu2 / tension sensing / 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 / condensed chromosome, centromeric region / attachment of mitotic spindle microtubules to kinetochore / protein localization to kinetochore ...centromere clustering / Ndc80 complex / mitotic sister chromatid biorientation / kinetochore organization / sister chromatid biorientation / meiotic chromosome segregation / outer kinetochore / condensed chromosome, centromeric region / attachment of mitotic spindle microtubules to kinetochore / 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
Spc24, Fungi, globular domain superfamily / Kinetochore protein Nuf2, N-terminal / Kinetochore-Ndc80 subunit Spc24 / Nuf2, N-terminal domain superfamily / Nuf2 family / Spc24 subunit of Ndc80 / Kinetochore protein Ndc80 / Ndc80 domain superfamily / Domain of unknown function DUF5595 / : ...Spc24, Fungi, globular domain superfamily / Kinetochore protein Nuf2, N-terminal / Kinetochore-Ndc80 subunit Spc24 / Nuf2, N-terminal domain superfamily / Nuf2 family / Spc24 subunit of Ndc80 / Kinetochore protein Ndc80 / Ndc80 domain superfamily / Domain of unknown function DUF5595 / : / HEC/Ndc80p family / Domain of unknown function (DUF5595)
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 / MOLECULAR REPLACEMENT / Resolution: 3.95 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: Ipl1/Nuf2 chimera protein
C: Kinetochore protein SPC24
D: Kinetochore protein SPC25
E: Kinetochore protein NDC80
F: Ipl1/Nuf2 chimera protein
G: Kinetochore protein SPC24
H: Kinetochore protein SPC25


Theoretical massNumber of molelcules
Total (without water)166,9408
Polymers166,9408
Non-polymers00
Water00
1
A: Kinetochore protein NDC80
B: Ipl1/Nuf2 chimera protein
C: Kinetochore protein SPC24
D: Kinetochore protein SPC25


Theoretical massNumber of molelcules
Total (without water)83,4704
Polymers83,4704
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13390 Å2
ΔGint-119 kcal/mol
Surface area41170 Å2
MethodPISA
2
E: Kinetochore protein NDC80
F: Ipl1/Nuf2 chimera protein
G: Kinetochore protein SPC24
H: Kinetochore protein SPC25


Theoretical massNumber of molelcules
Total (without water)83,4704
Polymers83,4704
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13700 Å2
ΔGint-117 kcal/mol
Surface area40930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.757, 114.757, 423.841
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 113 through 275 or resid 277 through 312 or resid 314 through 684))
d_2ens_1(chain "E" and (resid 113 through 275 or resid 277 through 312 or resid 314 through 684))
d_1ens_2chain "B"
d_2ens_2chain "F"
d_1ens_3chain "C"
d_2ens_3chain "G"
d_1ens_4(chain "D" and resid 3 through 220)
d_2ens_4chain "H"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1ALAALAVALVALAA113 - 2753 - 165
d_12ens_1LYSLYSVALVALAA277 - 312167 - 202
d_13ens_1ILEILEGLUGLUAA314 - 684204 - 272
d_21ens_1ALAALAVALVALEE113 - 2753 - 165
d_22ens_1LYSLYSVALVALEE277 - 312167 - 202
d_23ens_1ILEILEGLUGLUEE314 - 684204 - 272
d_11ens_2ILEILEGLNGLNBB48 - 145119 - 227
d_21ens_2ILEILEGLNGLNFF48 - 145119 - 227
d_11ens_3ASNASNGLYGLYCC6 - 2126 - 99
d_21ens_3ASNASNGLYGLYGG6 - 2126 - 99
d_11ens_4SERSERSERSERDD3 - 2203 - 114
d_21ens_4SERSERSERSERHH3 - 2203 - 114

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4

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Components

#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: 32460.154 Da / Num. of mol.: 2
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 Ipl1/Nuf2 chimera protein


Mass: 26548.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: IPL1, NUF2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P33895
#3: Protein Kinetochore protein SPC24


Mass: 11752.278 Da / Num. of mol.: 2
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: 12709.465 Da / Num. of mol.: 2
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

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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: 4.18 Å3/Da / Density % sol: 70.57 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% polyethylene glycol 2000 monomethyl ether,500 mM sodium chloride,50 mM Tris pH 7.5

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: Liquid nitrogen cryostream / 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: 3.95→48.53 Å / Num. obs: 10981 / % possible obs: 42.6 % / Redundancy: 17.4 % / Biso Wilson estimate: 98.15 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.556 / Rpim(I) all: 0.135 / Rrim(I) all: 0.573 / Net I/σ(I): 6.7
Reflection shellResolution: 3.95→4.448 Å / Redundancy: 19 % / Rmerge(I) obs: 3.899 / Num. unique obs: 785 / CC1/2: 0.609 / Rpim(I) all: 0.909 / Rrim(I) all: 4.006 / % possible all: 10.5

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.95→48.53 Å / SU ML: 0.7326 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 45.7832
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3266 559 5.1 %
Rwork0.2666 10412 -
obs0.2696 10971 42.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 162.25 Å2
Refinement stepCycle: LAST / Resolution: 3.95→48.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11239 0 0 0 11239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005711461
X-RAY DIFFRACTIONf_angle_d1.125715467
X-RAY DIFFRACTIONf_chiral_restr0.05921731
X-RAY DIFFRACTIONf_plane_restr0.00542013
X-RAY DIFFRACTIONf_dihedral_angle_d15.1524385
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS2.21255604163
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS2.63049277242
ens_3d_2CCX-RAY DIFFRACTIONTorsion NCS1.81705749813
ens_4d_2DDX-RAY DIFFRACTIONTorsion NCS1.89725207791
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.95-4.350.3173320.2383522X-RAY DIFFRACTION8.84
4.35-4.980.3083910.21571501X-RAY DIFFRACTION25.15
4.98-6.270.35431100.32232155X-RAY DIFFRACTION35.25
6.28-48.530.32513260.2656234X-RAY DIFFRACTION97.26

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