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- PDB-8g0p: Crystal structure of the human Ndc80:Nuf2 loop region -

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Basic information

Entry
Database: PDB / ID: 8g0p
TitleCrystal structure of the human Ndc80:Nuf2 loop region
Components
  • Kinetochore protein NDC80 homolog
  • Kinetochore protein Nuf2
KeywordsCELL CYCLE / Cell division / chromosome segregation / kinetochore / Ndc80 complex / Ndc80 / Nuf2 / loop / hinge / human
Function / homology
Function and homology information


G2/MI transition of meiotic cell cycle / kinetochore adaptor activity / skeletal muscle satellite cell proliferation / Ndc80 complex / kinetochore organization / positive regulation of mitotic cell cycle spindle assembly checkpoint / metaphase chromosome alignment / meiotic chromosome segregation / attachment of spindle microtubules to kinetochore / outer kinetochore ...G2/MI transition of meiotic cell cycle / kinetochore adaptor activity / skeletal muscle satellite cell proliferation / Ndc80 complex / kinetochore organization / positive regulation of mitotic cell cycle spindle assembly checkpoint / metaphase chromosome alignment / meiotic chromosome segregation / attachment of spindle microtubules to kinetochore / outer kinetochore / spindle assembly involved in female meiosis I / attachment of mitotic spindle microtubules to kinetochore / mitotic spindle assembly checkpoint signaling / centrosome duplication / mitotic sister chromatid segregation / establishment of mitotic spindle orientation / chromosome, centromeric region / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / cyclin binding / Resolution of Sister Chromatid Cohesion / mitotic spindle organization / chromosome segregation / RHO GTPases Activate Formins / regulation of protein stability / kinetochore / Separation of Sister Chromatids / mitotic cell cycle / microtubule binding / nuclear speck / cell division / centrosome / protein-containing complex binding / nucleoplasm / identical protein binding / nucleus / membrane / cytosol
Similarity search - Function
Kinetochore protein NDC80 loop region / 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)
Similarity search - Domain/homology
Kinetochore protein NDC80 homolog / Kinetochore protein Nuf2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZahm, J.A. / Jenni, S. / Harrison, S.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)GM124165 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: Open Biology / Year: 2023
Title: Structure of the Ndc80 complex and its interactions at the yeast kinetochore-microtubule interface.
Authors: Zahm, J.A. / Jenni, S. / Harrison, S.C.
History
DepositionFeb 1, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kinetochore protein NDC80 homolog
B: Kinetochore protein Nuf2


Theoretical massNumber of molelcules
Total (without water)28,2192
Polymers28,2192
Non-polymers00
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-67 kcal/mol
Surface area16120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.903, 72.259, 80.065
Angle α, β, γ (deg.)90.000, 98.560, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Kinetochore protein NDC80 homolog / Highly expressed in cancer protein / Kinetochore protein Hec1 / HsHec1 / Kinetochore-associated ...Highly expressed in cancer protein / Kinetochore protein Hec1 / HsHec1 / Kinetochore-associated protein 2 / Retinoblastoma-associated protein HEC


Mass: 16652.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NDC80, HEC, HEC1, KNTC2 / Production host: Escherichia coli (E. coli) / References: UniProt: O14777
#2: Protein Kinetochore protein Nuf2 / hNuf2 / hNuf2R / hsNuf2 / Cell division cycle-associated protein 1


Mass: 11567.251 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUF2, CDCA1, NUF2R / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BZD4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
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: 2.53 Å3/Da / Density % sol: 51.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% (w/v) polyethylene glycol 4000, 0.1 M TRIS pH 8.6, and 0.2 M magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.84→40.75 Å / Num. obs: 36742 / % possible obs: 98.7 % / Redundancy: 6.8 % / Biso Wilson estimate: 47.1 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.05 / Rrim(I) all: 0.132 / Net I/σ(I): 9.5
Reflection shellResolution: 1.84→1.87 Å / Redundancy: 5.7 % / Rmerge(I) obs: 4.03 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1005 / CC1/2: 0.33 / Rpim(I) all: 1.82 / Rrim(I) all: 4.44 / % possible all: 84.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→40.75 Å / SU ML: 0.3084 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.4717
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2968 1836 5 %
Rwork0.26 34906 -
obs0.262 36742 98.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.66 Å2
Refinement stepCycle: LAST / Resolution: 2→40.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1970 0 0 13 1983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00261995
X-RAY DIFFRACTIONf_angle_d0.45622668
X-RAY DIFFRACTIONf_chiral_restr0.0277297
X-RAY DIFFRACTIONf_plane_restr0.0033346
X-RAY DIFFRACTIONf_dihedral_angle_d3.6001260
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.4991280.51492440X-RAY DIFFRACTION91.39
2.05-2.110.44241310.48232657X-RAY DIFFRACTION97.76
2.11-2.180.42891780.44762723X-RAY DIFFRACTION99.18
2.18-2.260.40391390.38192664X-RAY DIFFRACTION98.94
2.26-2.350.37011640.32972655X-RAY DIFFRACTION98.22
2.35-2.460.33091550.3012716X-RAY DIFFRACTION98.59
2.46-2.590.3311230.28362763X-RAY DIFFRACTION99.38
2.59-2.750.36231510.28882712X-RAY DIFFRACTION99.51
2.75-2.960.3521420.2562686X-RAY DIFFRACTION99.4
2.96-3.260.27781110.27092740X-RAY DIFFRACTION99.41
3.26-3.730.30121390.25152704X-RAY DIFFRACTION98.96
3.73-4.70.21091270.2012741X-RAY DIFFRACTION99.86
4.7-40.750.27571480.22662705X-RAY DIFFRACTION98.72
Refinement TLS params.Method: refined / Origin x: -15.5160948454 Å / Origin y: 3.20932480929 Å / Origin z: 29.4258775818 Å
111213212223313233
T0.673901053404 Å20.0321103241127 Å20.0158146086533 Å2-0.687879151338 Å2-0.0450110512032 Å2--0.558401897984 Å2
L-0.0061328170901 °2-0.314891142814 °2-0.787308253579 °2-0.287526116768 °20.979972770059 °2--1.84164670038 °2
S0.166046357282 Å °-0.026156265894 Å °0.0729343219773 Å °-0.184470327445 Å °0.0145180593242 Å °-0.0810856715833 Å °-0.614391857945 Å °-0.0566112890914 Å °0.0153445629062 Å °
Refinement TLS groupSelection details: all

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