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- PDB-9n9g: Cryo-EM structure of the human Hec1-Nuf2 dimer bound to the pacli... -

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Basic information

Entry
Database: PDB / ID: 9n9g
TitleCryo-EM structure of the human Hec1-Nuf2 dimer bound to the paclitaxel-stabilized microtubule
Components
  • (Kinetochore protein ...) x 2
  • Tubulin alpha-1B chain
  • Tubulin beta chain
KeywordsCELL CYCLE / microtubule / kinetochore / Ndc80 complex / mitosis
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 / meiotic chromosome segregation / metaphase chromosome alignment / positive regulation of mitotic cell cycle spindle assembly checkpoint / 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 / meiotic chromosome segregation / metaphase chromosome alignment / positive regulation of mitotic cell cycle spindle assembly checkpoint / attachment of spindle microtubules to kinetochore / outer kinetochore / spindle assembly involved in female meiosis I / attachment of mitotic spindle microtubules to kinetochore / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Resolution of Sister Chromatid Cohesion / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Mitotic Prometaphase / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / EML4 and NUDC in mitotic spindle formation / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / COPI-mediated anterograde transport / mitotic spindle assembly checkpoint signaling / centrosome duplication / establishment of mitotic spindle orientation / mitotic sister chromatid segregation / 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 / regulation of protein stability / RHO GTPases Activate Formins / kinetochore / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / Separation of Sister Chromatids / mitotic cell cycle / microtubule cytoskeleton / microtubule binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / nuclear speck / cell division / GTPase activity / centrosome / GTP binding / protein-containing complex binding / nucleoplasm / metal ion binding / identical protein binding / membrane / nucleus / cytoplasm / 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) ...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) / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / TAXOL / Kinetochore protein NDC80 homolog / Tubulin beta chain / Tubulin alpha-1B chain / Kinetochore protein Nuf2
Similarity search - Component
Biological speciesHomo sapiens (human)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsFunabiki, H. / Niu, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM132111 United States
CitationJournal: Sci Adv / Year: 2026
Title: Cryo-EM structure of the human Hec1-Nuf2 dimer bound to the paclitaxel-stabilized microtubule
Authors: Funabiki, H. / Niu, Y.
History
DepositionFeb 10, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: Kinetochore protein NDC80 homolog
A: Tubulin alpha-1B chain
B: Tubulin beta chain
F: Kinetochore protein Nuf2
N: Kinetochore protein NDC80 homolog
a: Tubulin alpha-1B chain
b: Tubulin beta chain
f: Kinetochore protein Nuf2
n: Kinetochore protein NDC80 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)535,94619
Polymers532,2089
Non-polymers3,73810
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Kinetochore protein ... , 2 types, 5 molecules 1NnFf

#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: 74247.945 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NDC80, HEC, HEC1, KNTC2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: O14777
#4: Protein Kinetochore protein Nuf2 / hNuf2 / hNuf2R / hsNuf2 / Cell division cycle-associated protein 1


Mass: 54619.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUF2, CDCA1, NUF2R / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: Q9BZD4

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Protein , 2 types, 4 molecules AaBb

#2: Protein Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 50204.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Brain / Plasmid details: https://www.cytoskeleton.com/t240 / References: UniProt: Q2XVP4
#3: Protein Tubulin beta chain / Beta-tubulin


Mass: 49907.770 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Brain / Plasmid details: https://www.cytoskeleton.com/t240 / References: UniProt: P02554

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Non-polymers , 4 types, 10 molecules

#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#8: Chemical ChemComp-TA1 / TAXOL


Mass: 853.906 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C47H51NO14 / Comment: medication, chemotherapy*YM

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: The human Hec1-Nuf2 dimer bound to the paclitaxel-stabilized microtubule
Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightValue: 4.3 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: Rosetta2(DE3)
Buffer solutionpH: 6.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 54.6 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategoryFitting-ID
7Cootmodel fitting1
9PHENIXmodel refinement1
10ISOLDEmodel refinement1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 284470 / Symmetry type: POINT
Atomic model building
IDProtocolSpaceTarget criteria
1AB INITIO MODELREALFSC=0.5
2
Atomic model building
IDPDB-IDPdb chain-ID 3D fitting-IDAccession codeChain-IDInitial refinement model-IDSource nameTypeChain residue rangeDetails
17SGS

7sgs

A17SGSA1PDBexperimental model
27SGS

7sgs

a17SGSa1PDBexperimental model
37SGS

7sgs

B17SGSB1PDBexperimental model
47SGS

7sgs

b17SGSb1PDBexperimental model
51NOtherother51-79Manually built in COOT and refined in ISOLDE
61NAlphaFoldin silico model80-289Alphafold structure is manually adjusted in COOT and refined in ISOLDE
71NAlphaFoldin silico model13-36Alphafold prediction consistently placed this peptide here and based on the truncation data published in PMID: 23085714, the Alphafold structure is manually adjusted in COOT and refined in ISOLDE
81nAlphaFoldin silico modelAlphafold structure is manually adjusted in COOT and refined in ISOLDE
91fAlphaFoldin silico modelAlphafold structure is manually adjusted in COOT and refined in ISOLDE
1011AlphaFoldin silico modelAlphafold prediction consistently placed this peptide here and based on the truncation data published in PMID: 23085714, the Alphafold structure is manually adjusted in COOT and refined in ISOLDE
112
122
132
142
152
162
172
182
192
202

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