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- EMDB-49168: Cryo-EM structure of the human Hec1-Nuf2 dimer bound to the pacli... -

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Basic information

Entry
Database: EMDB / ID: EMD-49168
TitleCryo-EM structure of the human Hec1-Nuf2 dimer bound to the paclitaxel-stabilized microtubule
Map data
Sample
  • Complex: The human Hec1-Nuf2 dimer bound to the paclitaxel-stabilized microtubule
    • Protein or peptide: Kinetochore protein NDC80 homolog
    • Protein or peptide: Tubulin alpha-1B chain
    • Protein or peptide: Tubulin beta chain
    • Protein or peptide: Kinetochore protein Nuf2
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: TAXOL
Keywordsmicrotubule / kinetochore / Ndc80 complex / mitosis / cell cycle
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 / attachment of spindle microtubules to kinetochore / positive regulation of mitotic cell cycle spindle assembly checkpoint / spindle assembly involved in female meiosis I ...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 / attachment of spindle microtubules to kinetochore / positive regulation of mitotic cell cycle spindle assembly checkpoint / spindle assembly involved in female meiosis I / outer kinetochore / 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 / establishment of mitotic spindle orientation / centrosome duplication / 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 / structural constituent of cytoskeleton / kinetochore / 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 / membrane / metal ion binding / identical protein binding / 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 ...: / 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
Kinetochore protein NDC80 homolog / Tubulin beta chain / Tubulin alpha-1B chain / Kinetochore protein Nuf2
Similarity search - Component
Biological speciesHomo sapiens (human) / Sus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsFunabiki H / Niu Y
Funding support United States, 1 items
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, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49168.png

Downloads & links

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Map

FileDownload / File: emd_49168.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 320 pix.
= 346.112 Å		1.08 Å/pix.
x 320 pix.
= 346.112 Å		1.08 Å/pix.
x 320 pix.
= 346.112 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0816 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.21363682 - 0.50840473
Average (Standard dev.)0.0008009466 (±0.015180993)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 346.112 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49168_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_49168_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49168_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The human Hec1-Nuf2 dimer bound to the paclitaxel-stabilized micr...

EntireName: The human Hec1-Nuf2 dimer bound to the paclitaxel-stabilized microtubule
Components
  • Complex: The human Hec1-Nuf2 dimer bound to the paclitaxel-stabilized microtubule
    • Protein or peptide: Kinetochore protein NDC80 homolog
    • Protein or peptide: Tubulin alpha-1B chain
    • Protein or peptide: Tubulin beta chain
    • Protein or peptide: Kinetochore protein Nuf2
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: TAXOL

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Supramolecule #1: The human Hec1-Nuf2 dimer bound to the paclitaxel-stabilized micr...

SupramoleculeName: The human Hec1-Nuf2 dimer bound to the paclitaxel-stabilized microtubule
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.3 kDa/nm

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Macromolecule #1: Kinetochore protein NDC80 homolog

MacromoleculeName: Kinetochore protein NDC80 homolog / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 74.247945 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: AGTMKRSSVS SGGAGRLSMQ ELRSQDVNKQ GLYTPQTKEK PTFGKLSINK PTSERKVSLF GKRTSGHGSR NSQLGIFSSS EKIKDPRPL NDKAFIQQCI RQLCEFLTEN GYAHNVSMKS LQAPSVKDFL KIFTFLYGFL CPSYELPDTK FEEEVPRIFK D LGYPFALS ...String:
AGTMKRSSVS SGGAGRLSMQ ELRSQDVNKQ GLYTPQTKEK PTFGKLSINK PTSERKVSLF GKRTSGHGSR NSQLGIFSSS EKIKDPRPL NDKAFIQQCI RQLCEFLTEN GYAHNVSMKS LQAPSVKDFL KIFTFLYGFL CPSYELPDTK FEEEVPRIFK D LGYPFALS KSSMYTVGAP HTWPHIVAAL VWLIDCIKIH TAMKESSPLF DDGQPWGEET EDGIMHNKLF LDYTIKCYES FM SGADSFD EMNAELQSKL KDLFNVDAFK LESLEAKNRA LNEQIARLEQ EREKEPNRLE SLRKLKASLQ GDVQKYQAYM SNL ESHSAI LDQKLNGLNE EIARVELECE TIKQENTRLQ NIIDNQKYSV ADIERINHER NELQQTINKL TKDLEAEQQK LWNE ELKYA RGKEAIETQL AEYHKLARKL KLIPKGAENS KGYDFEIKFN PEAGANCLVK YRAQVYVPLK ELLNETEEEI NKALN KKMG LEDTLEQLNA MITESKRSVR TLKEEVQKLD DLYQQKIKEA EEEDEKCASE LESLEKHKHL LESTVNQGLS EAMNEL DAV QREYQLVVQT TTEERRKVGN NLQRLLEMVA THVGSVEKHL EEQIAKVDRE YEECMSEDLS ENIKEIRDKY EKKATLI KS SEE

UniProtKB: Kinetochore protein NDC80 homolog

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Macromolecule #2: Tubulin alpha-1B chain

MacromoleculeName: Tubulin alpha-1B chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig) / Organ: Brain
Molecular weightTheoretical: 50.204445 KDa
SequenceString: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFLVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE ...String:
MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFLVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE FSIYPAPQVS TAVVEPYNSI LTTHTTLEHS DCAFMVDNEA IYDICRRNLD IERPTYTNLN RLISQIVSSI TA SLRFDGA LNVDLTEFQT NLVPYPRIHF PLATYAPVIS AEKAYHEQLS VAEITNACFE PANQMVKCDP RHGKYMACCL LYR GDVVPK DVNAAIATIK TKRSIQFVDW CPTGFKVGIN YQPPTVVPGG DLAKVQRAVC MLSNTTAIAE AWARLDHKFD LMYA KRAFV HWYVGEGMEE GEFSEAREDM AALEKDYEEV GVDSVEGEGE EEGEEY

UniProtKB: Tubulin alpha-1B chain

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Macromolecule #3: Tubulin beta chain

MacromoleculeName: Tubulin beta chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig) / Organ: Brain
Molecular weightTheoretical: 49.90777 KDa
SequenceString: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEAAGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKESESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS ...String:
MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEAAGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKESESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS VVPSPKVSDT VVEPYNATLS VHQLVENTDE TYCIDNEALY DICFRTLKLT TPTYGDLNHL VSATMSGVTT CL RFPGQLN ADLRKLAVNM VPFPRLHFFM PGFAPLTSRG SQQYRALTVP ELTQQMFDAK NMMAACDPRH GRYLTVAAVF RGR MSMKEV DEQMLNVQNK NSSYFVEWIP NNVKTAVCDI PPRGLKMSAT FIGNSTAIQE LFKRISEQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QDATADEQGE FEEEGEEDEA

UniProtKB: Tubulin beta chain

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Macromolecule #4: Kinetochore protein Nuf2

MacromoleculeName: Kinetochore protein Nuf2 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.619875 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: AGTMETLSFP RYNVAEIVIH IRNKILTGAD GKNLTKNDLY PNPKPEVLHM IYMRALQIVY GIRLEHFYMM PVNSEVMYPH LMEGFLPFS NLVTHLDSFL PICRVNDFET ADILCPKAKR TSRFLSGIIN FIHFREACRE TYMEFLWQYK SSADKMQQLN A AHQEALMK ...String:
AGTMETLSFP RYNVAEIVIH IRNKILTGAD GKNLTKNDLY PNPKPEVLHM IYMRALQIVY GIRLEHFYMM PVNSEVMYPH LMEGFLPFS NLVTHLDSFL PICRVNDFET ADILCPKAKR TSRFLSGIIN FIHFREACRE TYMEFLWQYK SSADKMQQLN A AHQEALMK LERLDSVPVE EQEEFKQLSD GIQELQQSLN QDFHQKTIVL QEGNSQKKSN ISEKTKRLNE LKLSVVSLKE IQ ESLKTKI VDSPEKLKNY KEKMKDTVQK LKNARQEVVE KYEIYGDSVD CLPSCQLEVQ LYQKKIQDLS DNREKLASIL KES LNLEDQ IESDESELKK LKTEENSFKR LMIVKKEKLA TAQFKINKKH EDVKQYKRTV IEDCNKVQEK RGAVYERVTT INQE IQKIK LGIQQLKDAA EREKLKSQEI FLNLKTALEK YHDGIEKAAE DSYAKIDEKT AELKRKMFKM ST

UniProtKB: Kinetochore protein Nuf2

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Macromolecule #5: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #7: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 2 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

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Macromolecule #8: TAXOL

MacromoleculeName: TAXOL / type: ligand / ID: 8 / Number of copies: 2 / Formula: TA1
Molecular weightTheoretical: 853.906 Da
Chemical component information

ChemComp-TA1:
TAXOL / medication*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 6.8
GridModel: Quantifoil / Material: GOLD / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 54.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: AlphaFold
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 284470
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChainDetails

7sgs

chain_id: A, source_name: PDB, initial_model_type: experimental model

7sgs

chain_id: a, source_name: PDB, initial_model_type: experimental model

7sgs

chain_id: B, source_name: PDB, initial_model_type: experimental model

7sgs

chain_id: b, source_name: PDB, initial_model_type: experimental model
chain_id: N, residue_range: 51-79, source_name: Other, initial_model_type: otherManually built in COOT and refined in ISOLDE
chain_id: N, residue_range: 80-289, source_name: AlphaFold, initial_model_type: in silico modelAlphafold structure is manually adjusted in COOT and refined in ISOLDE
chain_id: N, residue_range: 13-36, source_name: AlphaFold, initial_model_type: in 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
chain_id: n, source_name: AlphaFold, initial_model_type: in silico modelAlphafold structure is manually adjusted in COOT and refined in ISOLDE
chain_id: f, source_name: AlphaFold, initial_model_type: in silico modelAlphafold structure is manually adjusted in COOT and refined in ISOLDE
chain_id: 1, source_name: AlphaFold, initial_model_type: in 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
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Target criteria: FSC=0.5
Output model

PDB-9n9g:
Cryo-EM structure of the human Hec1-Nuf2 dimer bound to the paclitaxel-stabilized microtubule

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