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- EMDB-49166: Cryo-EM structure of the SAH domain of Caenorhabditis elegans ICP... -

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Basic information

Entry
Database: EMDB / ID: EMD-49166
TitleCryo-EM structure of the SAH domain of Caenorhabditis elegans ICP-1 bound to the paclitaxel-stabilized microtubule
Map data
Sample
  • Complex: The SAH domain of Caenorhabditis elegans ICP-1 bound to the paclitaxel-stabilized microtubule
    • Protein or peptide: Tubulin alpha-1B chain
    • Protein or peptide: Tubulin beta chain
    • Protein or peptide: Incenp-like protein ICP-1
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: TAXOL
  • Ligand: water
Keywordsmicrotubule / CPC / chromosomal passenger complex / INCENP / mitosis / cell cycle
Function / homology
Function and homology information


nuclear chromosome segregation / positive regulation of mitotic sister chromatid separation / mitotic chromosome movement towards spindle pole / positive regulation of mitotic cell cycle spindle assembly checkpoint / mitotic spindle midzone assembly / female meiotic nuclear division / chromosome passenger complex / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Resolution of Sister Chromatid Cohesion / Hedgehog 'off' state ...nuclear chromosome segregation / positive regulation of mitotic sister chromatid separation / mitotic chromosome movement towards spindle pole / positive regulation of mitotic cell cycle spindle assembly checkpoint / mitotic spindle midzone assembly / female meiotic nuclear division / chromosome passenger complex / 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 metaphase chromosome alignment / mitotic cytokinesis / mitotic spindle assembly / protein kinase activator activity / protein serine/threonine kinase activator activity / kinetochore / structural constituent of cytoskeleton / microtubule cytoskeleton organization / spindle / neuron migration / mitotic cell cycle / chromosome / microtubule cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / GTPase activity / GTP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Inner centromere protein, ARK-binding domain / Inner centromere protein, ARK binding region / 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 ...Inner centromere protein, ARK-binding domain / Inner centromere protein, ARK binding region / 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
Incenp-like protein ICP-1 / Tubulin beta chain / Tubulin alpha-1B chain
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata) / Sus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 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_49166.png

Downloads & links

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Map

FileDownload / File: emd_49166.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 256 pix.
= 279.04 Å		1.09 Å/pix.
x 256 pix.
= 279.04 Å		1.09 Å/pix.
x 256 pix.
= 279.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.374
Minimum - Maximum-1.6240698 - 6.594271
Average (Standard dev.)0.023585353 (±0.17737342)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 279.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49166_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_49166_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_49166_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : The SAH domain of Caenorhabditis elegans ICP-1 bound to the pacli...

EntireName: The SAH domain of Caenorhabditis elegans ICP-1 bound to the paclitaxel-stabilized microtubule
Components
  • Complex: The SAH domain of Caenorhabditis elegans ICP-1 bound to the paclitaxel-stabilized microtubule
    • Protein or peptide: Tubulin alpha-1B chain
    • Protein or peptide: Tubulin beta chain
    • Protein or peptide: Incenp-like protein ICP-1
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: TAXOL
  • Ligand: water

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Supramolecule #1: The SAH domain of Caenorhabditis elegans ICP-1 bound to the pacli...

SupramoleculeName: The SAH domain of Caenorhabditis elegans ICP-1 bound to the paclitaxel-stabilized microtubule
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 8.6 kDa/nm

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Macromolecule #1: Tubulin alpha-1B chain

MacromoleculeName: Tubulin alpha-1B chain / type: protein_or_peptide / ID: 1 / 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 #2: Tubulin beta chain

MacromoleculeName: Tubulin beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / 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 #3: Incenp-like protein ICP-1

MacromoleculeName: Incenp-like protein ICP-1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 72.831859 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPPKKRAVSR KPAEPTIKLF SSIPKISSIF DEVSEAHDDA AAKVFADLYK RMSSITEELA TPQFSAEQLL NAVLKPGRID AEFVELISR QKAKPAQPSS SSHRGDDDME TDEVETDQAG PITPRAGSVA TDGDFEEDIL PVTLKRMQQM SISKKKTEGS I SRNAAYSG ...String:
MPPKKRAVSR KPAEPTIKLF SSIPKISSIF DEVSEAHDDA AAKVFADLYK RMSSITEELA TPQFSAEQLL NAVLKPGRID AEFVELISR QKAKPAQPSS SSHRGDDDME TDEVETDQAG PITPRAGSVA TDGDFEEDIL PVTLKRMQQM SISKKKTEGS I SRNAAYSG TPRRNPPREA HNQATPRNIF SSTPGRMAGT PGRAAVVPRT PHRVIPFNDA EKDPNARMKH ADELRMKELE KK REKARKD EEKRNAVMER RKEQERVRQE KLDQLKQKEE RNANLAKLHN SAKSPTRARL MQDHAPNKAA SRKIFPTAES TST PGRGPA KKGKVEILIG SDGQKTAPVA QPTVELSPSR ELQRNGSRQV KMEPMSCDDS TPPARQHKPK AKATKRSAHA ASSS TSNVE AAAALAALQE QQRIQLEQEQ YLLQLAEDER RKREQKEMKE KAEKERQLRA REEQEHFLAV QREEQAQLEK QRERE EAEL QATLARCAEK QARQEALRKT PPPAAYEMTP PRTYQNNSKN DYGLNDLNSD DETDQEDDPR KDVPAWAEFA VVRENV RRH AINPPFDVAQ FFGSIGKPNL KEIFSDAVKV KKRGSSAVWK KSPSTLNTSS RTILQDISEP SRLEEELRRR LTESNSL EV LFQ

UniProtKB: Incenp-like protein ICP-1

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Macromolecule #4: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / 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 #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 3 / 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: 1 / 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: 1 / Formula: TA1
Molecular weightTheoretical: 853.906 Da
Chemical component information

ChemComp-TA1:
TAXOL / medication, chemotherapy*YM

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Macromolecule #9: water

MacromoleculeName: water / type: ligand / ID: 9 / Number of copies: 4 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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
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: 50.5 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: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 792640
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: B, source_name: PDB, initial_model_type: experimental model

7sgs

chain_id: C, source_name: PDB, initial_model_type: experimental model
chain_id: S, residue_range: 221-273, source_name: AlphaFold, initial_model_type: in silico modelAlphafold structure is manually adjusted in COOT and refined in ISOLDE
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Target criteria: FSC=0.5
Output model

PDB-9n9e:
Cryo-EM structure of the SAH domain of Caenorhabditis elegans ICP-1 bound to the paclitaxel-stabilized microtubule

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