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- PDB-9n9e: Cryo-EM structure of the SAH domain of Caenorhabditis elegans ICP... -

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Basic information

Entry
Database: PDB / ID: 9n9e
TitleCryo-EM structure of the SAH domain of Caenorhabditis elegans ICP-1 bound to the paclitaxel-stabilized microtubule
Components
  • Incenp-like protein ICP-1
  • Tubulin alpha-1B chain
  • Tubulin beta chain
KeywordsCELL CYCLE / microtubule / CPC / chromosomal passenger complex / INCENP / mitosis
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
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / TAXOL / Incenp-like protein ICP-1 / Tubulin beta chain / Tubulin alpha-1B chain
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 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
A: Tubulin alpha-1B chain
B: Tubulin beta chain
C: Tubulin alpha-1B chain
S: Incenp-like protein ICP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,69613
Polymers223,1494
Non-polymers2,5479
Water724
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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Protein , 3 types, 4 molecules ACBS

#1: 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
#2: Protein Tubulin beta chain / Beta-tubulin


Mass: 49907.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Brain / Plasmid details: https://www.cytoskeleton.com/t240 / References: UniProt: P02554
#3: Protein Incenp-like protein ICP-1 / Inner centromere protein ARK-binding domain-containing protein


Mass: 72831.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: icp-1, CELE_Y39G10AR.13, Y39G10AR.13 / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: G5EE37

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Non-polymers , 6 types, 13 molecules

#4: 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
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#8: Chemical ChemComp-TA1 / TAXOL


Mass: 853.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H51NO14 / Comment: medication, chemotherapy*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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 SAH domain of Caenorhabditis elegans ICP-1 bound to the paclitaxel-stabilized microtubule
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 8.6 kDa/nm / Experimental value: NO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293S GnTI-
Buffer solutionpH: 6.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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: 50.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategoryFitting-ID
7Cootmodel fitting1
13PHENIXmodel refinement1
14ISOLDEmodel refinement1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 792640 / 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

B17SGSB1PDBexperimental model
37SGS

7sgs

C17SGSC1PDBexperimental model
41SAlphaFoldin silico model221-273Alphafold structure is manually adjusted in COOT and refined in ISOLDE
52
62
72
82
92
102
112
122
132
142
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00310752
ELECTRON MICROSCOPYf_angle_d0.52314569
ELECTRON MICROSCOPYf_dihedral_angle_d39.4351460
ELECTRON MICROSCOPYf_chiral_restr0.0421597
ELECTRON MICROSCOPYf_plane_restr0.0051914

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