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- PDB-9zmk: Cartwheel Assembly of T. agilis SAS-6 -

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Basic information

Entry
Database: PDB / ID: 9zmk
TitleCartwheel Assembly of T. agilis SAS-6
ComponentsSpindle assembly abnormal 6
KeywordsSTRUCTURAL PROTEIN / Trichonympha / Centriole / Cartwheel / Tetramer
Function / homologySpindle assembly abnormal protein 6, N-terminal / SAS-6, N-terminal domain superfamily / Centriolar protein SAS N-terminal domain / centrosome / Spindle assembly abnormal 6
Function and homology information
Biological speciesTrichonympha (eukaryote)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 7.6 Å
AuthorsRowsell, C.M. / Arin, A. / Bui, K.H.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-156354 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2022-04774 Canada
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2026
Title: The Native Structure of the Trichonympha Centriole Cartwheel Reveals a Zig-Zag Stacking Pattern
Authors: Rowsell, C.M. / Arin, A. / Bui, K.H.
History
DepositionDec 10, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 2, 2026Data content type: EM metadata / Data content type: EM metadata / 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: Spindle assembly abnormal 6
B: Spindle assembly abnormal 6
C: Spindle assembly abnormal 6
D: Spindle assembly abnormal 6
E: Spindle assembly abnormal 6
F: Spindle assembly abnormal 6
G: Spindle assembly abnormal 6
H: Spindle assembly abnormal 6


Theoretical massNumber of molelcules
Total (without water)153,1098
Polymers153,1098
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1chain "E"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "A"
d_6ens_1chain "F"
d_7ens_1chain "G"
d_8ens_1chain "H"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ASN / End label comp-ID: ASN / Auth seq-ID: 1 - 160 / Label seq-ID: 1 - 160

Dom-IDAuth asym-IDLabel asym-ID
d_1EE
d_2BB
d_3CC
d_4DD
d_5AA
d_6FF
d_7GG
d_8HH

NCS oper:
IDCodeMatrixVector
1given(-0.999862804209, -0.000529604645769, -0.0165557324858), (0.00191030088731, 0.989132892412, -0.147011808704), (0.0164536776966, -0.147023265733, -0.988996175839)336.865425361, 27.7587306143, 356.42404479
2given(0.765556421408, -0.643086053477, 0.0190707489375), (0.642990316066, 0.765786452846, 0.0116000897729), (-0.022063977134, 0.00338178367234, 0.999750841186)208.300890855, -46.687810947, 1.96507556913
3given(-0.995777180839, 0.0687623626495, -0.0608238736364), (0.0666210175333, 0.997108256199, 0.0365618030665), (0.0631620625385, 0.032355260832, -0.997478666916)322.920853453, -17.8859821674, 362.210585373
4given(0.720434267491, -0.692942964894, -0.0283639494593), (0.684291284919, 0.703598346357, 0.191558879687), (-0.112782550106, -0.15741478459, 0.981071191089)241.382542341, -73.5029838659, 3.75756254251
5given(-0.72251714394, 0.691349508609, 0.00219855817469), (0.690161743457, 0.721081934025, 0.0609722255722), (0.0405677776075, 0.0455708390231, -0.998137041719)98.1575100871, -50.017924733, 363.129600684
6given(0.994182171175, -0.0763772101229, 0.0759495377936), (0.0625222973851, 0.983373533954, 0.170491803467), (-0.0877084536799, -0.16475137175, 0.982427713707)9.14413134744, -42.5198258331, 2.08825532944
7given(-0.766623824918, 0.636999651965, -0.0807425195501), (0.64206312909, 0.759217024592, -0.106510317965), (-0.00654594002324, -0.133495142104, -0.991027849106)138.29109069, -24.287072089, 357.883924717

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Components

#1: Protein
Spindle assembly abnormal 6


Mass: 19138.650 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Trichonympha (eukaryote) / References: UniProt: R4WPE9
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: 8 nm Cartwheel Subunit from the Proximal Centriole of Trichonympha spp.
Type: ORGANELLE OR CELLULAR COMPONENT
Details: Subunit of the proximal centriole cartwheel of Trichonympha spp., isolated from the hindgut of Z. angusticollis.
Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Trichonympha (eukaryote) / Organelle: Centriole
Buffer solutionpH: 8 / Details: TE Buffer: 10mM Tris pH 8, 1mM EDTA pH 8
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMTris BufferC4H11NO31
21 mMEDTAEDTA1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Grid was plasma discharged prior to use / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
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: DIFFRACTION / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 3 e/Å2 / Avg electron dose per subtomogram: 123 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 1

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Processing

EM software
IDNameVersionCategory
1Warp2volume selection
2SerialEMimage acquisition
4Warp2CTF correction
7UCSF ChimeraXmodel fitting
10RELION5final Euler assignment
11RELION5classification
12RELION53D reconstruction
13M3D reconstruction
14PHENIX1.21_5207model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 7.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 58707 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 61 / Num. of volumes extracted: 58707
Atomic model buildingProtocol: RIGID BODY FIT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 41.85 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003110968
ELECTRON MICROSCOPYf_angle_d0.76114776
ELECTRON MICROSCOPYf_chiral_restr0.04781648
ELECTRON MICROSCOPYf_plane_restr0.00461896
ELECTRON MICROSCOPYf_dihedral_angle_d5.48951408
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2EEELECTRON MICROSCOPYNCS constraints9.11671960027E-13
ens_1d_3EEELECTRON MICROSCOPYNCS constraints1.14907971704E-12
ens_1d_4EEELECTRON MICROSCOPYNCS constraints5.61998116885E-13
ens_1d_5EEELECTRON MICROSCOPYNCS constraints9.37003497477E-11
ens_1d_6EEELECTRON MICROSCOPYNCS constraints1.30745360227E-12
ens_1d_7EEELECTRON MICROSCOPYNCS constraints3.73566647409E-13
ens_1d_8EEELECTRON MICROSCOPYNCS constraints2.97719256269E-11

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