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- PDB-6z26: Structure of the Danio rerio SAS-6 coiled-coil domain -

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Basic information

Entry
Database: PDB / ID: 6z26
TitleStructure of the Danio rerio SAS-6 coiled-coil domain
ComponentsSpindle assembly abnormal protein 6 homolog
KeywordsSTRUCTURAL PROTEIN / centriole / centrosome / cartwheel / coiled coil / complex / alpha helical
Function / homology
Function and homology information


positive regulation of mitotic spindle organization / deuterosome / procentriole replication complex / positive regulation of centriole replication / nuclear division / positive regulation of spindle assembly / embryonic cleavage / centriole replication / centrosome duplication / positive regulation of G1/S transition of mitotic cell cycle ...positive regulation of mitotic spindle organization / deuterosome / procentriole replication complex / positive regulation of centriole replication / nuclear division / positive regulation of spindle assembly / embryonic cleavage / centriole replication / centrosome duplication / positive regulation of G1/S transition of mitotic cell cycle / centriole / mitotic spindle organization / spermatogenesis / centrosome / cytoplasm
Similarity search - Function
SAS-6 coiled-coil domain / Sas6/XLF/XRCC4 coiled-coil domain / Spindle assembly abnormal protein 6, N-terminal / SAS-6, N-terminal domain superfamily / Centriolar protein SAS N-terminal domain
Similarity search - Domain/homology
Spindle assembly abnormal protein 6 homolog
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.32 Å
AuthorsKantsadi, A.L. / Vakonakis, I.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
European CommissionMSCA 752069 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/N009274/1 United Kingdom
CitationJournal: Structure / Year: 2022
Title: Structures of SAS-6 coiled coil hold implications for the polarity of the centriolar cartwheel.
Authors: Kantsadi, A.L. / Hatzopoulos, G.N. / Gonczy, P. / Vakonakis, I.
History
DepositionMay 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Database references / Category: citation / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 18, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spindle assembly abnormal protein 6 homolog
B: Spindle assembly abnormal protein 6 homolog
C: Spindle assembly abnormal protein 6 homolog
D: Spindle assembly abnormal protein 6 homolog


Theoretical massNumber of molelcules
Total (without water)55,4694
Polymers55,4694
Non-polymers00
Water45025
1
A: Spindle assembly abnormal protein 6 homolog
D: Spindle assembly abnormal protein 6 homolog


Theoretical massNumber of molelcules
Total (without water)27,7352
Polymers27,7352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-55 kcal/mol
Surface area15340 Å2
MethodPISA
2
B: Spindle assembly abnormal protein 6 homolog
C: Spindle assembly abnormal protein 6 homolog


Theoretical massNumber of molelcules
Total (without water)27,7352
Polymers27,7352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-59 kcal/mol
Surface area15920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.380, 70.306, 98.736
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Spindle assembly abnormal protein 6 homolog


Mass: 13867.258 Da / Num. of mol.: 4 / Mutation: L286M, L321M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: sass6, sas6, zgc:55668 / Plasmid: pFLOAT2
Details (production host): pET30 derivative, N-terminal His6-tag
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7ZVT3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 4 mM of alkalis mixture (barium acetate, caesium acetate, rubidium chloride, strontium acetate) 0.1 M BES / Triehylamine buffer 50% v/v of a precipitant mix (25% w/v PEG 4000 and 40% w/v 1,2,6- Hexanetriol)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.31→57.27 Å / Num. obs: 14143 / % possible obs: 65.1 % / Observed criterion σ(F): 3 / Redundancy: 13 % / Biso Wilson estimate: 44.55 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.121 / Rrim(I) all: 0.127 / Net I/σ(I): 9.9
Reflection shellResolution: 2.31→2.37 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 840 / CC1/2: 0.887 / Rrim(I) all: 0.624 / % possible all: 4.2

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.32→57.27 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.894 / SU R Cruickshank DPI: 1.514 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.615 / SU Rfree Blow DPI: 0.379 / SU Rfree Cruickshank DPI: 0.385
RfactorNum. reflection% reflectionSelection details
Rfree0.297 708 5.01 %RANDOM
Rwork0.277 ---
obs0.278 14142 65.4 %-
Displacement parametersBiso mean: 57.78 Å2
Baniso -1Baniso -2Baniso -3
1-9.4695 Å20 Å20 Å2
2---2.757 Å20 Å2
3----6.7124 Å2
Refine analyzeLuzzati coordinate error obs: 0.5 Å
Refinement stepCycle: 1 / Resolution: 2.32→57.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3302 0 0 25 3327
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013322HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.194435HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1377SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes576HARMONIC5
X-RAY DIFFRACTIONt_it3322HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2
X-RAY DIFFRACTIONt_other_torsion18.88
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion443SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3632SEMIHARMONIC4
LS refinement shellResolution: 2.32→2.49 Å / Total num. of bins used: 35
RfactorNum. reflection% reflection
Rfree0.3566 -6.67 %
Rwork0.3406 378 -
all0.3417 405 -
obs--9.71 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3745-0.27993.67380.5597-0.812211.27860.08930.08180.06440.153-0.191-0.13760.61140.22050.1018-0.0131-0.0892-0.0047-0.25160.0163-0.378574.581410.379940.1438
21.10640.13323.54750.74640.421914.5511-0.0271-0.06290.13740.097-0.19190.05040.5996-0.21440.219-0.15750.1201-0.0183-0.3969-0.0747-0.413245.78838.78028.464
31.15820.39243.58920.59132.015419.8421-0.0449-0.090.05090.0323-0.03450.0349-0.2637-0.43650.07930.01930.0909-0.0045-0.2375-0.0007-0.258246.22968.71378.1449
41.86760.20855.63610.35030.810319.46460.14320.0002-0.120.21320.007-0.0750.2588-0.1213-0.1502-0.0186-0.0145-0.0355-0.24980.0225-0.276674.486210.463438.1154
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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