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- PDB-6ys4: Structure of the Homo sapiens SAS-6 coiled-coil domain -

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Basic information

Entry
Database: PDB / ID: 6ys4
TitleStructure of the Homo sapiens 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


deuterosome / procentriole replication complex / positive regulation of centriole replication / positive regulation of spindle assembly / centriole replication / centrosome duplication / positive regulation of G1/S transition of mitotic cell cycle / regulation of mitotic spindle organization / centriole / 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
GLYCINE / Spindle assembly abnormal protein 6 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.11 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
DepositionApr 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 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 1.2Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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
E: Spindle assembly abnormal protein 6 homolog
F: Spindle assembly abnormal protein 6 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,35611
Polymers73,7436
Non-polymers6145
Water3,351186
1
A: Spindle assembly abnormal protein 6 homolog
B: Spindle assembly abnormal protein 6 homolog


Theoretical massNumber of molelcules
Total (without water)24,5812
Polymers24,5812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-46 kcal/mol
Surface area15580 Å2
MethodPISA
2
C: Spindle assembly abnormal protein 6 homolog
D: Spindle assembly abnormal protein 6 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0006
Polymers24,5812
Non-polymers4194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-40 kcal/mol
Surface area14010 Å2
MethodPISA
3
E: Spindle assembly abnormal protein 6 homolog
F: Spindle assembly abnormal protein 6 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7753
Polymers24,5812
Non-polymers1941
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-47 kcal/mol
Surface area15370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.004, 62.004, 153.748
Angle α, β, γ (deg.)90.00, 96.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Spindle assembly abnormal protein 6 homolog / HsSAS-6


Mass: 12290.455 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SASS6, SAS6 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6UVJ0
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C2H5NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.7 Å3/Da / Density % sol: 54.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM amino acids mixture, 0.1 M Gly-Gly / AMPD buffer, 50% v/v of 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: ESRF / Beamline: ID29 / Wavelength: 0.979155 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979155 Å / Relative weight: 1
ReflectionResolution: 2.11→57.46 Å / Num. obs: 37930 / % possible obs: 85.1 % / Redundancy: 6.5 % / Biso Wilson estimate: 40.89 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.106 / Net I/σ(I): 7.14
Reflection shellResolution: 2.11→2.17 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.917 / Mean I/σ(I) obs: 1.66 / Num. unique obs: 939 / CC1/2: 0.578 / Rrim(I) all: 1.087 / % possible all: 27.9

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.11→48.15 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.896 / SU R Cruickshank DPI: 0.296 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.289 / SU Rfree Blow DPI: 0.233 / SU Rfree Cruickshank DPI: 0.238
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1842 5 %RANDOM
Rwork0.239 ---
obs0.242 36857 85.5 %-
Displacement parametersBiso mean: 61.4 Å2
Baniso -1Baniso -2Baniso -3
1-3.0356 Å20 Å2-0.2571 Å2
2---4.341 Å20 Å2
3---1.3054 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: 1 / Resolution: 2.11→48.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4885 0 8 186 5079
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014955HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.136617HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1996SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes894HARMONIC5
X-RAY DIFFRACTIONt_it4955HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.25
X-RAY DIFFRACTIONt_other_torsion19.4
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion625SEMIHARMONIC5
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_contact5393SEMIHARMONIC4
LS refinement shellResolution: 2.11→2.16 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3232 -4.07 %
Rwork0.2529 708 -
all0.2558 738 -
obs--26.93 %
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)
10.67370.01213.16490.5147-1.264121.6741-0.01770.036-0.0032-0.0726-0.0896-0.09650.94480.81320.1073-0.07240.0734-0.0119-0.20670.0071-0.24277.3096.5277100.1445
21.57570.24263.88850.41280.684415.08360.0233-0.2412-0.0669-0.02240.03550.00480.1958-0.6781-0.0588-0.01910.0533-0.03-0.3705-0.0037-0.19762.10677.0969100.906
31.9956-0.42424.46420.4516-2.071815.942-0.0252-0.16940.02050.1290.09280.0023-0.15110.0112-0.0676-0.02970.1048-0.0213-0.2631-0.0238-0.1347-8.382322.702293.0563
41.4918-0.56285.86931.1201-5.444240.34310.0288-0.24030.01820.0277-0.00940.0380.5334-0.2491-0.0193-0.11560.1330.0055-0.1962-0.0308-0.1304-9.76717.851390.01
50.36920.3373.79660.35872.338329.7248-0.1412-0.06280.1240.0972-0.28050.0432-0.155-0.42760.4217-0.0109-0.23-0.0710.00220.0296-0.3125-20.1125.4451155.3716
60.3977-0.01972.75980-0.648318.047-0.04510.20320.04410.0622-0.2146-0.03190.00761.38760.25970.0334-0.2069-0.07130.04760.0669-0.3316-16.206921.3143156.8514
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|0 - B|101 }
3X-RAY DIFFRACTION3{ C|7 - C|101 }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }

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