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- PDB-8arf: Crystal structure of the N-terminal parallel dimeric coiled-coil ... -

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Basic information

Entry
Database: PDB / ID: 8arf
TitleCrystal structure of the N-terminal parallel dimeric coiled-coil region of the human kinetochore associated protein Spindly
ComponentsProtein Spindly
KeywordsCELL CYCLE / kinetochore / dynein / dynactin
Function / homology
Function and homology information


kinetochore binding / outer kinetochore / protein localization to kinetochore / microtubule organizing center / mitotic metaphase chromosome alignment / mitotic spindle assembly checkpoint signaling / establishment of mitotic spindle orientation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation ...kinetochore binding / outer kinetochore / protein localization to kinetochore / microtubule organizing center / mitotic metaphase chromosome alignment / mitotic spindle assembly checkpoint signaling / establishment of mitotic spindle orientation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / RHO GTPases Activate Formins / spindle pole / Separation of Sister Chromatids / cell migration / cell division / enzyme binding / nucleus / cytosol
Similarity search - Function
Protein Spindly, chordates
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.8 Å
AuthorsPerrakis, A. / Ahmad, M.U.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Cell Biol. / Year: 2022
Title: Conformational transitions of the Spindly adaptor underlie its interaction with Dynein and Dynactin.
Authors: d'Amico, E.A. / Ud Din Ahmad, M. / Cmentowski, V. / Girbig, M. / Muller, F. / Wohlgemuth, S. / Brockmeyer, A. / Maffini, S. / Janning, P. / Vetter, I.R. / Carter, A.P. / Perrakis, A. / Musacchio, A.
History
DepositionAug 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Protein Spindly
A: Protein Spindly


Theoretical massNumber of molelcules
Total (without water)24,2882
Polymers24,2882
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-43 kcal/mol
Surface area14130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.507, 112.507, 49.642
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Protein Spindly / hSpindly / Arsenite-related gene 1 protein / Coiled-coil domain-containing protein 99 / ...hSpindly / Arsenite-related gene 1 protein / Coiled-coil domain-containing protein 99 / Rhabdomyosarcoma antigen MU-RMS-40.4A / Spindle apparatus coiled-coil domain-containing protein 1


Mass: 12143.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPDL1, CCDC99 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96EA4

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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: 3.73 Å3/Da / Density % sol: 67.06 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Bis-Tris Propane pH 6.5; 19% PEG3350; 0.2M KSCN

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.8→48.72 Å / Num. obs: 9079 / % possible obs: 99.3 % / Redundancy: 5.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.05 / Net I/σ(I): 10.8
Reflection shellResolution: 2.8→2.95 Å / Rmerge(I) obs: 1.558 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1312 / CC1/2: 0.718 / Rpim(I) all: 0.97

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.8→48.72 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.926 / SU B: 42.122 / SU ML: 0.338 / Cross valid method: FREE R-VALUE / ESU R: 0.6 / ESU R Free: 0.356
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2898 432 4.764 %
Rwork0.2492 8636 -
all0.251 --
obs-9068 99.191 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 92.609 Å2
Baniso -1Baniso -2Baniso -3
1--3.132 Å2-1.566 Å2-0 Å2
2---3.132 Å20 Å2
3---10.159 Å2
Refinement stepCycle: LAST / Resolution: 2.8→48.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1598 0 0 0 1598
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191606
X-RAY DIFFRACTIONr_bond_other_d0.0020.021561
X-RAY DIFFRACTIONr_angle_refined_deg1.8871.9362139
X-RAY DIFFRACTIONr_angle_other_deg1.3812.9383617
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4715191
X-RAY DIFFRACTIONr_dihedral_angle_2_deg47.42126.52292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg28.29115366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.6721512
X-RAY DIFFRACTIONr_chiral_restr0.1020.2236
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021805
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02339
X-RAY DIFFRACTIONr_nbd_refined0.3960.2397
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2610.21548
X-RAY DIFFRACTIONr_nbtor_refined0.1880.2769
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.090.21260
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.221
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2020.224
X-RAY DIFFRACTIONr_nbd_other0.2590.289
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1950.22
X-RAY DIFFRACTIONr_mcbond_it5.3836.424770
X-RAY DIFFRACTIONr_mcbond_other5.3346.424769
X-RAY DIFFRACTIONr_mcangle_it7.7249.667959
X-RAY DIFFRACTIONr_mcangle_other7.739.671960
X-RAY DIFFRACTIONr_scbond_it8.8947.955835
X-RAY DIFFRACTIONr_scbond_other8.8897.956836
X-RAY DIFFRACTIONr_scangle_it14.1611.4171179
X-RAY DIFFRACTIONr_scangle_other14.15411.4181180
X-RAY DIFFRACTIONr_lrange_it18.02129.1566740
X-RAY DIFFRACTIONr_lrange_other18.018129.1556741
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.8730.346220.364646X-RAY DIFFRACTION99.8505
2.873-2.9520.358220.349621X-RAY DIFFRACTION99.0755
2.952-3.0370.372280.359585X-RAY DIFFRACTION98.7118
3.037-3.130.375220.346597X-RAY DIFFRACTION99.3579
3.13-3.2330.353280.362557X-RAY DIFFRACTION99.6593
3.233-3.3460.431210.32554X-RAY DIFFRACTION99.481
3.346-3.4720.303280.314531X-RAY DIFFRACTION99.8214
3.472-3.6140.349260.263512X-RAY DIFFRACTION99.8145
3.614-3.7750.337220.241493X-RAY DIFFRACTION99.8062
3.775-3.9580.247400.225449X-RAY DIFFRACTION99.3902
3.958-4.1720.269130.191462X-RAY DIFFRACTION99.3724
4.172-4.4250.239280.18404X-RAY DIFFRACTION99.0826
4.425-4.730.254170.184403X-RAY DIFFRACTION99.0566
4.73-5.1080.224290.203365X-RAY DIFFRACTION98.7469
5.108-5.5940.315240.296345X-RAY DIFFRACTION98.6631
5.594-6.2510.375190.346304X-RAY DIFFRACTION98.7768
6.251-7.2130.549150.292272X-RAY DIFFRACTION97.619
7.213-8.8220.236130.204234X-RAY DIFFRACTION98.0159
8.822-12.4260.21190.172191X-RAY DIFFRACTION98.0392
12.426-48.720.27360.288111X-RAY DIFFRACTION98.3193
Refinement TLS params.Method: refined / Origin x: -40.09 Å / Origin y: 36.044 Å / Origin z: -11.789 Å
111213212223313233
T0.2556 Å20.0271 Å20.0317 Å2-0.0188 Å20.013 Å2--0.0334 Å2
L0.3263 °20.2077 °20.007 °2-12.7628 °2-0.7488 °2--0.1972 °2
S0.0235 Å °-0.0285 Å °0.0368 Å °0.3316 Å °-0.0813 Å °-0.4239 Å °-0.0293 Å °0.0446 Å °0.0577 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA2 - 97
2X-RAY DIFFRACTION1ALLB2 - 98

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