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- PDB-4ca0: Structural Basis for the microtubule binding of the human kinetoc... -

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Basic information

Entry
Database: PDB / ID: 4ca0
TitleStructural Basis for the microtubule binding of the human kinetochore Ska complex
ComponentsSPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 1
KeywordsCELL CYCLE / CELL DIVISON / KINETOCHORE-MICROTUBULE ATTACHMENT / WINGED-HELIX DOMAIN
Function / homology
Function and homology information


negative regulation of mitotic spindle assembly checkpoint signaling / SKA complex / establishment of meiotic spindle orientation / metaphase chromosome alignment / mitotic spindle microtubule / outer kinetochore / attachment of mitotic spindle microtubules to kinetochore / spindle assembly involved in female meiosis / mitotic metaphase chromosome alignment / mitotic sister chromatid segregation ...negative regulation of mitotic spindle assembly checkpoint signaling / SKA complex / establishment of meiotic spindle orientation / metaphase chromosome alignment / mitotic spindle microtubule / outer kinetochore / attachment of mitotic spindle microtubules to kinetochore / spindle assembly involved in female meiosis / mitotic metaphase chromosome alignment / mitotic sister chromatid segregation / regulation of microtubule polymerization or depolymerization / intercellular bridge / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / positive regulation of microtubule polymerization / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / spindle microtubule / chromosome segregation / RHO GTPases Activate Formins / kinetochore / centriolar satellite / mitotic spindle / Separation of Sister Chromatids / mitotic cell cycle / microtubule cytoskeleton / microtubule binding / ciliary basal body / cilium / cell division / centrosome / nucleoplasm / cytosol
Similarity search - Function
Ska1 microtubule binding domain-like / Spindle and kinetochore-associated protein 1 / SKA1 microtubule binding domain / Spindle and kinetochore-associated protein 1 / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
SKA complex subunit 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.259 Å
AuthorsAbad, M. / Medina, B. / Santamaria, A. / Zou, J. / Plasberg-Hill, C. / Madhumalar, A. / Jayachandran, U. / Redli, P.M. / Rappsilber, J. / Nigg, E.A. / Jeyaprakash, A.A.
CitationJournal: Nat.Commun. / Year: 2014
Title: Structural Basis for Microtubule Recognition by the Human Kinetochore Ska Complex.
Authors: Abad, M.A. / Medina, B. / Santamaria, A. / Zou, J. / Plasberg-Hill, C. / Madhumalar, A. / Jayachandran, U. / Redli, P.M. / Rappsilber, J. / Nigg, E.A. / Jeyaprakash, A.A.
History
DepositionOct 4, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 1
B: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)29,2882
Polymers29,2882
Non-polymers00
Water72140
1
A: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)14,6441
Polymers14,6441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)14,6441
Polymers14,6441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.180, 47.180, 116.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 1 / SKA1


Mass: 14644.111 Da / Num. of mol.: 2 / Fragment: MT-BINDING DOMAIN, RESDUES 133-255
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PEC-CDF-HIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: Q96BD8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
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: 2.58 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growpH: 7 / Details: 24% PEG 1500 AND 20% GLYCEROL, pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.541
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 21, 2012 / Details: VARIMAX HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 2.25→2.37 Å / Num. obs: 13570 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 41.98 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.3
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 4 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.6 / % possible all: 90.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.259→15.443 Å / SU ML: 0.33 / σ(F): 1.01 / Phase error: 32.73 / Stereochemistry target values: ML / Details: 52-56 UNSTRUCTURED
RfactorNum. reflection% reflection
Rfree0.2675 2381 9.1 %
Rwork0.2252 --
obs0.2292 13467 96.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.8 Å2
Refinement stepCycle: LAST / Resolution: 2.259→15.443 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1962 0 0 40 2002
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081997
X-RAY DIFFRACTIONf_angle_d1.1172678
X-RAY DIFFRACTIONf_dihedral_angle_d16.638766
X-RAY DIFFRACTIONf_chiral_restr0.081304
X-RAY DIFFRACTIONf_plane_restr0.005332
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2587-2.30460.3681070.30431119X-RAY DIFFRACTION79
2.3046-2.35460.29411510.2691426X-RAY DIFFRACTION96
2.3546-2.40910.30691310.25731400X-RAY DIFFRACTION96
2.4091-2.46910.3021500.27031407X-RAY DIFFRACTION96
2.4691-2.53560.31821330.25911346X-RAY DIFFRACTION97
2.5356-2.60990.39511620.26971449X-RAY DIFFRACTION97
2.6099-2.69370.32811190.28671363X-RAY DIFFRACTION97
2.6937-2.78940.35671310.29481481X-RAY DIFFRACTION97
2.7894-2.90040.40161430.2781398X-RAY DIFFRACTION97
2.9004-3.03150.34631460.30541380X-RAY DIFFRACTION98
3.0315-3.190.39251440.26541414X-RAY DIFFRACTION98
3.19-3.38790.31861390.23331443X-RAY DIFFRACTION98
3.3879-3.64630.31461680.23261420X-RAY DIFFRACTION99
3.6463-4.00740.22641370.2141396X-RAY DIFFRACTION98
4.0074-4.5740.20531240.17941469X-RAY DIFFRACTION99
4.574-5.71390.21561350.18711458X-RAY DIFFRACTION99
5.7139-15.44360.17861610.17741422X-RAY DIFFRACTION98
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)
12.0043-0.7481-0.16983.21811.34344.6160.0084-0.4597-0.0216-0.0457-0.27130.2321-0.4506-0.18910.24490.22820.08930.01551.13-0.04340.354-22.818736.640354.1555
27.25731.5876-1.09421.54020.90651.26590.1116-0.6374-0.22560.0548-0.09020.11720.0029-0.4791-0.04910.29450.05470.021.1368-0.04760.3226-27.369837.500860.9674
30.43970.1810.05031.4551.18730.9924-0.2087-0.3795-0.20750.25540.09110.37820.22130.06550.15180.30820.03450.04071.21010.0230.4253-27.496328.604456.8584
41.78661.3842-0.08674.11231.24655.19310.01270.4-0.15330.0093-0.28290.28340.4114-0.28530.22940.2064-0.0771-0.0241.1196-0.05660.35930.804631.461261.9824
52.4571-1.88150.07542.66441.25912.5444-0.0680.75280.3747-0.03420.08930.17130.0945-0.6627-0.05580.2902-0.08950.00561.19640.00830.3526-3.775530.581755.1451
60.9747-1.0458-0.9071.13540.94870.8878-0.17480.3760.145-0.23440.13520.2458-0.22750.0390.06490.2996-0.0177-0.05851.1710.00780.4563-3.921639.51259.2654
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN B AND (RESID 2 THROUGH 69 )
2X-RAY DIFFRACTION2CHAIN B AND (RESID 70 THROUGH 94 )
3X-RAY DIFFRACTION3CHAIN B AND (RESID 95 THROUGH 124 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 2 THROUGH 69 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 70 THROUGH 94 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 95 THROUGH 124 )

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