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- PDB-5m9e: Interactions between the Mal3 EB1-like domain and Dis1 -

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Basic information

Entry
Database: PDB / ID: 5m9e
TitleInteractions between the Mal3 EB1-like domain and Dis1
Components
  • Microtubule integrity protein mal3
  • Phosphoprotein p93
KeywordsCELL CYCLE / EB1 domain / microtubule-binding / coiled-coil
Function / homology
Function and homology information


meiotic centromere clustering / static microtubule bundle / dynein-driven meiotic oscillatory nuclear movement / post-anaphase array microtubule end / thigmotropism / kinetochore => GO:0000776 / microtubule plus end polymerase / nuclear migration involved in conjugation with cellular fusion / cortical microtubule / cell cortex of cell tip ...meiotic centromere clustering / static microtubule bundle / dynein-driven meiotic oscillatory nuclear movement / post-anaphase array microtubule end / thigmotropism / kinetochore => GO:0000776 / microtubule plus end polymerase / nuclear migration involved in conjugation with cellular fusion / cortical microtubule / cell cortex of cell tip / karyogamy involved in conjugation with cellular fusion / mitotic spindle astral microtubule / establishment or maintenance of microtubule cytoskeleton polarity / mitotic spindle elongation / mitotic spindle pole body / mitotic spindle midzone / nuclear microtubule / protein localization to microtubule / astral microtubule / microtubule plus-end / cytoskeletal anchor activity / attachment of mitotic spindle microtubules to kinetochore / microtubule bundle formation / microtubule plus-end binding / spindle pole body / microtubule depolymerization / microtubule organizing center / microtubule lateral binding / microtubule polymerization / cytoplasmic microtubule / ATPase activator activity / chromosome, centromeric region / regulation of microtubule polymerization or depolymerization / spindle assembly / spindle midzone / mitotic spindle organization / molecular condensate scaffold activity / mitotic spindle / kinetochore / spindle pole / microtubule cytoskeleton / microtubule binding / cell division / protein-containing complex / nucleus / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1430 / EB1, C-terminal / Microtubule-associated protein RP/EB / EB1, C-terminal domain superfamily / EB1-C terminal (EB1-C) domain profile. / EB1-like C-terminal motif / TOG domain / TOG / Calponin homology domain / CH domain superfamily ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1430 / EB1, C-terminal / Microtubule-associated protein RP/EB / EB1, C-terminal domain superfamily / EB1-C terminal (EB1-C) domain profile. / EB1-like C-terminal motif / TOG domain / TOG / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Armadillo-like helical / Armadillo-type fold / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Phosphoprotein p93 / Microtubule integrity protein mal3
Similarity search - Component
Biological speciesSchizosaccharomyces pombe 972h- (yeast)
Schizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsZakian, S. / Singleton, M.R.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Cancer Research UKFC001155 United Kingdom
Wellcome TrustFC001155 United Kingdom
Medical Research Council (United Kingdom)FC001155 United Kingdom
CitationJournal: J. Cell. Sci. / Year: 2016
Title: An unconventional interaction between Dis1/TOG and Mal3/EB1 in fission yeast promotes the fidelity of chromosome segregation.
Authors: Matsuo, Y. / Maurer, S.P. / Yukawa, M. / Zakian, S. / Singleton, M.R. / Surrey, T. / Toda, T.
History
DepositionNov 1, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references
Revision 1.2Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Microtubule integrity protein mal3
B: Microtubule integrity protein mal3
C: Microtubule integrity protein mal3
D: Microtubule integrity protein mal3
E: Phosphoprotein p93
F: Phosphoprotein p93
G: Phosphoprotein p93
H: Phosphoprotein p93


Theoretical massNumber of molelcules
Total (without water)45,3158
Polymers45,3158
Non-polymers00
Water00
1
A: Microtubule integrity protein mal3
B: Microtubule integrity protein mal3
E: Phosphoprotein p93
H: Phosphoprotein p93


Theoretical massNumber of molelcules
Total (without water)22,6584
Polymers22,6584
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Microtubule integrity protein mal3
D: Microtubule integrity protein mal3
F: Phosphoprotein p93
G: Phosphoprotein p93


Theoretical massNumber of molelcules
Total (without water)22,6584
Polymers22,6584
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.305, 93.305, 196.545
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein
Microtubule integrity protein mal3


Mass: 9030.100 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe 972h- (yeast)
Gene: mal3, SPAC18G6.15 / Production host: Escherichia coli (E. coli) / References: UniProt: Q10113
#2: Protein/peptide
Phosphoprotein p93


Mass: 2298.667 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q09933

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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: 3.1 Å3/Da / Density % sol: 60.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.2 M MgCl2, 0.1 M HEPES pH 7, 20% PEG 6K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.83→80.8 Å / Num. obs: 12733 / % possible obs: 97 % / Redundancy: 18.3 % / Rmerge(I) obs: 0.1766 / Net I/σ(I): 9.13
Reflection shellResolution: 2.83→2.931 Å / Redundancy: 19 % / Rmerge(I) obs: 2.937 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.58 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
PDB_EXTRACT3.1data extraction
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M97

5m97


Resolution: 2.83→80.8 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 38.07
RfactorNum. reflection% reflectionSelection details
Rfree0.3245 603 4.88 %RANDOM
Rwork0.266 ---
obs0.2691 12366 97.12 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.83→80.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2805 0 0 0 2805
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122839
X-RAY DIFFRACTIONf_angle_d1.5243807
X-RAY DIFFRACTIONf_dihedral_angle_d14.0771777
X-RAY DIFFRACTIONf_chiral_restr0.073432
X-RAY DIFFRACTIONf_plane_restr0.009490
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8301-3.11490.43831480.38382836X-RAY DIFFRACTION96
3.1149-3.56560.4161400.35162894X-RAY DIFFRACTION98
3.5656-4.49230.31691510.27582831X-RAY DIFFRACTION94
4.4923-80.83740.29151640.21953202X-RAY DIFFRACTION100
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)
10.318-0.27490.13240.5159-0.01240.2150.1028-0.25980.39240.3119-0.08670.2719-0.3083-0.27230.00660.7113-0.2368-0.21270.68390.15520.480839.0814-10.2516-22.2239
20.01160.0043-0.01850.33130.16810.118-0.0737-0.08810.14110.1842-0.23440.0106-0.0424-0.1761-0.07441.032-0.5415-0.21681.0483-0.00240.410656.0007-4.0698-6.614
30.37760.28030.15810.42950.14520.6838-0.0480.05520.00640.0991-0.1183-0.31980.0633-0.0803-0.90220.6658-0.3056-0.92010.56770.55960.782142.4992-16.577-24.8951
40.32810.0499-0.2010.0806-0.02330.28030.05120.0883-0.33010.0037-0.2244-0.25810.07330.1075-0.41710.5052-0.1315-0.30780.59840.28090.782263.9389-8.3975-19.2457
50.22420.06-0.02880.0338-0.06590.5726-0.1169-0.62390.13830.51710.3173-0.1213-0.2373-0.29520.26770.89580.0169-0.33130.6781-0.27220.795240.27859.7695-29.6843
60.0809-0.12550.09310.56-0.00270.1871-0.0208-0.1324-0.08410.08710.1590.33110.1371-0.75420.04030.5196-0.0664-0.53780.95440.25971.182119.1764-1.2809-45.0715
70.31160.1004-0.37310.3649-0.18840.4664-0.1449-0.1810.2216-0.02860.0719-0.0048-0.1351-0.17320.05670.7657-0.0573-0.51630.4113-0.03350.645942.518910.2773-36.8997
80.2018-0.2133-0.12350.48780.28530.16960.27580.2653-0.0217-0.18660.3902-0.25010.1926-0.15410.07580.9356-0.2007-0.36250.71060.11530.760331.3222-2.6733-53.0599
90.0071-0.01660.05030.0297-0.09770.3189-0.15540.07930.32740.0986-0.3911-0.023-0.15390.1372-0.02640.5128-0.1144-0.21960.43470.0370.78152.30431.5467-25.0767
100.02020.0439-0.01730.0883-0.03740.01420.1476-0.07010.04390.00940.2320.4068-0.1011-0.1948-0.00050.6667-0.00840.01620.95640.20450.730439.8465-5.1937-30.6502
110.14980.1286-0.15690.134-0.12290.1945-0.035-0.071-0.09890.0584-0.12870.12670.2238-0.0473-0.12041.1001-0.2446-0.38340.49780.21750.979934.3682-8.1732-37.7478
120.1032-0.00780.01290.04090.01980.4245-0.132-0.36940.22590.28470.0367-0.043-0.14870.12530.0020.83530.1544-0.07410.4680.00860.754343.89970.1146-27.7932
130.0468-0.0117-0.00270.060.03070.0276-0.0578-0.17950.08640.0845-0.1624-0.0196-0.12210.1911-0.00551.15620.0728-0.44030.7919-0.05511.220532.005114.8078-43.7083
140.10180.01540.01390.00280.00030.01770.0129-0.0738-0.2774-0.0147-0.15570.2077-0.03830.175-0.00161.0724-0.5366-0.21041.31320.36180.961242.4046-19.5866-14.5439
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 173 through 226 )
2X-RAY DIFFRACTION2chain 'A' and (resid 227 through 241 )
3X-RAY DIFFRACTION3chain 'B' and (resid 172 through 226 )
4X-RAY DIFFRACTION4chain 'B' and (resid 227 through 242 )
5X-RAY DIFFRACTION5chain 'C' and (resid 174 through 220 )
6X-RAY DIFFRACTION6chain 'C' and (resid 221 through 241 )
7X-RAY DIFFRACTION7chain 'D' and (resid 173 through 226 )
8X-RAY DIFFRACTION8chain 'D' and (resid 227 through 242 )
9X-RAY DIFFRACTION9chain 'E' and (resid 833 through 842 )
10X-RAY DIFFRACTION10chain 'E' and (resid 843 through 851 )
11X-RAY DIFFRACTION11chain 'F' and (resid 833 through 842 )
12X-RAY DIFFRACTION12chain 'F' and (resid 843 through 852 )
13X-RAY DIFFRACTION13chain 'G' and (resid 834 through 846 )
14X-RAY DIFFRACTION14chain 'H' and (resid 838 through 849 )

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