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- PDB-3co1: Crystal structure of microtubule binding domain of human EB3 -

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Basic information

Entry
Database: PDB / ID: 3co1
TitleCrystal structure of microtubule binding domain of human EB3
ComponentsMicrotubule-associated protein RP/EB family member 3
KeywordsPROTEIN BINDING / RP/EB family / CH domain / microtubule-binding / +TIP protein / Cell cycle / Cell division / Mitosis / Phosphoprotein
Function / homology
Function and homology information


mitotic spindle astral microtubule end / protein localization to microtubule / microtubule plus-end / microtubule plus-end binding / microtubule organizing center / regulation of microtubule polymerization / positive regulation of cyclin-dependent protein serine/threonine kinase activity / spindle assembly / regulation of microtubule polymerization or depolymerization / spindle midzone ...mitotic spindle astral microtubule end / protein localization to microtubule / microtubule plus-end / microtubule plus-end binding / microtubule organizing center / regulation of microtubule polymerization / positive regulation of cyclin-dependent protein serine/threonine kinase activity / spindle assembly / regulation of microtubule polymerization or depolymerization / spindle midzone / positive regulation of protein kinase activity / protein localization / microtubule cytoskeleton / midbody / microtubule binding / cell division / protein kinase binding / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / identical protein binding / cytoplasm
Similarity search - Function
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 / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily ...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 / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Microtubule-associated protein RP/EB family member 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsDe Groot, C.O. / Honnappa, S. / Steinmetz, M.O.
CitationJournal: J.Cell Biol. / Year: 2009
Title: Mammalian end binding proteins control persistent microtubule growth.
Authors: Komarova, Y. / De Groot, C.O. / Grigoriev, I. / Gouveia, S.M. / Munteanu, E.L. / Schober, J.M. / Honnappa, S. / Buey, R.M. / Hoogenraad, C.C. / Dogterom, M. / Borisy, G.G. / Steinmetz, M.O. / Akhmanova, A.
History
DepositionMar 27, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Microtubule-associated protein RP/EB family member 3


Theoretical massNumber of molelcules
Total (without water)15,4031
Polymers15,4031
Non-polymers00
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.188, 85.365, 32.161
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Microtubule-associated protein RP/EB family member 3 / End-binding protein 3 / EB3 / EB1 protein family member 3 / EBF3 / RP3


Mass: 15402.819 Da / Num. of mol.: 1 / Fragment: CH domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Invitrogen Gateway / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE(3) / References: UniProt: Q9UPY8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O

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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: 2.1 Å3/Da / Density % sol: 41.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.04M potassium phosphate, 16% PEG 8000, 20% glycerol anhydrous, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.009 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2007
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. all: 25525 / Num. obs: 25525 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rsym value: 0.107 / Net I/σ(I): 10.85
Reflection shellResolution: 1.4→1.45 Å / % possible all: 92.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata scaling
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PA7

1pa7


Resolution: 1.4→42.68 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.015 / SU ML: 0.058 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23355 1296 5.1 %RANDOM
Rwork0.20001 ---
all0.20161 24229 --
obs0.20161 24229 96.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.734 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å20 Å2
2--0.62 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.4→42.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1083 0 0 151 1234
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221124
X-RAY DIFFRACTIONr_angle_refined_deg1.0671.9321514
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4945135
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.13724.64356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.34615206
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.078153
X-RAY DIFFRACTIONr_chiral_restr0.080.2158
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02850
X-RAY DIFFRACTIONr_nbd_refined0.1890.2538
X-RAY DIFFRACTIONr_nbtor_refined0.3090.2786
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2107
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.218
X-RAY DIFFRACTIONr_mcbond_it1.9362673
X-RAY DIFFRACTIONr_mcangle_it2.69831065
X-RAY DIFFRACTIONr_scbond_it4.4414.5506
X-RAY DIFFRACTIONr_scangle_it6.396447
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 84 -
Rwork0.302 1651 -
obs--92.29 %
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)
13.0131-0.1531-0.011.49470.07972.1750.0444-0.05420.2084-0.0522-0.01650.0586-0.0574-0.0362-0.02790.0528-0.0269-0.01060.0244-0.00840.0882-3.580420.4453-1.2461
213.9048.04883.912622.5753.91051.84250.1982-0.1199-0.28220.3633-0.0655-0.16870.2656-0.0132-0.13280.12860.01930.00020.06140.03560.0915-3.66891.0339-1.2856
33.81750.0599-0.04523.417-0.58143.0131-0.02570.1133-0.1219-0.00710.0544-0.05450.1069-0.0855-0.02870.0565-0.00810.0014-0.00430.01730.0626-14.47651.4105-4.7855
41.4429-1.0855-0.5062.97391.34331.50410.0354-0.0252-0.0348-0.0716-0.07290.06760.0391-0.09030.03740.04270.003-0.00560.00920.00980.0272-17.104212.9572-7.9309
59.1566-0.7339-0.7716.5915-0.40155.3454-0.0371-0.08260.0411-0.0018-0.1872-0.07330.051-0.40580.22440.0449-0.035-0.01470.10920.01550.0433-24.687112.9974-15.2186
62.1287-0.5964-0.88794.02-0.48998.2607-0.05980.1296-0.2834-0.20810.09780.12270.638-0.193-0.0380.0777-0.0157-0.00070.0024-0.01450.0159-17.1738.2391-21.6999
75.7151.21452.3167.67346.023913.4067-0.20070.2430.1305-0.6090.0911-0.1283-0.15860.33880.10960.0934-0.00310.01080.02630.00930.0192-14.919418.8306-15.6205
85.82720.8135-0.58695.61111.83933.9405-0.0670.0871-0.0358-0.26590.0188-0.1432-0.14910.110.04820.0599-0.01690.01320.00860.02020.0545-9.43921.9488-11.0851
910.4714-1.13540.725413.81694.36729.15010.05960.69720.2385-0.4872-0.0647-0.51460.07330.46190.00510.03820.02840.05240.02690.02090.0216-6.7879.0369-20.6638
1012.7885-1.13060.889815.15770.22031.3010.23470.6737-0.6327-0.6002-0.1648-0.73310.23990.3908-0.06990.0450.06270.02270.0487-0.03870.0915-2.56084.1633-13.6876
112.5594-1.2057-0.27410.85940.37761.51960.0191-0.1497-0.0390.0596-0.0117-0.0540.0715-0.0433-0.00740.0271-0.004-0.00160.00860.01230.0565-9.729813.5459-1.7207
122.99283.0507-1.56613.15818.027327.3543-0.0481-0.001-0.3755-0.4207-0.1933-0.4179-0.00310.37470.24140.0004-0.00230.02570.03270.03370.054-26.971410.2364-3.456
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-1 - 121 - 14
2X-RAY DIFFRACTION2AA13 - 1815 - 20
3X-RAY DIFFRACTION3AA19 - 3621 - 38
4X-RAY DIFFRACTION4AA37 - 5639 - 58
5X-RAY DIFFRACTION5AA57 - 6459 - 66
6X-RAY DIFFRACTION6AA65 - 7567 - 77
7X-RAY DIFFRACTION7AA76 - 8178 - 83
8X-RAY DIFFRACTION8AA82 - 9184 - 93
9X-RAY DIFFRACTION9AA92 - 9994 - 101
10X-RAY DIFFRACTION10AA100 - 106102 - 108
11X-RAY DIFFRACTION11AA107 - 122109 - 124
12X-RAY DIFFRACTION12AA123 - 130125 - 132

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