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- PDB-1pa7: Crystal structure of amino-terminal microtubule binding domain of EB1 -

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Basic information

Entry
Database: PDB / ID: 1pa7
TitleCrystal structure of amino-terminal microtubule binding domain of EB1
ComponentsMicrotubule-associated protein RP/EB family member 1
KeywordsSTRUCTURAL PROTEIN / CH domain
Function / homology
Function and homology information


protein localization to astral microtubule / protein localization to mitotic spindle / cortical microtubule cytoskeleton / mitotic spindle astral microtubule end / protein localization to microtubule / microtubule plus-end / mitotic spindle microtubule / cell projection membrane / attachment of mitotic spindle microtubules to kinetochore / microtubule bundle formation ...protein localization to astral microtubule / protein localization to mitotic spindle / cortical microtubule cytoskeleton / mitotic spindle astral microtubule end / protein localization to microtubule / microtubule plus-end / mitotic spindle microtubule / cell projection membrane / attachment of mitotic spindle microtubules to kinetochore / microtubule bundle formation / non-motile cilium assembly / microtubule plus-end binding / protein localization to centrosome / negative regulation of microtubule polymerization / mitotic spindle pole / microtubule organizing center / microtubule polymerization / establishment of mitotic spindle orientation / regulation of microtubule polymerization or depolymerization / spindle midzone / spindle assembly / cytoplasmic microtubule / 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 / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / protein serine/threonine kinase binding / Resolution of Sister Chromatid Cohesion / AURKA Activation by TPX2 / RHO GTPases Activate Formins / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / Regulation of PLK1 Activity at G2/M Transition / intracellular protein localization / cell migration / microtubule / ciliary basal body / cadherin binding / cell division / focal adhesion / centrosome / Golgi apparatus / RNA binding / identical protein binding / cytosol
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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.45 Å
AuthorsHayashi, I. / Ikura, M.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal structure of the amino-terminal microtubule-binding domain of end-binding protein 1 (EB1)
Authors: Hayashi, I. / Ikura, M.
History
DepositionMay 13, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 21, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Microtubule-associated protein RP/EB family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2433
Polymers15,0501
Non-polymers1922
Water2,450136
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.856, 48.453, 44.968
Angle α, β, γ (deg.)90.00, 103.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Microtubule-associated protein RP/EB family member 1 / APC-binding protein EB1


Mass: 15050.383 Da / Num. of mol.: 1 / Fragment: N-terminal domain, EB1 microtubule-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EB1 (amino acids 1-130) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15691
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG4K, ammonium sulfate, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMTris1droppH8.0
20.1 M1dropNaCl
31 mMdithiothreitol1drop
415 mg/mlprotein1drop
520 %PEG33501reservoir
60.2 Mammonium sulfate1reservoir
70.1 MMES1reservoirpH6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 7, 2002 / Details: mirror
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.45→20 Å / Num. obs: 23798 / Rmerge(I) obs: 0.042
Reflection shellResolution: 1.45→1.5 Å / Rmerge(I) obs: 0.228 / Num. unique all: 2278
Reflection
*PLUS
% possible obs: 99 %
Reflection shell
*PLUS
% possible obs: 97.8 % / Rmerge(I) obs: 0.192 / Mean I/σ(I) obs: 6.99

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 1.45→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.946 / SU B: 0.932 / SU ML: 0.037 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1886 1211 5.1 %RANDOM
Rwork0.17272 ---
obs0.17358 22304 98.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.199 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å20.17 Å2
2---0.03 Å20 Å2
3---0.47 Å2
Refinement stepCycle: LAST / Resolution: 1.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1058 0 10 136 1204
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221067
X-RAY DIFFRACTIONr_bond_other_d0.0020.02943
X-RAY DIFFRACTIONr_angle_refined_deg1.2471.9411438
X-RAY DIFFRACTIONr_angle_other_deg0.7832184
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1465129
X-RAY DIFFRACTIONr_chiral_restr0.0810.2154
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021177
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02223
X-RAY DIFFRACTIONr_nbd_refined0.2290.2222
X-RAY DIFFRACTIONr_nbd_other0.2180.21018
X-RAY DIFFRACTIONr_nbtor_other0.0830.2578
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.27
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0710.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2760.214
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0540.22
X-RAY DIFFRACTIONr_mcbond_it0.7881.5646
X-RAY DIFFRACTIONr_mcangle_it1.44621037
X-RAY DIFFRACTIONr_scbond_it2.3723421
X-RAY DIFFRACTIONr_scangle_it3.5544.5401
LS refinement shellResolution: 1.448→1.486 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.205 90
Rwork0.182 1554
Refinement TLS params.Method: refined / Origin x: 2.8131 Å / Origin y: 23.293 Å / Origin z: 32.6876 Å
111213212223313233
T0.0038 Å20.0012 Å20.0007 Å2-0.0033 Å2-0.0013 Å2--0.001 Å2
L0.2538 °2-0.0316 °20.0281 °2-0.109 °20.0767 °2--0.1425 °2
S-0.0045 Å °-0.0235 Å °0.0116 Å °-0.0094 Å °-0.0044 Å °0.0137 Å °0.0069 Å °-0.005 Å °0.0089 Å °
Refinement
*PLUS
Num. reflection obs: 21093 / % reflection Rfree: 5 % / Rfactor Rfree: 0.189 / Rfactor Rwork: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.022
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.25

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