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- PDB-1txq: Crystal structure of the EB1 C-terminal domain complexed with the... -

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Basic information

Entry
Database: PDB / ID: 1txq
TitleCrystal structure of the EB1 C-terminal domain complexed with the CAP-Gly domain of p150Glued
Components
  • Dynactin 1
  • Microtubule-associated protein RP/EB family member 1
KeywordsSTRUCTURAL PROTEIN/PROTEIN BINDING / PROTEIN COMPLEX / STRUCTURAL PROTEIN-PROTEIN BINDING COMPLEX
Function / homology
Function and homology information


centriolar subdistal appendage / positive regulation of neuromuscular junction development / centriole-centriole cohesion / cell cortex region / protein localization to mitotic spindle / protein localization to astral microtubule / cortical microtubule cytoskeleton / microtubule anchoring at centrosome / mitotic spindle astral microtubule end / ventral spinal cord development ...centriolar subdistal appendage / positive regulation of neuromuscular junction development / centriole-centriole cohesion / cell cortex region / protein localization to mitotic spindle / protein localization to astral microtubule / cortical microtubule cytoskeleton / microtubule anchoring at centrosome / mitotic spindle astral microtubule end / ventral spinal cord development / maintenance of synapse structure / melanosome transport / protein localization to microtubule / nuclear membrane disassembly / positive regulation of microtubule nucleation / microtubule plus-end / mitotic spindle microtubule / cell projection membrane / XBP1(S) activates chaperone genes / dynein complex / attachment of mitotic spindle microtubules to kinetochore / COPI-independent Golgi-to-ER retrograde traffic / microtubule plus-end binding / non-motile cilium assembly / microtubule bundle formation / retrograde transport, endosome to Golgi / nuclear migration / protein localization to centrosome / microtubule organizing center / motor behavior / microtubule associated complex / neuromuscular process / negative regulation of microtubule polymerization / neuromuscular junction development / intercellular bridge / mitotic spindle pole / cytoplasmic microtubule / cell leading edge / establishment of mitotic spindle orientation / microtubule polymerization / spindle midzone / spindle assembly / regulation of microtubule polymerization or depolymerization / COPI-mediated anterograde transport / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / EML4 and NUDC in mitotic spindle formation / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / regulation of mitotic spindle organization / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / positive regulation of microtubule polymerization / neuron projection maintenance / MHC class II antigen presentation / Resolution of Sister Chromatid Cohesion / centriole / AURKA Activation by TPX2 / tubulin binding / ciliary basal body / RHO GTPases Activate Formins / tau protein binding / mitotic spindle / kinetochore / spindle pole / spindle / neuron cellular homeostasis / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / protein localization / Signaling by ALK fusions and activated point mutants / cell migration / nuclear envelope / mitotic cell cycle / nervous system development / cell cortex / microtubule binding / microtubule / neuron projection / cadherin binding / axon / cell division / focal adhesion / neuronal cell body / centrosome / protein kinase binding / Golgi apparatus / RNA binding / identical protein binding / membrane / cytosol / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1430 / Dynein associated protein / Dynein associated protein / CAP Gly-rich-like domain / 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 / CAP-Gly domain signature. ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1430 / Dynein associated protein / Dynein associated protein / CAP Gly-rich-like domain / 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 / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / SH3 type barrels. / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Dynactin subunit 1 / Microtubule-associated protein RP/EB family member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsHayashi, I. / Ikura, M.
CitationJournal: Mol.Cell / Year: 2005
Title: Structural Basis for the Activation of Microtubule Assembly by the EB1 and p150(Glued) Complex
Authors: Hayashi, I. / Wilde, A. / Mal, T.K. / Ikura, M.
History
DepositionJul 6, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 13, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Dynactin 1
B: Microtubule-associated protein RP/EB family member 1


Theoretical massNumber of molelcules
Total (without water)19,7072
Polymers19,7072
Non-polymers00
Water1,45981
1
A: Dynactin 1
B: Microtubule-associated protein RP/EB family member 1

A: Dynactin 1
B: Microtubule-associated protein RP/EB family member 1


Theoretical massNumber of molelcules
Total (without water)39,4134
Polymers39,4134
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)53.085, 80.210, 39.239
Angle α, β, γ (deg.)90.00, 108.52, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-131-

HOH

DetailsThe biological assembly is a hetero-tetramer.

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Components

#1: Protein Dynactin 1 / 150 kDa dynein-associated polypeptide / DP-150 / DAP-150 / p150-glued / p135


Mass: 9928.076 Da / Num. of mol.: 1 / Fragment: p150Glued CAP-Gly domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: p150Glued / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q14203
#2: Protein Microtubule-associated protein RP/EB family member 1 / APC-binding protein EB1


Mass: 9778.598 Da / Num. of mol.: 1 / Fragment: EB1 C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EB1 / Plasmid: pGEX4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q15691
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.01 Å3/Da / Density % sol: 38.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: ammonium sulphate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9513 Å
DetectorDetector: CCD / Date: Jul 10, 2003
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9513 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 14411 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Biso Wilson estimate: 22.7 Å2
Reflection shellResolution: 1.8→1.91 Å / % possible all: 99.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→17.93 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 769082.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1408 10.1 %RANDOM
Rwork0.203 ---
obs0.203 13953 96.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.5391 Å2 / ksol: 0.433519 e/Å3
Displacement parametersBiso mean: 32 Å2
Baniso -1Baniso -2Baniso -3
1-7.4 Å20 Å20.17 Å2
2---1.26 Å20 Å2
3----6.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.8→17.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1094 0 0 81 1175
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.251.5
X-RAY DIFFRACTIONc_mcangle_it3.412
X-RAY DIFFRACTIONc_scbond_it2.692
X-RAY DIFFRACTIONc_scangle_it4.182.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.312 230 10.3 %
Rwork0.269 2008 -
obs--99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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