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- PDB-1wu9: Crystal structure of the C-terminal domain of the end-binding pro... -

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Basic information

Entry
Database: PDB / ID: 1wu9
TitleCrystal structure of the C-terminal domain of the end-binding protein 1 (EB1)
ComponentsMicrotubule-associated protein RP/EB family member 1
KeywordsSTRUCTURAL PROTEIN / EB1-like structural motif / APC/dynactin binding domain / Coiled coil
Function / homology
Function and homology information


protein localization to astral microtubule / cortical microtubule cytoskeleton / mitotic spindle astral microtubule end / protein localization to microtubule / microtubule plus-end / cell projection membrane / attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end binding / non-motile cilium assembly / microtubule bundle formation ...protein localization to astral microtubule / cortical microtubule cytoskeleton / mitotic spindle astral microtubule end / protein localization to microtubule / microtubule plus-end / cell projection membrane / attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end binding / non-motile cilium assembly / microtubule bundle formation / protein localization to centrosome / microtubule organizing center / negative regulation of microtubule polymerization / mitotic spindle pole / microtubule polymerization / establishment of mitotic spindle orientation / spindle assembly / regulation of microtubule polymerization or depolymerization / spindle midzone / cytoplasmic microtubule / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / positive regulation of microtubule polymerization / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / ciliary basal body / RHO GTPases Activate Formins / protein localization / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / Regulation of PLK1 Activity at G2/M Transition / cell migration / microtubule / molecular adaptor activity / cadherin binding / cell division / focal adhesion / centrosome / protein kinase binding / Golgi apparatus / RNA binding / identical protein binding / cytosol
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 / 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 - #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 / 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 / Up-down 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 / SIRAS / Resolution: 1.54 Å
AuthorsHonnappa, S. / John, C.M. / Kostrewa, D. / Winkler, F.K. / Steinmetz, M.O.
CitationJournal: Embo J. / Year: 2005
Title: Structural insights into the EB1-APC interaction
Authors: Honnappa, S. / John, C.M. / Kostrewa, D. / Winkler, F.K. / Steinmetz, M.O.
History
DepositionDec 2, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 1
B: Microtubule-associated protein RP/EB family member 1


Theoretical massNumber of molelcules
Total (without water)18,4242
Polymers18,4242
Non-polymers00
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-33 kcal/mol
Surface area8620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.0, 37.3, 56.5
Angle α, β, γ (deg.)90.0, 105.4, 90.0
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is the dimer in the asymmetric unit.

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Components

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


Mass: 9212.031 Da / Num. of mol.: 2 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EB1 / Plasmid: pET-15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15691
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 1.76 Å3/Da / Density % sol: 30 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: sodium citrate, PEG 3350, gamma-butyrolactone, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 12, 2004 / Details: Osmic mirrors
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.54→55 Å / Num. all: 18705 / Num. obs: 18705 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 24 Å2 / Rsym value: 0.04 / Net I/σ(I): 14.8
Reflection shellResolution: 1.54→1.6 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 5.4 / Num. unique all: 1850 / Rsym value: 0.188 / % possible all: 90.1

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Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
MAR345data collection
XDSdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.54→54.23 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.675 / SU ML: 0.072 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.085 / ESU R Free: 0.088 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22 959 5.1 %RANDOM
Rwork0.181 ---
all0.183 17745 --
obs0.183 17745 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21 Å2
Baniso -1Baniso -2Baniso -3
1-1.6 Å20 Å2-0.45 Å2
2---0.24 Å20 Å2
3----1.6 Å2
Refine analyzeLuzzati sigma a free: 0.07 Å
Refinement stepCycle: LAST / Resolution: 1.54→54.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1030 0 0 119 1149
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221040
X-RAY DIFFRACTIONr_bond_other_d0.0010.02951
X-RAY DIFFRACTIONr_angle_refined_deg1.1771.9781404
X-RAY DIFFRACTIONr_angle_other_deg0.74332221
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0985124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.55326.61362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.89115198
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.41156
X-RAY DIFFRACTIONr_chiral_restr0.0630.2161
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021156
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02186
X-RAY DIFFRACTIONr_nbd_refined0.2270.2247
X-RAY DIFFRACTIONr_nbd_other0.1580.2963
X-RAY DIFFRACTIONr_nbtor_other0.0840.2621
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.257
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2020.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.211
X-RAY DIFFRACTIONr_mcbond_it2.6252831
X-RAY DIFFRACTIONr_mcbond_other0.6432258
X-RAY DIFFRACTIONr_mcangle_it2.83631014
X-RAY DIFFRACTIONr_scbond_it5.6344.5460
X-RAY DIFFRACTIONr_scangle_it7.6416390
LS refinement shellResolution: 1.54→1.58 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.343 57
Rwork0.268 1155

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