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- PDB-6evq: solution NMR structure of EB1 C terminus (191-260) with a small m... -

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Basic information

Entry
Database: PDB / ID: 6evq
Titlesolution NMR structure of EB1 C terminus (191-260) with a small molecule bound into the SxIP binding site
ComponentsMicrotubule-associated protein RP/EB family member 1
KeywordsPROTEIN BINDING / End-binding protein / EB1 / microtubules / SxIP / Microtubule-associated protein RP/EB family member 1 / MAPRE1 / APC-binding protein EB1
Function / homology
Function and homology information


protein localization to astral microtubule / cortical microtubule cytoskeleton / mitotic spindle astral microtubule end / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / The role of GTSE1 in G2/M progression after G2 checkpoint / RHO GTPases Activate Formins / protein localization to microtubule ...protein localization to astral microtubule / cortical microtubule cytoskeleton / mitotic spindle astral microtubule end / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / The role of GTSE1 in G2/M progression after G2 checkpoint / RHO GTPases Activate Formins / protein localization to microtubule / Separation of Sister Chromatids / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / microtubule plus-end / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / cell projection membrane / Regulation of PLK1 Activity at G2/M Transition / 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 / positive regulation of microtubule polymerization / ciliary basal body / cell projection / microtubule cytoskeleton / cell migration / microtubule / molecular adaptor activity / cell division / focal adhesion / centrosome / protein kinase binding / Golgi apparatus / identical protein binding
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
Chem-C05 / Microtubule-associated protein RP/EB family member 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsBarsukov, I.L. / Almeida, T.B.
CitationJournal: Sci Rep / Year: 2017
Title: Targeting SxIP-EB1 interaction: An integrated approach to the discovery of small molecule modulators of dynamic binding sites.
Authors: Almeida, T.B. / Carnell, A.J. / Barsukov, I.L. / Berry, N.G.
History
DepositionNov 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7434
Polymers16,1002
Non-polymers6432
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area3370 Å2
ΔGint-35 kcal/mol
Surface area9540 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1closest to the average

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Components

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


Mass: 8049.979 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mapre1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q61166
#2: Chemical ChemComp-C05 / (2~{R})-2-[(1-cyclopentyl-1,2,3,4-tetrazol-5-yl)sulfanyl]-~{N}-(furan-2-ylmethyl)propanamide


Mass: 321.398 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H19N5O2S

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
121isotropic22D 1H-13C HSQC aliphatic
131isotropic22D 1H-13C HSQC aromatic
141isotropic23D CBCA(CO)NH
151isotropic23D HBHA(CO)NH
1101isotropic23D 1H-13C NOESY aliphatic
191isotropic23D 1H-13C NOESY aromatic
181isotropic22D 1H-1H NOESY
171isotropic22D 1H-1H TOCSY
161isotropic23D (H)CCH-TOCSY
1111isotropic23D 1H-15N NOESY

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-13C; U-15N] EB1, 5 mM 2-(1-cyclopentyltetrazol-5-yl)sulfanyl-N-(2-furylmethyl)propanamide, 90% H2O/10% D2O
Label: 15N, 13C / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMEB1[U-13C; U-15N]1
5 mM2-(1-cyclopentyltetrazol-5-yl)sulfanyl-N-(2-furylmethyl)propanamidenatural abundance1
Sample conditionsIonic strength: 50 mM / Label: H2O / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceIIIBrukerAvanceIII6001
Bruker AvanceIIIBrukerAvanceIII8002

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
ARIALinge, O'Donoghue and Nilgesstructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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