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- PDB-7olg: EB1 bound to MACF peptide -

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Basic information

Entry
Database: PDB / ID: 7olg
TitleEB1 bound to MACF peptide
Components
  • 11MACF
  • Microtubule-associated protein RP/EB family member 1
KeywordsPROTEIN BINDING / microtubule / +TIPs / homodimer / Leucine zipper
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 / protein localization to microtubule / RHO GTPases Activate Formins ...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 / protein localization to microtubule / RHO GTPases Activate Formins / 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 / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / microtubule plus-end / cell projection membrane / Regulation of PLK1 Activity at G2/M Transition / attachment of mitotic spindle microtubules to kinetochore / non-motile cilium assembly / microtubule bundle formation / microtubule plus-end binding / protein localization to centrosome / microtubule organizing center / negative regulation of microtubule polymerization / mitotic spindle pole / microtubule polymerization / cytoplasmic microtubule / establishment of mitotic spindle orientation / regulation of microtubule polymerization or depolymerization / spindle assembly / spindle midzone / positive regulation of microtubule polymerization / ciliary basal body / cell projection / microtubule cytoskeleton / cell migration / microtubule / cell division / focal adhesion / centrosome / protein kinase binding / Golgi apparatus / identical protein binding
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 homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile.
Similarity search - Domain/homology
Microtubule-associated protein RP/EB family member 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsAlmeida, T.B. / Barsukov, I.L.
CitationJournal: To Be Published
Title: EB1 bound to MACF peptide
Authors: Almeida, T.B. / Barsukov, I.L.
History
DepositionMay 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.2Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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
C: 11MACF
D: 11MACF


Theoretical massNumber of molelcules
Total (without water)18,6674
Polymers18,6674
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area6790 Å2
ΔGint-46 kcal/mol
Surface area9340 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 160all calculated structures submitted
RepresentativeModel #1lowest energy

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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: Protein/peptide 11MACF


Mass: 1283.561 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-13C HSQC
121isotropic22D 1H-13C HSQC aromatic
131isotropic22D 1H-1H NOESY
141isotropic22D 1H-15N HSQC
151isotropic23D CBCA(CO)NH
1111isotropic23D HBHA(CO)NH
1101isotropic23D 1H-13C NOESY
191isotropic23D (H)CCH-TOCSY
181isotropic13D 1H-15N NOESY

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Sample preparation

DetailsType: solution
Contents: 1.15 mM [U-13C; U-15N] cEB1, 1.265 mM 11MACF, 95% H2O/5% D2O
Label: 15N-13C_sample / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.15 mMcEB1[U-13C; U-15N]1
1.265 mM11MACFnatural abundance1
Sample conditionsIonic strength: 50 mM / Label: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIBrukerAVANCE II6001
Bruker AVANCE IIBrukerAVANCE II8002

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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: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 160 / Conformers submitted total number: 20

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