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- PDB-2k76: Solution structure of a paralog-specific Mena binder by NMR -

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Basic information

Entry
Database: PDB / ID: 2k76
TitleSolution structure of a paralog-specific Mena binder by NMR
ComponentspGolemi
KeywordsDE NOVO PROTEIN / protein design / miniature protein / aPP / beta-hairpin / ActA homolog
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsLink, N.M. / Hunke, C. / Eichler, J. / Bayer, P.
Citation
Journal: Biol.Chem. / Year: 2009
Title: The solution structure of pGolemi, a high affinity Mena EVH1 binding miniature protein, suggests explanations for paralog-specific binding to Ena/VASP homology (EVH) 1 domains.
Authors: Link, N.M. / Hunke, C. / Mueller, J.W. / Eichler, J. / Bayer, P.
#1: Journal: J.Am.Chem.Soc. / Year: 2004
Title: High Affinity, Paralog-Specific Recognition of the Mena EVH1 domain by a miniature protein
Authors: Golemi-Kotra, D. / Mahaffy, R. / Footer, M.J. / Holtzman, J.H. / Pollard, T.D. / Theriot, J.A. / Schepartz, A.
#2: Journal: Biochemistry / Year: 2007
Title: Miniature Protein Ligands for EVH1 Domains: Interplay between Affinity, Specificity, and Cell Motility
Authors: Holtzman, J.H. / Woronowicz, K. / Golemi-Kotra, D. / Schepartz, A.
History
DepositionAug 3, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: pGolemi


Theoretical massNumber of molelcules
Total (without water)3,4601
Polymers3,4601
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200lowest energy
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide pGolemi


Mass: 3459.831 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Solid-phase peptide synthesis. The original sequence comes from Meleagris gallopavo (Wild Turkey)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111COSY
121TOCSY
131NOESY

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Sample preparation

DetailsContents: 1 mM pGolemi, 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: pGolemi
Sample conditionsIonic strength: 45 / pH: 7 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: DRX / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
AUREMOL2Bruker Biospinchemical shift assignment
AUREMOL2Bruker Biospinpeak picking
X-PLOR NIH2.18Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.18Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 373 / NOE intraresidue total count: 203 / NOE long range total count: 12 / NOE medium range total count: 63 / NOE sequential total count: 95 / Hydrogen bond constraints total count: 26 / Protein other angle constraints total count: 50
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: lowest energy / Conformers calculated total number: 200 / Conformers submitted total number: 10

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