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- PDB-6yet: Second EH domain of AtEH1/Pan1 -

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Basic information

Entry
Database: PDB / ID: 6yet
TitleSecond EH domain of AtEH1/Pan1
ComponentsCalcium-binding EF hand family protein
KeywordsLIPID BINDING PROTEIN / EF-hand / EH domain / lipid binding / Adaptor protein / Calcium binding
Function / homology
Function and homology information


calcium ion binding / nucleus
Similarity search - Function
EH domain / EH domain profile. / Eps15 homology domain / EH domain / EF hand / EF-hand / Recoverin; domain 1 / EF-hand, calcium binding motif / EF-hand calcium-binding domain profile. / EF-hand domain ...EH domain / EH domain profile. / Eps15 homology domain / EH domain / EF hand / EF-hand / Recoverin; domain 1 / EF-hand, calcium binding motif / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Calcium-binding EF hand family protein
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / simulated annealing
AuthorsYperman, K. / Papageorgiou, A. / Evangelidis, T. / Van Damme, D. / Tripsianes, K.
Funding support1items
OrganizationGrant numberCountry
European Research Council (ERC)682436
CitationJournal: Nat Commun / Year: 2021
Title: Distinct EH domains of the endocytic TPLATE complex confer lipid and protein binding.
Authors: Yperman, K. / Papageorgiou, A.C. / Merceron, R. / De Munck, S. / Bloch, Y. / Eeckhout, D. / Jiang, Q. / Tack, P. / Grigoryan, R. / Evangelidis, T. / Van Leene, J. / Vincze, L. / ...Authors: Yperman, K. / Papageorgiou, A.C. / Merceron, R. / De Munck, S. / Bloch, Y. / Eeckhout, D. / Jiang, Q. / Tack, P. / Grigoryan, R. / Evangelidis, T. / Van Leene, J. / Vincze, L. / Vandenabeele, P. / Vanhaecke, F. / Potocky, M. / De Jaeger, G. / Savvides, S.N. / Tripsianes, K. / Pleskot, R. / Van Damme, D.
History
DepositionMar 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3Jun 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: Calcium-binding EF hand family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3762
Polymers12,3361
Non-polymers401
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6220 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Calcium-binding EF hand family protein / F2D10.25


Mass: 12336.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g20760, F2D10.25, F2D10_25 / Plasmid: pET22b_EH12 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9LM78
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic14D HC(CC TOCSY(CO))NH
121isotropic14D 13C,15N edited HMQC-NOESY-HSQC
131isotropic14D 13C,13C edited HMQC-NOESY-HSQC
141isotropic13D 13C edited NOESY-HSQC

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Sample preparation

DetailsType: solution / Contents: 1 mM [U-99% 13C; U-99% 15N] EH12, 90% H2O/10% D2O / Label: sample_1 / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: EH12 / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 150 mM / Label: sample_conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 850 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
4D-CHAINSEvangelidis and Tripsianeschemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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