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- PDB-2rt9: Solution structure of a regulatory domain of meiosis inhibitor -

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Basic information

Entry
Database: PDB / ID: 2rt9
TitleSolution structure of a regulatory domain of meiosis inhibitor
ComponentsF-box only protein 43
KeywordsMETAL BINDING PROTEIN / zinc-finger domain
Function / homology
Function and homology information


meiotic nuclear division / negative regulation of cell cycle process / negative regulation of meiotic nuclear division / regulation of meiotic nuclear division / female germ cell nucleus / regulation of mitotic nuclear division / protein catabolic process / negative regulation of protein catabolic process / protein ubiquitination / zinc ion binding / nucleus
Similarity search - Function
N-terminal domain of TfIIb - #20 / Zinc finger ZBR-type domain / : / Zinc finger ZBR-type profile. / IBR domain / In Between Ring fingers / N-terminal domain of TfIIb / Single Sheet / Mainly Beta
Similarity search - Domain/homology
F-box only protein 43
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model1
AuthorsShoji, S. / Muto, Y. / Ikeda, M. / He, F. / Tsuda, K. / Ohsawa, N. / Akasaka, R. / Terada, T. / Wakiyama, M. / Shirouzu, M. / Yokoyama, S.
CitationJournal: FEBS Open Bio / Year: 2014
Title: The zinc-binding region (ZBR) fragment of Emi2 can inhibit APC/C by targeting its association with the coactivator Cdc20 and UBE2C-mediated ubiquitylation
Authors: Shoji, S. / Muto, Y. / Ikeda, M. / He, F. / Tsuda, K. / Ohsawa, N. / Akasaka, R. / Terada, T. / Wakiyama, M. / Shirouzu, M. / Yokoyama, S.
History
DepositionJul 5, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: F-box only protein 43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4813
Polymers6,3501
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein F-box only protein 43 / Endogenous meiotic inhibitor 2


Mass: 6350.284 Da / Num. of mol.: 1 / Fragment: UNP residues 565-616
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fbxo43 / Production host: E. coli CELL FREE PROTEIN SYNTHESIS / References: UniProt: Q8CDI2
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY

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Sample preparation

DetailsContents: 0.47 mM [U-100% 13C; U-100% 15N] protein-1, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.47 mM / Component: protein-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 120 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
KUJIRAKobayashi, Ndata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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