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- PDB-7x9u: Type-II KH motif of human mitochondrial RbfA -

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Basic information

Entry
Database: PDB / ID: 7x9u
TitleType-II KH motif of human mitochondrial RbfA
ComponentsPutative ribosome-binding factor A, mitochondrial
KeywordsRNA BINDING PROTEIN / Ribosome / mitochondria / maturation / Structural Genomics / PSI-2 / Protein Structure Initiative / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


rRNA processing / mitochondrion
Similarity search - Function
Putative ribosome-binding factor A, mitochondrial / Ribosome-binding factor A, conserved site / Ribosome-binding factor A signature. / Ribosome-binding factor A / Ribosome-binding factor A domain superfamily / Ribosome-binding factor A / K homology domain-like, alpha/beta
Similarity search - Domain/homology
Putative ribosome-binding factor A, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsKuwasako, K. / Suzuki, S. / Furue, M. / Takizawa, M. / Takahashi, M. / Tsuda, K. / Nagata, T. / Watanabe, S. / Tanaka, A. / Kobayashi, N. ...Kuwasako, K. / Suzuki, S. / Furue, M. / Takizawa, M. / Takahashi, M. / Tsuda, K. / Nagata, T. / Watanabe, S. / Tanaka, A. / Kobayashi, N. / Kigawa, T. / Guntert, P. / Shirouzu, M. / Yokoyama, S. / Muto, Y. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biomol.Nmr Assign. / Year: 2022
Title: 1 H, 13 C, and 15 N resonance assignments and solution structures of the KH domain of human ribosome binding factor A, mtRbfA, involved in mitochondrial ribosome biogenesis.
Authors: Kuwasako, K. / Suzuki, S. / Nameki, N. / Takizawa, M. / Takahashi, M. / Tsuda, K. / Nagata, T. / Watanabe, S. / Tanaka, A. / Kobayashi, N. / Kigawa, T. / Guntert, P. / Shirouzu, M. / Yokoyama, S. / Muto, Y.
History
DepositionMar 16, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1May 15, 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

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Assembly

Deposited unit
A: Putative ribosome-binding factor A, mitochondrial


Theoretical massNumber of molelcules
Total (without water)14,0101
Polymers14,0101
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Putative ribosome-binding factor A, mitochondrial


Mass: 14009.806 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBFA, C18orf22 / Plasmid: P050905-10 / Details (production host): CELL-FREE PROTEIN SYNTHESIS
Production host: Cell-free gateway cloning vector N-term 8xHis pCellFree_G01 (others)
References: UniProt: Q8N0V3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic23D 13C,15N-SEPARATED NOESY SPECTRA
121isotropic13D CBCA(CO)NH
131isotropic13D HN(CA)CB
141isotropic13D (H)CCH-COSY
151isotropic13D (H)CCH-TOCSY

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Sample preparation

DetailsType: solution
Contents: 0.79 mM [U-99% 13C; U-99% 15N] human mitochondrial RbfA, 100 mM non NaCl, 1 mM [U-99% 2H] d-DTT, 20 mM [U-99% 2H] d-Tris HCl, 0.02 % w/v non NaN3, 90% H2O/10% D2O
Details: 1mM D-DTT;0.02% NaN3 were used to keep the protein condition
Label: 13C,15N_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.79 mMhuman mitochondrial RbfA[U-99% 13C; U-99% 15N]1
100 mMNaClnon1
1 mMd-DTT[U-99% 2H]1
20 mMd-Tris HCl[U-99% 2H]1
0.02 % w/vNaN3non1
Sample conditionsDetails: 20mM d-Tris-HCL (PH7.0); 100mM NaCl; 1mM d-DTT;0.02% NaN3
Ionic strength: 100 mM / Label: condition_1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE6001Assignment (CBCACONH etc)
Bruker AVANCEBrukerAVANCE800213C,15N-edited NOESY

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Processing

NMR software
NameVersionDeveloperClassification
Amber12Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANA2-1Guntert, Mumenthaler and Wuthrichstructure calculation
KUJIRA0.863N. Kobayashi, T. Kigawa, S. Yokoyamachemical shift assignment
NMRView5.0.4Johnson, One Moon Scientificpeak picking
NMRPipe2007Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOS2007Cornilescu, Delaglio and Baxgeometry optimization
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are refined based on 1463 distant constraints derived from NOE and estimated hydrogen bonds, and 212 dihedral constraints estimated from NOE data and TALOS program.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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