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- PDB-2mez: Flexible anchoring of archaeal MBF1 on ribosomes suggests role as... -

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Basic information

Entry
Database: PDB / ID: 2mez
TitleFlexible anchoring of archaeal MBF1 on ribosomes suggests role as recruitment factor
ComponentsMultiprotein Bridging Factor (MBP-like)
KeywordsRNA BINDING PROTEIN / Multiple Binding Factor MBF1 / Helix-turn-Helix domain
Function / homology
Function and homology information


Conserved hypothetical protein CHP00270 / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / lambda repressor-like DNA-binding domains / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Multiprotein Bridging Factor (MBP-like), putative (MBP-like)
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodSOLUTION NMR / molecular dynamics
Model type detailsminimized average
AuthorsLaunay, H. / Blombarch, F. / Camilloni, C. / Vendruscolo, M. / van des Oost, J. / Christodoulou, J.
CitationJournal: Biochem.J. / Year: 2014
Title: Archaeal MBF1 binds to 30S and 70S ribosomes via its helix-turn-helix domain.
Authors: Blombach, F. / Launay, H. / Snijders, A.P. / Zorraquino, V. / Wu, H. / de Koning, B. / Brouns, S.J. / Ettema, T.J. / Camilloni, C. / Cavalli, A. / Vendruscolo, M. / Dickman, M.J. / Cabrita, ...Authors: Blombach, F. / Launay, H. / Snijders, A.P. / Zorraquino, V. / Wu, H. / de Koning, B. / Brouns, S.J. / Ettema, T.J. / Camilloni, C. / Cavalli, A. / Vendruscolo, M. / Dickman, M.J. / Cabrita, L.D. / La Teana, A. / Benelli, D. / Londei, P. / Christodoulou, J. / van der Oost, J.
History
DepositionOct 3, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Multiprotein Bridging Factor (MBP-like)


Theoretical massNumber of molelcules
Total (without water)12,1881
Polymers12,1881
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)16 / 1756one structure per cluster
RepresentativeModel #1minimized average structure

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Components

#1: Protein Multiprotein Bridging Factor (MBP-like)


Mass: 12187.833 Da / Num. of mol.: 1
Fragment: C-terminal Helix-turn-Helix domain (UNP residues 68-165)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: MBP-like, SSO0270 / Plasmid: pWUR557 / Production host: Escherichia coli (E. coli) / References: UniProt: Q980M2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HN(CA)CO
1413D HN(CA)CB
1513D CBCA(CO)NH

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Sample preparation

DetailsContents: 1 mM [U-100% 13C; U-100% 15N] MBF1-C, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: MBF1-C-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0.05 / pH: 7.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX7001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Zhengrong and Baxprocessing
CamShift-MDKohlhoff, K.J. et al.refinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: one structure per cluster / Conformers calculated total number: 1756 / Conformers submitted total number: 16

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