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- PDB-7c36: c-Myc DNA binding protein structure -

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Basic information

Entry
Database: PDB / ID: 7c36
Titlec-Myc DNA binding protein structure
ComponentsRNA-binding motif, single-stranded-interacting protein 1
KeywordsDNA BINDING PROTEIN / DNA Binding / c-myc binding
Function / homology
Function and homology information


poly(A) binding / poly(U) RNA binding / RNA processing / mRNA 3'-UTR binding / single-stranded DNA binding / double-stranded DNA binding / DNA replication / ribonucleoprotein complex / RNA binding / nucleus / cytosol
Similarity search - Function
MSSP-1, RNA recognition motif 1 / Paraneoplastic encephalomyelitis antigen / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
RNA-binding motif, single-stranded-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsAggarwal, P. / Bhavesh, N.S.
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Hinge like domain motion facilitates human RBMS1 protein binding to proto-oncogene c-myc promoter.
Authors: Aggarwal, P. / Bhavesh, N.S.
History
DepositionMay 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.3May 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

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-binding motif, single-stranded-interacting protein 1


Theoretical massNumber of molelcules
Total (without water)18,0781
Polymers18,0781
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9500 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 10000structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein RNA-binding motif, single-stranded-interacting protein 1 / Single-stranded DNA-binding protein MSSP-1 / Suppressor of CDC2 with RNA-binding motif 2


Mass: 18077.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBMS1, C2orf12, MSSP, MSSP1, SCR2 / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / References: UniProt: P29558

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
1143isotropic11D 1H
121isotropic12D 1H-15N HSQC
131isotropic12D 1H-13C HSQC aliphatic
141isotropic12D 1H-13C HSQC aromatic
111isotropic13D HNCA
151isotropic13D CBCA(CO)NH
171isotropic13D C(CO)NH
161isotropic13D HNCO
191isotropic13D HN(CA)CB
1121isotropic13D HN(CA)CO
181isotropic13D 15N-edited [1H,1H]-NOESY
1111isotropic13D 13Caro-edited [1H,1H]-NOESY
1132isotropic13D 13Cali-edited [1H,1H]-NOESY
1101isotropic23D 13Cali-edited [1H,1H]-NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM [U-13C; U-15N] protein, 90% H2O/10% D2O15N 13C labelled sample90% H2O/10% D2O
solution21 mM [U-13C; U-15N] protein, 100% D2O15N 13C labelled sample100% D2O
solution31 mM [U-15N] protein, 90% H2O/10% D2O15N90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMprotein[U-13C; U-15N]1
1 mMprotein[U-13C; U-15N]2
1 mMprotein[U-15N]3
Sample conditionsIonic strength: 100 mM / Label: Conditions 1 / pH: 7.1 / PH err: 0.1 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 303 K / Temperature err: 1

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III500.151
Bruker AVANCE IIIBrukerAVANCE III800.182

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.1Bruker Biospincollection
TopSpin3.1Bruker Biospinprocessing
CARAKeller and Wuthrichpeak picking
CARAKeller and Wuthrichdata analysis
CYANA3.98.13Guntert, Mumenthaler and Wuthrichstructure calculation
Amber18Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CARAKeller and Wuthrichchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 6
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 10000 / Conformers submitted total number: 20

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