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- PDB-2mpu: Structural and Functional analysis of the Hordeum vulgare L. HvGR... -

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Basic information

Entry
Database: PDB / ID: 2mpu
TitleStructural and Functional analysis of the Hordeum vulgare L. HvGR-RBP1 protein, a glycine-rich RNA binding protein implicated in the regulation of barley leaf senescence and environmental adaptation
ComponentsRBP1
KeywordsRNA BINDING PROTEIN / RNA recognition motif / RRM / RNP1 / RNP2 / glycine rich protein / nucleic acid binding protein
Function / homology
Function and homology information


RRM (RNA recognition motif) domain / 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 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHordeum vulgare (barley)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model1
AuthorsMason, K.E. / Tripet, B.P. / Eilers, B.J. / Powell, P. / Fischer, A.M. / Copie, V.
Citation
Journal: Biochemistry / Year: 2014
Title: Structural and Biochemical Analysis of the Hordeum vulgare L. HvGR-RBP1 Protein, a Glycine-Rich RNA-Binding Protein Involved in the Regulation of Barley Plant Development and Stress Response.
Authors: Tripet, B.P. / Mason, K.E. / Eilers, B.J. / Burns, J. / Powell, P. / Fischer, A.M. / Copie, V.
#1: Journal: Biomol.Nmr Assign. / Year: 2014
Title: 1H, 13C, 15N backbone and side chain NMR resonance assignments for the N-terminal RNA recognition motif of the HvGR-RBP1 protein involved in the regulation of barley (Hordeum vulgare L.) senescence.
Authors: Mason, K.E. / Tripet, B.P. / Parrott, D. / Fischer, A.M. / Copie, V.
History
DepositionJun 2, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name
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: RBP1


Theoretical massNumber of molelcules
Total (without water)9,9901
Polymers9,9901
Non-polymers00
Water0
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 lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein RBP1


Mass: 9989.825 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hordeum vulgare (barley) / Gene: rbp1 / Production host: Escherichia coli (E. coli) / References: UniProt: J7FTI7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D (H)CCH-TOCSY
1413D H(CCO)NH
1513D CBCA(CO)NH
1613D C(CO)NH
1713D HN(CA)CB
1813D HBHA(CO)NH
1913D 1H-15N NOESY
11013D 1H-13C NOESY

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Sample preparation

DetailsContents: 15 mM [U-99% 13C; U-99% 15N] RBP1, 0.01 % sodium azide, 50 mM potassium phosphate, 5 % D2O, 1 mM EDTA, 500 mM sodium chloride, 1 mM PMSF, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
15 mMRBP1-1[U-99% 13C; U-99% 15N]1
0.01 %sodium azide-21
50 mMpotassium phosphate-31
5 %D2O-41
1 mMEDTA-51
500 mMsodium chloride-61
1 mMPMSF-71
Sample conditionsIonic strength: 1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker BioSpincollection
Sparky3.114Goddardchemical shift assignment
Sparky3.114Goddarddata analysis
Sparky3.114Goddardpeak picking
NMRPipe3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxstructure solution
AmberDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxrefinement
RefinementMethod: molecular dynamics / 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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