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- PDB-8tg0: Solution NMR structure of the cold shock domain of the Arabidopsi... -

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Basic information

Entry
Database: PDB / ID: 8tg0
TitleSolution NMR structure of the cold shock domain of the Arabidopsis thaliana glycine-rich protein AtGRP2
ComponentsCold shock protein 2
KeywordsRNA BINDING PROTEIN / Glycine-rich protein / cold shock
Function / homology
Function and homology information


response to desiccation / : / vegetative to reproductive phase transition of meristem / seed development / stamen development / cold acclimation / response to abscisic acid / response to water deprivation / regulation of cellular respiration / response to cold ...response to desiccation / : / vegetative to reproductive phase transition of meristem / seed development / stamen development / cold acclimation / response to abscisic acid / response to water deprivation / regulation of cellular respiration / response to cold / single-stranded DNA binding / double-stranded DNA binding / vesicle / nucleic acid binding / mRNA binding / nucleolus / zinc ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Cold-shock (CSD) domain / Cold-shock (CSD) domain signature. / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold-shock (CSD) domain profile. / Cold shock domain / Cold shock protein domain / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily ...Cold-shock (CSD) domain / Cold-shock (CSD) domain signature. / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold-shock (CSD) domain profile. / Cold shock domain / Cold shock protein domain / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Cold shock protein 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / simulated annealing
AuthorsPougy, K.C. / Almeida, F.C.L. / Pinheiro, A.S.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq) Brazil
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Structural basis of nucleic acid recognition by the N-terminal cold shock domain of the plant glycine-rich protein AtGRP2.
Authors: Pougy, K.C. / Moraes, B.S. / Malizia-Motta, C.L.F. / Lima, L.M.T.R. / Sachetto-Martins, G. / Almeida, F.C.L. / Pinheiro, A.S.
History
DepositionJul 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cold shock protein 2


Theoretical massNumber of molelcules
Total (without water)9,6651
Polymers9,6651
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 400structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Cold shock protein 2 / AtCSP2 / Cold shock domain-containing protein 2 / Glycine-rich protein 2 / AtGRP2


Mass: 9665.299 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CSP2, CSDP2, GRP2, At4g38680, F20M13.240 / Plasmid: pET-RP1B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q41188
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic12D 1H-15N HSQC
124isotropic23D HN(CA)CB
134isotropic23D CBCA(CO)NH
144isotropic23D HNCA
154isotropic23D HNCO
164isotropic23D HN(CA)CO
174isotropic23D HBHA(CO)NH
184isotropic12D 1H-13C HSQC
194isotropic13D CC(CO)NH
1104isotropic13D (H)CCH-TOCSY
1114isotropic13D (H)CCH-TOCSY
1124isotropic12D (HB)CB(CGCD)HD
1134isotropic12D (HB)CB(CGCDCE)HE
1143isotropic12D 1H-1H TOCSY
1154isotropic13D 1H-13C NOESY aliphatic
1164isotropic13D 1H-15N NOESY
1173isotropic12D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution220 mM sodium phosphate, 50 mM sodium chloride, 250 uM PMSF, 3 mM sodium azide, 1.3 mM [U-100% 15N] cold shock protein 2, 95% H2O/5% D2O15N_ sample95% H2O/5% D2O
solution420 mM sodium phosphate, 50 mM sodium chloride, 250 uM PMSF, 3 mM sodium azide, 1.3 mM [U-13C; U-15N] cold shock protein 2, 95% H2O/5% D2O15N_13C_ sample95% H2O/5% D2O
solution320 mM sodium phosphate, 50 mM sodium chloride, 250 uM PMSF, 3 mM sodium azide, 1.3 mM cold shock protein 2, 100% D2O1H_ sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMsodium phosphatenatural abundance2
50 mMsodium chloridenatural abundance2
250 uMPMSFnatural abundance2
3 mMsodium azidenatural abundance2
20 mMsodium phosphatenatural abundance4
50 mMsodium chloridenatural abundance4
250 uMPMSFnatural abundance4
3 mMsodium azidenatural abundance4
20 mMsodium phosphatenatural abundance3
50 mMsodium chloridenatural abundance3
250 uMPMSFnatural abundance3
3 mMsodium azidenatural abundance3
1.3 mMcold shock protein 2[U-100% 15N]2
1.3 mMcold shock protein 2[U-13C; U-15N]4
1.3 mMcold shock protein 2natural abundance3
Sample conditionsIonic strength: NaCl 50 mM / Label: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE III HDBrukerAVANCE III HD9001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameDeveloperClassification
CARAKeller and Wuthrichchemical shift assignment
CcpNmr AnalysisCCPNchemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 3
Details: The structures are based on a total of 2216 restraints, 2150 of which are NOE-derived distance constraints and 66 are dihedral angle restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 20

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