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- PDB-2mqh: Solution structure of the Chlamydomonas reinhardtii NAB1 cold sho... -

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Basic information

Entry
Database: PDB / ID: 2mqh
TitleSolution structure of the Chlamydomonas reinhardtii NAB1 cold shock domain, CSD1
ComponentsNucleic acid binding protein
KeywordsDNA BINDING PROTEIN / protein / cold shock domain / RNA-binding / Chlamydomonas reinhardtii / algae
Function / homology
Function and homology information


response to cold / ribonucleoprotein complex / mRNA binding / zinc ion binding / nucleus / 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 / Nucleic acid-binding proteins / RNA recognition motif / RNA recognition motif ...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 / Nucleic acid-binding proteins / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleotide-binding alpha-beta plait domain superfamily / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Putative nucleic acid binding protein
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsSawyer, A. / Mobli, M.
Citation
Journal: Biochem.J. / Year: 2015
Title: Solution structure of the RNA-binding cold-shock domain of the Chlamydomonas reinhardtii NAB1 protein and insights into RNA recognition.
Authors: Sawyer, A.L. / Landsberg, M.J. / Ross, I.L. / Kruse, O. / Mobli, M. / Hankamer, B.
#2: Journal: Plant Cell / Year: 2005
Title: NAB1 is an RNA binding protein involved in the light-regulated differential expression of the light-harvesting antenna of Chlamydomonas reinhardtii
Authors: Mussgnug, J. / Wobbe, L. / Elles, I. / Claus, C. / Hamilton, M. / Fink, A. / Kahmann, U. / Kapazoglou, A. / Mullineaux, C. / Hippler, M. / Nickelsen, J. / Nixon, P. / Kruse, O.
History
DepositionJun 20, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Dec 20, 2017Group: Database references / Category: pdbx_database_related
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 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: Nucleic acid binding protein


Theoretical massNumber of molelcules
Total (without water)8,9981
Polymers8,9981
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)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Nucleic acid binding protein / Putative nucleic acid binding protein


Mass: 8997.812 Da / Num. of mol.: 1 / Fragment: cold shock domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant)
Gene: CHLREDRAFT_126810, Nab1, NAB1 nucleic acid binding protein
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8GV23

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D CBCA(CO)NH
1213D HN(CA)CB
1313D HNCO
1413D 1H-15N NOESY
1513D 1H-13C NOESY aliphatic
1612D 1H-15N HSQC
2713D (H)CCH-TOCSY
1813D 1H-13C NOESY aromatic
NMR detailsText: All non NOE 3D experiments acquired using NUS and processed using MaxEnt.

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Sample preparation

DetailsContents: 267 uM [U-100% 13C; U-100% 15N] NAB1 cold shock domain, 20 mM sodium phosphate, 300 mM sodium chloride, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
267 uMNAB1 cold shock domain-1[U-100% 13C; U-100% 15N]1
20 mMsodium phosphate-21
300 mMsodium chloride-31
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.37ambient atm298 K
20.37ambient atm303 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr2.4.0CCPNdata analysis
CcpNmr2.4.0CCPNchemical shift assignment
CcpNmr2.4.0CCPNpeak picking
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
TopSpin3.1Bruker Biospincollection
Rowland_NMR_Toolkit3A. Stern, J. C. Hochprocessing
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: Automated noe assignment
NMR constraintsNOE constraints total: 679 / NOE intraresidue total count: 192 / NOE long range total count: 194 / NOE medium range total count: 33 / NOE sequential total count: 260
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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