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- PDB-1x32: Three Dimensional Solution Structure of the Chromo1 domain of cpSRP43 -

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Basic information

Entry
Database: PDB / ID: 1x32
TitleThree Dimensional Solution Structure of the Chromo1 domain of cpSRP43
Componentschloroplast signal recognition particle component
KeywordsSIGNALING PROTEIN / Signal recognition particle / cpSRP43 / Chromo domain 1 / LHCP / thylakoid
Function / homology
Function and homology information


protein import into chloroplast thylakoid membrane / protein heterotrimerization / response to high light intensity / signal recognition particle, endoplasmic reticulum targeting / chloroplast envelope / chloroplast stroma / chloroplast thylakoid membrane / chloroplast / disordered domain specific binding / protein-macromolecule adaptor activity ...protein import into chloroplast thylakoid membrane / protein heterotrimerization / response to high light intensity / signal recognition particle, endoplasmic reticulum targeting / chloroplast envelope / chloroplast stroma / chloroplast thylakoid membrane / chloroplast / disordered domain specific binding / protein-macromolecule adaptor activity / protein domain specific binding / protein-containing complex / identical protein binding / metal ion binding / cytosol
Similarity search - Function
Signal recognition particle 43kDa protein / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. ...Signal recognition particle 43kDa protein / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Signal recognition particle 43 kDa protein, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / Torsional angle dynamics, simulated annealing
AuthorsSivaraja, V. / Kumar, T.K. / Henry, R. / Yu, C.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Three-dimensional solution structures of the chromodomains of cpSRP43
Authors: Sivaraja, V. / Kumar, T.K. / Leena, P.S. / Chang, A.N. / Vidya, C. / Goforth, R.L. / Rajalingam, D. / Arvind, K. / Ye, J.L. / Chou, J. / Henry, R. / Yu, C.
History
DepositionApr 28, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: chloroplast signal recognition particle component


Theoretical massNumber of molelcules
Total (without water)5,0491
Polymers5,0491
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 / 100structures with the lowest energy
RepresentativeModel #20lowest energy

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Components

#1: Protein/peptide chloroplast signal recognition particle component / cpSRP43 / CAO


Mass: 5048.510 Da / Num. of mol.: 1 / Fragment: Chromo domain 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Escherichia coli (E. coli) / References: UniProt: O22265

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1313D N15 NOESY-HSQC
1413D 15N-separated HSQC-TOCSY
151HNHA
1613D 13C-separated NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear, 3D heteronuclear NMR experiments

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Sample preparation

DetailsContents: unlabeled Chromo 1 domain, Uniformly labeled 15N chromo domain 1, Uniformly 15N and 13C labeled Chromo 1 domain
Solvent system: HOH
Sample conditionsIonic strength: 10mM phosphate ,100mM NaCL / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukerprocessing
CNS1.1structure solution
CNS1.1refinement
RefinementMethod: Torsional angle dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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