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- PDB-2hug: 3D Solution Structure of the Chromo-2 Domain of cpSRP43 complexed... -

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Basic information

Entry
Database: PDB / ID: 2hug
Title3D Solution Structure of the Chromo-2 Domain of cpSRP43 complexed with cpSRP54 peptide
Components
  • Signal recognition particle 43 kDa protein, chloroplast
  • Signal recognition particle 54 kDa protein, chloroplast
KeywordsPLANT PROTEIN / Chromo-2 domain / cpSRP43 / LHCP / thylakoid / protein translocation / cpSRP54
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 / endoplasmic reticulum signal peptide binding / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane, translocation / chloroplast envelope / chloroplast stroma ...protein import into chloroplast thylakoid membrane / protein heterotrimerization / response to high light intensity / signal recognition particle, endoplasmic reticulum targeting / endoplasmic reticulum signal peptide binding / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane, translocation / chloroplast envelope / chloroplast stroma / chloroplast thylakoid membrane / chloroplast / disordered domain specific binding / protein-macromolecule adaptor activity / protein domain specific binding / GTPase activity / GTP binding / ATP hydrolysis activity / protein-containing complex / identical protein binding / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Signal recognition particle 43kDa protein / Signal recognition particle protein / Signal recognition particle, SRP54 subunit / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP54 subunit, M-domain superfamily / Signal peptide binding domain / SRP54-type proteins GTP-binding domain signature. / Signal recognition particle SRP54, helical bundle / Signal recognition particle SRP54, N-terminal domain superfamily / SRP54-type protein, helical bundle domain ...Signal recognition particle 43kDa protein / Signal recognition particle protein / Signal recognition particle, SRP54 subunit / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP54 subunit, M-domain superfamily / Signal peptide binding domain / SRP54-type proteins GTP-binding domain signature. / Signal recognition particle SRP54, helical bundle / Signal recognition particle SRP54, N-terminal domain superfamily / SRP54-type protein, helical bundle domain / SRP54-type protein, helical bundle domain / Signal recognition particle, SRP54 subunit, GTPase domain / SRP54-type protein, GTPase domain / SRP54-type protein, GTPase domain / 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) / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Signal recognition particle 43 kDa protein, chloroplastic / Signal recognition particle subunit SRP54, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
AuthorsKathir, K.M. / Vaithiyalingam, S. / Henry, R. / Thallapuranam, S.K.K.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Assembly of chloroplast signal recognition particle involves structural rearrangement in cpSRP43.
Authors: Kathir, K.M. / Rajalingam, D. / Sivaraja, V. / Kight, A. / Goforth, R.L. / Yu, C. / Henry, R. / Kumar, T.K.
History
DepositionJul 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jun 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 1.4May 8, 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: Signal recognition particle 43 kDa protein, chloroplast
B: Signal recognition particle 54 kDa protein, chloroplast


Theoretical massNumber of molelcules
Total (without water)8,0642
Polymers8,0642
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200
Representativelowest energy

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Components

#1: Protein Signal recognition particle 43 kDa protein, chloroplast / CpSRP43 / Chromo protein SRP43


Mass: 6548.151 Da / Num. of mol.: 1 / Fragment: Chromo-2 domain (residues 265-319)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CAO / Production host: Escherichia coli (E. coli) / References: UniProt: O22265
#2: Protein/peptide Signal recognition particle 54 kDa protein, chloroplast / SRP54 / 54 / chloroplast protein / 54CP / FFC


Mass: 1515.740 Da / Num. of mol.: 1 / Fragment: M-domain (residues 530-543)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Escherichia coli (E. coli) / References: UniProt: P37107

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

DetailsContents: 1.5mM Chromo domain-2;Uniform labeling with 13C, 15N at known labeling levels: U-95% 13C;U-98% 15N; PBS buffer.
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 150 mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukerprocessing
ARIA/CNSrefinement
RefinementMethod: distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformers calculated total number: 200 / Conformers submitted total number: 20

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