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- PDB-3ui2: Crystal structure of the cpSRP54 tail bound to cpSRP43 -

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Basic information

Entry
Database: PDB / ID: 3ui2
TitleCrystal structure of the cpSRP54 tail bound to cpSRP43
Components
  • Signal recognition particle 43 kDa protein, chloroplastic
  • Signal recognition particle 54 kDa protein, chloroplastic
KeywordsTRANSPORT PROTEIN / ankyrin repeat / chromodomain / aromatic cage / signal recognition particle / protein targeting / membrane protein chaperone / chloroplast
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 / signal-recognition-particle GTPase / chloroplast envelope / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / chloroplast stroma / chloroplast thylakoid membrane ...protein import into chloroplast thylakoid membrane / protein heterotrimerization / response to high light intensity / signal recognition particle, endoplasmic reticulum targeting / signal-recognition-particle GTPase / chloroplast envelope / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / 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 / Ankyrin repeat-containing domain / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / 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 / Mainly Alpha
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.178 Å
AuthorsHoldermann, I. / Wild, K. / Sinning, I.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Chromodomains read the arginine code of post-translational targeting.
Authors: Holdermann, I. / Meyer, N.H. / Round, A. / Wild, K. / Sattler, M. / Sinning, I.
History
DepositionNov 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Signal recognition particle 43 kDa protein, chloroplastic
B: Signal recognition particle 54 kDa protein, chloroplastic


Theoretical massNumber of molelcules
Total (without water)28,3382
Polymers28,3382
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-5 kcal/mol
Surface area14170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.230, 48.520, 57.850
Angle α, β, γ (deg.)90.00, 90.13, 90.00
Int Tables number5
Space group name H-MC121
Detailsthe biological unit corresponds to the asymmetric unit

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Components

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


Mass: 26838.002 Da / Num. of mol.: 1 / Fragment: UNP residues 84-327
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At2g47450, CAO, CPSRP43, T30B22.25 / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS / References: UniProt: O22265
#2: Protein/peptide Signal recognition particle 54 kDa protein, chloroplastic / 54 chloroplast protein / 54CP / SRP54 / cpSRP54 / FFC


Mass: 1499.806 Da / Num. of mol.: 1 / Fragment: RRKR motif, UNP residues 528-540
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g03940, CPSRP54, F8F6_150, FFC / Plasmid: pETtrx / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS / References: UniProt: P37107

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M BisTris, 25% (w/v) PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 3.178→57.831 Å / Num. all: 5401 / Num. obs: 5382 / % possible obs: 99.7 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 14.1
Reflection shellResolution: 3.178→3.35 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 2.2 / Num. unique all: 753 / % possible all: 98.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DEO

3deo


Resolution: 3.178→57.831 Å / SU ML: 0.42 / σ(F): 1.37 / Phase error: 32.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.268 246 4.58 %random
Rwork0.207 ---
obs0.2098 5372 99.46 %-
all-5401 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.469 Å2 / ksol: 0.309 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--11.049 Å2-0 Å228.0656 Å2
2--17.4879 Å20 Å2
3----6.439 Å2
Refinement stepCycle: LAST / Resolution: 3.178→57.831 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1923 0 0 0 1923
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091955
X-RAY DIFFRACTIONf_angle_d1.1562641
X-RAY DIFFRACTIONf_dihedral_angle_d19.299725
X-RAY DIFFRACTIONf_chiral_restr0.076287
X-RAY DIFFRACTIONf_plane_restr0.005348
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Num. reflection Rfree: 123

Resolution (Å)Rfactor RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
3.1781-4.00390.34760.28152536253699
4.0039-57.85940.23730.178725902590100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4659-1.52981.13262.0742-0.46091.5463-0.09720.8545-0.1547-0.65760.043-0.1293-1.08920.3460.00241.3675-0.01070.01381.48280.15540.9577-12.19642.5055-14.7677
24.0493-0.2688-1.96150.9547-1.23645.65410.09980.08780.32190.03450.01520.0979-0.11270.07210.00010.8761-0.1162-0.05870.7608-0.15470.9135-18.3985-0.436713.33
32.10870.32050.39421.30390.55350.81290.4434-0.11080.13560.4729-0.10280.80160.80420.17830.00081.16420.03440.06410.82930.06841.1992-47.60764.1337.1909
40.25270.12750.12910.19650.17870.1313-0.36190.960.42410.11220.05281.17670.7170.9261-0.0011.09930.21180.09981.02330.09821.1774-39.57436.946831.0828
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 85:120)
2X-RAY DIFFRACTION2(chain A and resid 121:265)
3X-RAY DIFFRACTION3(chain A and resid 266:318)
4X-RAY DIFFRACTION4(chain B and resid 528:540)

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