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- PDB-3ktw: Crystal structure of the SRP19/S-domain SRP RNA complex of Sulfol... -

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Basic information

Entry
Database: PDB / ID: 3ktw
TitleCrystal structure of the SRP19/S-domain SRP RNA complex of Sulfolobus solfataricus
Components
  • SRP RNA
  • Signal recognition particle 19 kDa protein
KeywordsRNA/RNA binding protein / ribonucleoprotein complex / RNA-RNA tertiary interactions / asymmetric loop / 7S RNA / signal recognition particle / structural RNA / RNA-binding / RNA-RNA binding protein complex
Function / homology
Function and homology information


signal recognition particle / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane
Similarity search - Function
Signal recognition particle, SRP19 subunit, archaeal-type / Signal recognition particle, SRP19-like subunit / Signal recognition particle, SRP19 subunit / Signal recognition particle, subunit SRP19-like superfamily / SRP19 protein / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / Signal recognition particle 19 kDa protein
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsWild, K. / Bange, G. / Bozkurt, G. / Sinning, I.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Structural insights into the assembly of the human and archaeal signal recognition particles.
Authors: Wild, K. / Bange, G. / Bozkurt, G. / Segnitz, B. / Hendricks, A. / Sinning, I.
History
DepositionNov 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: SRP RNA
D: SRP RNA
A: Signal recognition particle 19 kDa protein
B: Signal recognition particle 19 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,51214
Polymers88,2094
Non-polymers30210
Water00
1
C: SRP RNA
A: Signal recognition particle 19 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2808
Polymers44,1052
Non-polymers1756
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-68 kcal/mol
Surface area19060 Å2
MethodPISA
2
D: SRP RNA
B: Signal recognition particle 19 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2326
Polymers44,1052
Non-polymers1274
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-41 kcal/mol
Surface area19130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.307, 79.338, 114.067
Angle α, β, γ (deg.)90.000, 101.990, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: RNA chain SRP RNA


Mass: 31165.553 Da / Num. of mol.: 2 / Fragment: S domain
Source method: isolated from a genetically manipulated source
Details: in vitro transcription / Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: GenBank: X17239.1
#2: Protein Signal recognition particle 19 kDa protein / SRP19


Mass: 12939.142 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: srp19, SSO0165 / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q980W2
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg

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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: 3.58 Å3/Da / Density % sol: 65.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 100 mM Na cacodylate, 400 mM KCl, 10 mM CaCl2, 15% (w/v) PEG4000, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1Na cacodylate11
2KCl11
3CaCl211
4PEG400011
5Na cacodylate12
6KCl12
7CaCl212
8PEG400012

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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: Jun 23, 2006 / Details: mirrors
RadiationMonochromator: Diamond (111), Ge (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 3.2→64.7 Å / Num. all: 20744 / Num. obs: 20578 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rsym value: 0.092 / Net I/σ(I): 13.6
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 3.3 / Rsym value: 0.388 / % possible all: 99.2

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0066refinement
PDB_EXTRACT3.005data extraction
MxCuBEdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1LNG

1lng


Resolution: 3.2→64.68 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.896 / Occupancy max: 1 / Occupancy min: 1 / SU B: 23.527 / SU ML: 0.412 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.501 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1054 5.1 %RANDOM
Rwork0.24 ---
all0.242 20794 --
obs0.242 20563 98.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 184.16 Å2 / Biso mean: 86.721 Å2 / Biso min: 32.73 Å2
Baniso -1Baniso -2Baniso -3
1--7.56 Å20 Å2-4.77 Å2
2--3.6 Å20 Å2
3---1.98 Å2
Refinement stepCycle: LAST / Resolution: 3.2→64.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1537 4106 10 0 5653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0216163
X-RAY DIFFRACTIONr_angle_refined_deg1.6192.7729277
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3175183
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.47221.56264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.47615326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6251518
X-RAY DIFFRACTIONr_chiral_restr0.0730.21192
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.023131
X-RAY DIFFRACTIONr_mcbond_it0.5061.5929
X-RAY DIFFRACTIONr_mcangle_it0.96121523
X-RAY DIFFRACTIONr_scbond_it1.11635234
X-RAY DIFFRACTIONr_scangle_it1.954.57754
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 76 -
Rwork0.288 1432 -
all-1508 -
obs--98.76 %

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