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- PDB-1qzw: Crystal structure of the complete core of archaeal SRP and implic... -

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Basic information

Entry
Database: PDB / ID: 1qzw
TitleCrystal structure of the complete core of archaeal SRP and implications for inter-domain communication
Components
  • 7S RNA
  • Signal recognition 54 kDa protein
KeywordsSignaling Protein/RNA / Signal recognition particle / SRP / ribonucleoprotein complex / protein-RNA complex / protein targeting / Signaling Protein-RNA COMPLEX
Function / homology
Function and homology information


signal recognition particle / endoplasmic reticulum signal peptide binding / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane, translocation / GTPase activity / GTP binding / ATP hydrolysis activity / cytosol
Similarity search - Function
SRP/SRP receptor, N-terminal / Signal recognition particle, SRP54 subunit / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP54 subunit, M-domain superfamily / Signal peptide binding domain / 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 ...SRP/SRP receptor, N-terminal / Signal recognition particle, SRP54 subunit / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP54 subunit, M-domain superfamily / Signal peptide binding domain / 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
RNA / RNA (> 10) / Signal recognition particle 54 kDa protein
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.1 Å
AuthorsRosendal, K.R. / Wild, K. / Montoya, G. / Sinning, I.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Crystal structure of the complete core of archaeal signal recognition particle and implications for interdomain communication
Authors: Rosendal, K.R. / Wild, K. / Montoya, G. / Sinning, I.
History
DepositionSep 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_sheet.number_strands
Remark 650HELIX DETERMINED METHOD: Authors determined
Remark 700SHEET DETERMINED METHOD: Authors determined

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 7S RNA
D: 7S RNA
F: 7S RNA
H: 7S RNA
A: Signal recognition 54 kDa protein
C: Signal recognition 54 kDa protein
E: Signal recognition 54 kDa protein
G: Signal recognition 54 kDa protein


Theoretical massNumber of molelcules
Total (without water)260,0748
Polymers260,0748
Non-polymers00
Water00
1
B: 7S RNA
A: Signal recognition 54 kDa protein


Theoretical massNumber of molelcules
Total (without water)65,0192
Polymers65,0192
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: 7S RNA
C: Signal recognition 54 kDa protein


Theoretical massNumber of molelcules
Total (without water)65,0192
Polymers65,0192
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
F: 7S RNA
E: Signal recognition 54 kDa protein


Theoretical massNumber of molelcules
Total (without water)65,0192
Polymers65,0192
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
H: 7S RNA
G: Signal recognition 54 kDa protein


Theoretical massNumber of molelcules
Total (without water)65,0192
Polymers65,0192
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.763, 137.763, 307.894
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.9996, -0.0075, -0.02731), (0.0072, -0.99991, 0.01089), (-0.02739, 0.01069, 0.99957)-66.44145, 118.9755, -0.65354
3given(-0.49638, -0.86804, 0.01022), (-0.86794, 0.49602, -0.02543), (0.017, -0.02149, -0.99962)-0.16039, 1.77392, 207.51863
4given(0.4965, -0.86803, 0.00268), (-0.86802, -0.49647, 0.00788), (-0.00551, -0.00624, -0.99997)69.02411, 118.55315, 103.94876

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Components

#1: RNA chain
7S RNA


Mass: 15555.170 Da / Num. of mol.: 4 / Fragment: SRP RNA helix 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Description: in vitro translation / Gene: 7S RNA / Plasmid: pUC18
#2: Protein
Signal recognition 54 kDa protein / SRP54


Mass: 49463.430 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: SRP54 / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta pLysS / References: UniProt: Q97ZE7

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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: 6.49 Å3/Da / Density % sol: 81.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: Ammonium sulphate, sodium chloride, sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1Ammonium sulphate11
2sodium chloride11
3sodium acetate11
4H2O11
5Ammonium sulphate12
6sodium acetate12
7H2O12
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Rosendal, K.R., (2004) Acta Crystallogr.,Sect.D, 60, 140.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mg/mlprotein1drop
21.26 Mammonium sulfate1reservoirpH4.5
3200 mM1reservoirNaCl
41
51
61
71

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 14, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 4.1→30 Å / Num. obs: 50447 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Rsym value: 0.087 / Net I/σ(I): 4
Reflection shellResolution: 4.1→4.32 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 7462 / Rsym value: 0.481 / % possible all: 99.4
Reflection
*PLUS
Num. obs: 49660 / % possible obs: 97.2 % / Rmerge(I) obs: 0.087
Reflection shell
*PLUS
Lowest resolution: 4.31 Å / % possible obs: 98.1 % / Rmerge(I) obs: 0.481

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1J8M

1j8m


Resolution: 4.1→30 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1576917.54 / Data cutoff high rms absF: 1576917.54 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The structure factor data associated with this file is from twinned crystal. To use structure factor data, this data will have to be detwinned.
RfactorNum. reflection% reflectionSelection details
Rfree0.3869 4666 9.3 %SHELLS
Rwork0.3395 ---
all-51112 --
obs-49660 97.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.4117 Å2 / ksol: 0.105512 e/Å3
Displacement parametersBiso mean: 69.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.73 Å0.64 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 4.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13596 4124 0 0 17720
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0122
X-RAY DIFFRACTIONc_angle_deg2.266
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0.93
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection Rwork
4.1-4.290.474658590.43186729
4.29-4.510.44645890.399
4.51-4.790.43025880.3769
4.79-5.160.43075790.3948
5.16-5.680.42855990.4161
5.68-6.490.46346300.3929
6.49-8.150.3985530.3153
8.15-300.29545430.2575
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA-ALLATOM.PARAMDNA-RNA-ALLATOM.TOP
Refinement
*PLUS
Highest resolution: 4.1 Å / Lowest resolution: 30 Å / % reflection Rfree: 9 % / Rfactor Rfree: 0.387 / Rfactor Rwork: 0.34
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg2.26
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.93

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