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- PDB-3ktv: Crystal structure of the human SRP19/S-domain SRP RNA complex -

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Basic information

Entry
Database: PDB / ID: 3ktv
TitleCrystal structure of the human SRP19/S-domain SRP RNA complex
Components
  • (SRP RNA) x 2
  • Signal recognition particle 19 kDa protein
KeywordsRNA/RNA Binding Protein / ribonucleoprotein complex / RNA-RNA tertiary interactions / asymmetric loop / RNA-binding / Signal recognition particle / RNA-RNA Binding Protein complex
Function / homology
Function and homology information


SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / signal recognition particle, endoplasmic reticulum targeting / signal recognition particle / cotranslational protein targeting to membrane / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / nuclear body / nucleolus / RNA binding / cytosol
Similarity search - Function
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) / RNA (> 100) / Signal recognition particle 19 kDa protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 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
A: SRP RNA
B: Signal recognition particle 19 kDa protein
C: SRP RNA
D: Signal recognition particle 19 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,03410
Polymers99,8444
Non-polymers1906
Water00
1
A: SRP RNA
B: Signal recognition particle 19 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9454
Polymers49,8822
Non-polymers632
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-30 kcal/mol
Surface area22130 Å2
MethodPISA
2
C: SRP RNA
D: Signal recognition particle 19 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0896
Polymers49,9622
Non-polymers1274
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-30 kcal/mol
Surface area21680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.120, 100.120, 293.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: RNA chain SRP RNA


Mass: 35090.961 Da / Num. of mol.: 1 / Fragment: S domain
Source method: isolated from a genetically manipulated source
Details: in vitro transcription / Source: (gene. exp.) Homo sapiens (human) / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: GenBank: NR_002715.1
#2: Protein Signal recognition particle 19 kDa protein / SRP19


Mass: 14791.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRP19 / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P09132
#3: RNA chain SRP RNA


Mass: 35170.941 Da / Num. of mol.: 1 / Fragment: S domain
Source method: isolated from a genetically manipulated source
Details: in vitro transcription / Source: (gene. exp.) Homo sapiens (human) / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: GenBank: NR_002715.1
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / 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: 3.68 Å3/Da / Density % sol: 66.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 100 mM NaOAc, 0.75 M KF, 2.2 M (NH4)2SO4, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1NaOAc11
2KF11
3(NH4)2SO411
4NaOAc12
5KF12
6(NH4)2SO412

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 24, 2009 / Details: mirrors
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.8→70.2 Å / Num. all: 15622 / Num. obs: 14852 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.103 / Net I/σ(I): 7.3
Reflection shellResolution: 3.8→4.01 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.3 / Rsym value: 0.608 / % possible all: 97.9

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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: 3.8→70.01 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.9 / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.804 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.872 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.329 711 4.8 %RANDOM
Rwork0.291 ---
all0.293 0 --
obs0.293 14727 94.28 %-
Solvent computationSolvent model: NONE
Displacement parametersBiso max: 207.1 Å2 / Biso mean: 88.009 Å2 / Biso min: 30.13 Å2
Refinement stepCycle: LAST / Resolution: 3.8→70.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1725 4659 6 0 6390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0216970
X-RAY DIFFRACTIONr_angle_refined_deg1.3522.76910502
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6665212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.19323.57184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.28115331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0581518
X-RAY DIFFRACTIONCHIRAL-CENTER RESTRAINTS (A''3)0.0580.21339
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023594
X-RAY DIFFRACTIONMAIN-CHAIN BOND REFINED ATOMS (A''2)0.4941.51071
X-RAY DIFFRACTIONMAIN-CHAIN ANGLE REFINED ATOMS (A''2)0.92421737
X-RAY DIFFRACTIONSIDE-CHAIN BOND REFINED ATOMS (A''2)0.89435899
X-RAY DIFFRACTIONSIDE-CHAIN ANGLE REFINED ATOMS (A''2)1.5764.58765
LS refinement shellResolution: 3.8→3.885 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.497 47 -
Rwork0.384 969 -
all-1016 -
obs--93.38 %

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