+Open data
-Basic information
Entry | Database: PDB / ID: 3ktv | ||||||
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Title | Crystal structure of the human SRP19/S-domain SRP RNA complex | ||||||
Components |
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Keywords | RNA/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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å | ||||||
Authors | Wild, K. / Bange, G. / Bozkurt, G. / Sinning, I. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ktv.cif.gz | 177.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ktv.ent.gz | 132.7 KB | Display | PDB format |
PDBx/mmJSON format | 3ktv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ktv_validation.pdf.gz | 490.5 KB | Display | wwPDB validaton report |
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Full document | 3ktv_full_validation.pdf.gz | 615 KB | Display | |
Data in XML | 3ktv_validation.xml.gz | 36.4 KB | Display | |
Data in CIF | 3ktv_validation.cif.gz | 48.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kt/3ktv ftp://data.pdbj.org/pub/pdb/validation_reports/kt/3ktv | HTTPS FTP |
-Related structure data
Related structure data | 3ktwC 1lngS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: RNA chain | 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 | ||||||
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#2: Protein | 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 | | 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 | #5: Chemical | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.68 Å3/Da / Density % sol: 66.58 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 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 |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 24, 2009 / Details: mirrors |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 3.8→4.01 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.3 / Rsym value: 0.608 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 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
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Solvent computation | Solvent model: NONE | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 207.1 Å2 / Biso mean: 88.009 Å2 / Biso min: 30.13 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.8→70.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.8→3.885 Å / Total num. of bins used: 20
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