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Yorodumi- PDB-3qqc: Crystal structure of archaeal Spt4/5 bound to the RNAP clamp domain -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qqc | ||||||
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Title | Crystal structure of archaeal Spt4/5 bound to the RNAP clamp domain | ||||||
Components |
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Keywords | TRANSCRIPTION / fusion protein / chimera protein / multiprotein complex | ||||||
Function / homology | Function and homology information transcription elongation-coupled chromatin remodeling / RNA polymerase II activity / translation elongation factor activity / DNA-directed RNA polymerase complex / regulation of DNA-templated transcription elongation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / ribosome / structural constituent of ribosome ...transcription elongation-coupled chromatin remodeling / RNA polymerase II activity / translation elongation factor activity / DNA-directed RNA polymerase complex / regulation of DNA-templated transcription elongation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / ribosome / structural constituent of ribosome / mRNA binding / DNA-templated transcription / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Molecular Replacement with SAD / Resolution: 3.3 Å | ||||||
Authors | Martinez-Rucobo, F.W. | ||||||
Citation | Journal: Embo J. / Year: 2011 Title: Architecture of the RNA polymerase-Spt4/5 complex and basis of universal transcription processivity. Authors: Martinez-Rucobo, F.W. / Sainsbury, S. / Cheung, A.C. / Cramer, P. | ||||||
History |
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Remark 999 | Chain A is a fusion protein of three peptides. First peptide is DNA-directed RNA polymerase subunit ...Chain A is a fusion protein of three peptides. First peptide is DNA-directed RNA polymerase subunit b (residues 2-64 in this entry corresponding to UNP Q8U0M3 residues 1053-1115) which is linked (via two GLY GLY linker residues) to DNA-directed RNA polymerase subunit a' (residues 67-382 in this entry corresponding to UNP Q8U0M4 residues 3-318) which is then linked (via nine linker residues: GLY ALA GLY SER GLY ALA GLY SER GLY) to DNA-directed RNA polymerase subunit A'' (residues 392-429 in this entry corresponding to UNP Q8U0M5 residues 334-371). |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qqc.cif.gz | 232.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qqc.ent.gz | 187.7 KB | Display | PDB format |
PDBx/mmJSON format | 3qqc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/3qqc ftp://data.pdbj.org/pub/pdb/validation_reports/qq/3qqc | HTTPS FTP |
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-Related structure data
Related structure data | 1y1wS 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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Unit cell |
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-Components
#1: Protein | Mass: 49409.867 Da / Num. of mol.: 1 Fragment: DNA-directed RNA polymerase subunit B (residues 1053-1115), DNA-directed RNA polymerase subunit A' (residues 3-318), DNA-directed RNA polymerase subunit A'' (residues 334-371) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: PF1563 / Production host: Escherichia coli (E. coli) References: UniProt: Q8U0M3, UniProt: Q8U0M4, UniProt: Q8U0M5 |
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#2: Protein | Mass: 18100.988 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: PF1990 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TZK1 |
#3: Protein | Mass: 6965.045 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: PF0255 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U440 |
#4: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 10% PEG 8000, 0.1 M sodium/potassium phosphate, 0.15 M guanidinium hydrochloride, 0.2 M sodium chloride, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.2783 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 18, 2010 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2783 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→50.7 Å / Num. all: 13603 / Num. obs: 13603 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 92.3 Å2 / Rsym value: 0.14 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 3.3→3.48 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 1965 / Rsym value: 0.84 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: Molecular Replacement with SAD Starting model: PDB Entry 1Y1W Resolution: 3.3→50.7 Å / Cor.coef. Fo:Fc: 0.9259 / Cor.coef. Fo:Fc free: 0.893 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: The model was subdivided into five groups for TLS refinement.
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Displacement parameters | Biso mean: 131.01 Å2
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Refine analyze | Luzzati coordinate error obs: 0.82 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→50.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.56 Å / Total num. of bins used: 7
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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