+Open data
-Basic information
Entry | Database: PDB / ID: 5lm9 | ||||||
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Title | Structure of E. coli NusA | ||||||
Components | Transcription termination/antitermination protein NusA | ||||||
Keywords | TRANSCRIPTION / Transcription factor / Antitermination Termination / Nus proteins | ||||||
Function / homology | Function and homology information bacterial-type RNA polymerase core enzyme binding / protein complex oligomerization / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription termination / ribosome biogenesis / DNA-binding transcription factor activity / protein domain specific binding / nucleotide binding ...bacterial-type RNA polymerase core enzyme binding / protein complex oligomerization / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription termination / ribosome biogenesis / DNA-binding transcription factor activity / protein domain specific binding / nucleotide binding / RNA binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.143 Å | ||||||
Authors | Said, N. / Weber, G. / Santos, K. / Wahl, M.C. | ||||||
Citation | Journal: Nat Microbiol / Year: 2017 Title: Structural basis for λN-dependent processive transcription antitermination. Authors: Nelly Said / Ferdinand Krupp / Ekaterina Anedchenko / Karine F Santos / Olexandr Dybkov / Yong-Heng Huang / Chung-Tien Lee / Bernhard Loll / Elmar Behrmann / Jörg Bürger / Thorsten Mielke ...Authors: Nelly Said / Ferdinand Krupp / Ekaterina Anedchenko / Karine F Santos / Olexandr Dybkov / Yong-Heng Huang / Chung-Tien Lee / Bernhard Loll / Elmar Behrmann / Jörg Bürger / Thorsten Mielke / Justus Loerke / Henning Urlaub / Christian M T Spahn / Gert Weber / Markus C Wahl / Abstract: λN-mediated processive antitermination constitutes a paradigmatic transcription regulatory event, during which phage protein λN, host factors NusA, NusB, NusE and NusG, and an RNA nut site render ...λN-mediated processive antitermination constitutes a paradigmatic transcription regulatory event, during which phage protein λN, host factors NusA, NusB, NusE and NusG, and an RNA nut site render elongating RNA polymerase termination-resistant. The structural basis of the process has so far remained elusive. Here we describe a crystal structure of a λN-NusA-NusB-NusE-nut site complex and an electron cryo-microscopic structure of a complete transcription antitermination complex, comprising RNA polymerase, DNA, nut site RNA, all Nus factors and λN, validated by crosslinking/mass spectrometry. Due to intrinsic disorder, λN can act as a multiprotein/RNA interaction hub, which, together with nut site RNA, arranges NusA, NusB and NusE into a triangular complex. This complex docks via the NusA N-terminal domain and the λN C-terminus next to the RNA exit channel on RNA polymerase. Based on the structures, comparative crosslinking analyses and structure-guided mutagenesis, we hypothesize that λN mounts a multipronged strategy to reprogram the transcriptional machinery, which may include (1) the λN C terminus clamping the RNA exit channel, thus stabilizing the DNA:RNA hybrid; (2) repositioning of NusA and RNAP elements, thus redirecting nascent RNA and sequestering the upstream branch of a terminator hairpin; and (3) hindering RNA engagement of termination factor ρ and/or obstructing ρ translocation on the transcript. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lm9.cif.gz | 79.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lm9.ent.gz | 57.6 KB | Display | PDB format |
PDBx/mmJSON format | 5lm9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lm9_validation.pdf.gz | 439.1 KB | Display | wwPDB validaton report |
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Full document | 5lm9_full_validation.pdf.gz | 441 KB | Display | |
Data in XML | 5lm9_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 5lm9_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lm/5lm9 ftp://data.pdbj.org/pub/pdb/validation_reports/lm/5lm9 | HTTPS FTP |
-Related structure data
Related structure data | 3561C 5lm7C 5ms0C 1l2fS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 36295.043 Da / Num. of mol.: 1 / Fragment: UNP residues 101-426 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: nusA, b3169, JW3138 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AFF6 | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.67 Å3/Da / Density % sol: 66.52 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES, pH 7.5, 0.1 M NaCl, 1.6 M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 5, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→50 Å / Num. obs: 28443 / % possible obs: 99.1 % / Redundancy: 6.8 % / Rsym value: 0.01 / Net I/σ(I): 12.15 |
Reflection shell | Resolution: 2.14→2.27 Å |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1L2F Resolution: 2.143→46.949 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.34
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.143→46.949 Å
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Refine LS restraints |
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LS refinement shell |
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