+Open data
-Basic information
Entry | Database: PDB / ID: 1n03 | ||||||
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Title | Model for Active RecA Filament | ||||||
Components | RecA protein | ||||||
Keywords | DNA BINDING PROTEIN / helical polymer | ||||||
Function / homology | Function and homology information DNA polymerase V complex / homologous recombination / recombinational repair / ATP-dependent DNA damage sensor activity / response to ionizing radiation / SOS response / ATP-dependent activity, acting on DNA / translesion synthesis / cell motility / single-stranded DNA binding ...DNA polymerase V complex / homologous recombination / recombinational repair / ATP-dependent DNA damage sensor activity / response to ionizing radiation / SOS response / ATP-dependent activity, acting on DNA / translesion synthesis / cell motility / single-stranded DNA binding / DNA-binding transcription factor binding / DNA recombination / damaged DNA binding / DNA damage response / ATP hydrolysis activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / negative staining / Resolution: 20 Å | ||||||
Authors | VanLoock, M.S. / Yu, X. / Yang, S. / Lai, A.L. / Low, C. / Campbell, M.J. / Egelman, E.H. | ||||||
Citation | Journal: Structure / Year: 2003 Title: ATP-mediated conformational changes in the RecA filament. Authors: Margaret S VanLoock / Xiong Yu / Shixin Yang / Alex L Lai / Claudia Low / Michael J Campbell / Edward H Egelman / Abstract: The crystal structure of the E. coli RecA protein was solved more than 10 years ago, but it has provided limited insight into the mechanism of homologous genetic recombination. Using electron ...The crystal structure of the E. coli RecA protein was solved more than 10 years ago, but it has provided limited insight into the mechanism of homologous genetic recombination. Using electron microscopy, we have reconstructed five different states of RecA-DNA filaments. The C-terminal lobe of the RecA protein is modulated by the state of the distantly bound nucleotide, and this allosteric coupling can explain how mutations and truncations of this C-terminal lobe enhance RecA's activity. A model generated from these reconstructions shows that the nucleotide binding core is substantially rotated from its position in the RecA crystal filament, resulting in ATP binding between subunits. This simple rotation can explain the large cooperativity in ATP hydrolysis observed for RecA-DNA filaments. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 1n03.cif.gz | 74 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n03.ent.gz | 47.8 KB | Display | PDB format |
PDBx/mmJSON format | 1n03.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1n03_validation.pdf.gz | 682.4 KB | Display | wwPDB validaton report |
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Full document | 1n03_full_validation.pdf.gz | 695.3 KB | Display | |
Data in XML | 1n03_validation.xml.gz | 2 KB | Display | |
Data in CIF | 1n03_validation.cif.gz | 20.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n0/1n03 ftp://data.pdbj.org/pub/pdb/validation_reports/n0/1n03 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 37885.086 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7G6 #2: Chemical | ChemComp-ADP / |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: RecA Filament / Type: COMPLEX Details: The active form of the RecA protein is the helical polymer formed on DNA in the presence of ATP |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: NO |
EM staining | Type: NEGATIVE / Material: Uranyl Acetate |
Crystal grow | *PLUS Method: electron microscopy / Details: Electron Microscopy |
-Electron microscopy imaging
Microscopy | Model: FEI TECNAI 12 |
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Electron gun | Electron source: OTHER / Accelerating voltage: 80 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 30000 X |
Image recording | Film or detector model: GENERIC FILM |
Image scans | Scanner model: OTHER |
-Processing
EM software |
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3D reconstruction | Method: Iterative Helical Real Space Reconstruction method (Egelman, Ultramicroscopy 85, 225-234, 2000) was used. Resolution: 20 Å / Num. of particles: 60000 / Nominal pixel size: 3.9 Å / Actual pixel size: 3.9 Å / Magnification calibration: TMV PARTICLES / Symmetry type: HELICAL | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: best visual fit using the program O / Details: REFINEMENT PROTOCOL--rigid body | ||||||||||||
Atomic model building | PDB-ID: 1REA Accession code: 1REA / Source name: PDB / Type: experimental model | ||||||||||||
Refinement step | Cycle: LAST
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