+Open data
-Basic information
Entry | Database: PDB / ID: 5j0n | ||||||
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Title | Lambda excision HJ intermediate | ||||||
Components |
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Keywords | TRANSFERASE / HYDROLASE/DNA / bacteriophage lambda / excision / site-specific recombination / Holliday junction / HYDROLASE-DNA complex | ||||||
Function / homology | Function and homology information IHF-DNA complex / provirus excision / integrase activity / DNA-binding transcription activator activity / protein-DNA complex / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / structural constituent of chromatin / chromosome ...IHF-DNA complex / provirus excision / integrase activity / DNA-binding transcription activator activity / protein-DNA complex / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / structural constituent of chromatin / chromosome / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / regulation of translation / transferase activity / DNA recombination / transcription cis-regulatory region binding / Hydrolases; Acting on ester bonds / hydrolase activity / symbiont entry into host cell / DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Enterobacteria phage lambda (virus) Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 11 Å | ||||||
Authors | Van Duyne, G. / Grigorieff, N. / Landy, A. | ||||||
Citation | Journal: Elife / Year: 2016 Title: Structure of a Holliday junction complex reveals mechanisms governing a highly regulated DNA transaction. Authors: Gurunathan Laxmikanthan / Chen Xu / Axel F Brilot / David Warren / Lindsay Steele / Nicole Seah / Wenjun Tong / Nikolaus Grigorieff / Arthur Landy / Gregory D Van Duyne / Abstract: The molecular machinery responsible for DNA expression, recombination, and compaction has been difficult to visualize as functionally complete entities due to their combinatorial and structural ...The molecular machinery responsible for DNA expression, recombination, and compaction has been difficult to visualize as functionally complete entities due to their combinatorial and structural complexity. We report here the structure of the intact functional assembly responsible for regulating and executing a site-specific DNA recombination reaction. The assembly is a 240-bp Holliday junction (HJ) bound specifically by 11 protein subunits. This higher-order complex is a key intermediate in the tightly regulated pathway for the excision of bacteriophage λ viral DNA out of the E. coli host chromosome, an extensively studied paradigmatic model system for the regulated rearrangement of DNA. Our results provide a structural basis for pre-existing data describing the excisive and integrative recombination pathways, and they help explain their regulation. | ||||||
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 | 5j0n.cif.gz | 631.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5j0n.ent.gz | 492.5 KB | Display | PDB format |
PDBx/mmJSON format | 5j0n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5j0n_validation.pdf.gz | 821.2 KB | Display | wwPDB validaton report |
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Full document | 5j0n_full_validation.pdf.gz | 892.9 KB | Display | |
Data in XML | 5j0n_validation.xml.gz | 65.3 KB | Display | |
Data in CIF | 5j0n_validation.cif.gz | 100.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j0/5j0n ftp://data.pdbj.org/pub/pdb/validation_reports/j0/5j0n | HTTPS FTP |
-Related structure data
Related structure data | 3400MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10065 (Title: Lambda excision HJ intermediate / Data size: 4.0 Data #1: Particle stack and Frealign parameter file [picked particles - multiframe - processed]) |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-DNA chain , 4 types, 4 molecules ABCD
#1: DNA chain | Mass: 60790.953 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 1 / Source: (synth.) Enterobacteria phage lambda (virus) |
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#2: DNA chain | Mass: 42883.652 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 1 / Source: (synth.) Enterobacteria phage lambda (virus) |
#3: DNA chain | Mass: 12607.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 1 / Source: (synth.) Escherichia coli (E. coli) |
#4: DNA chain | Mass: 30552.629 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 1 / Source: (synth.) Enterobacteria phage lambda (virus) |
-Protein , 2 types, 7 molecules EFGHMNO
#5: Protein | Mass: 40373.168 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: 1 / Source: (gene. exp.) Enterobacteria phage lambda (virus) / Gene: int / Production host: Escherichia coli (E. coli) References: UniProt: P03700, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds #8: Protein | Mass: 6793.799 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: 1 / Source: (gene. exp.) Enterobacteria phage lambda (virus) / Gene: xis / Production host: Escherichia coli (E. coli) / References: UniProt: P03699 |
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-Integration host factor subunit ... , 2 types, 4 molecules IKJL
#6: Protein | Mass: 10998.554 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: 1 / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ihfA, himA, ECS88_1763 / Production host: Escherichia coli (E. coli) / References: UniProt: B7MAS3, UniProt: P0A6X7*PLUS #7: Protein | Mass: 10671.178 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: 1 / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ihfB, himD, ECS88_0940 / Production host: Escherichia coli (E. coli) / References: UniProt: B7MHM1, UniProt: P0A6Y1*PLUS |
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-Details
Sequence details | Chains F, G, and H include 20-residue linkers with essentially arbitrary conformations that were ...Chains F, G, and H include 20-residue linkers with essentially arbitrary conformations that were not determined experimentally. These linkers are retained in the model to aid in visualization of domain connectivity. |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Lambda excision HJ intermediate / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES | |||||||||||||||
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Molecular weight | Experimental value: NO | |||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: The sample was lightly crosslinked. | |||||||||||||||
Specimen support | Details: Glow discharge with EMITECH K100X / Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 85 % / Chamber temperature: 298 K Details: 10 second blot followed by plunging into liquid ethane (FEI VITROBOT MARK II). |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F30 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 78000 X / Calibrated magnification: 100000 X / Nominal defocus max: 4150 nm / Nominal defocus min: 2600 nm / Calibrated defocus min: 1627 nm / Calibrated defocus max: 4793 nm / Cs: 2 mm / C2 aperture diameter: 50 µm / Alignment procedure: BASIC |
Specimen holder | Cryogen: NITROGEN Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Temperature (max): 90 K / Temperature (min): 90 K |
Image recording | Average exposure time: 2 sec. / Electron dose: 35.5 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1359 |
Image scans | Sampling size: 14 µm / Movie frames/image: 25 / Used frames/image: 1-25 |
-Processing
EM software |
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CTF correction | Details: Built-in correction in Frealign v9 / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 66033 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10956 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: RECIPROCAL / Target criteria: MLHL / Details: Highly restrained DEN refinement in CNS |