+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-3400 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Lambda excision HJ intermediate | |||||||||
![]() | Map calculated from 10956 particles and fully CTF corrected | |||||||||
![]() |
| |||||||||
![]() | bacteriophage lambda / excision / site-specfific recombination / Holliday junction | |||||||||
Function / homology | ![]() 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 | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 11.0 Å | |||||||||
![]() | Laxmikanthan G / Xu C / Brilot AF / Warren D / Steele L / Seah N / Tong W / Grigorieff N / Landy A / Van Duyne G | |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 7 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 18.1 KB 18.1 KB | Display Display | ![]() |
Images | ![]() | 47 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5j0nMC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data | |
EM raw data | ![]() Data #1: Particle stack and Frealign parameter file [picked particles - multiframe - processed]) |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Map calculated from 10956 particles and fully CTF corrected | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
+Entire : Lambda excision HJ intermediate
+Supramolecule #1000: Lambda excision HJ intermediate
+Macromolecule #1: attB(-21) to attP(+117)
+Macromolecule #2: attB(-19 to +21)
+Macromolecule #3: attP(-79) to attB(+19)
+Macromolecule #4: attP (-117 to +79)
+Macromolecule #5: Int
+Macromolecule #6: Int
+Macromolecule #7: IHFa
+Macromolecule #8: IHFb
+Macromolecule #9: Xis
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Concentration | 2 mg/mL |
---|---|
Buffer | pH: 8 / Details: 10mM Tris, 50mM NaCl |
Grid | Details: 1.2/1.3 400-mesh copper C-flat |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 85 % / Instrument: FEI VITROBOT MARK II / Method: 10 seconds blotting (two-sided) |
-
Electron microscopy
Microscope | FEI TECNAI F30 |
---|---|
Temperature | Min: 90 K / Max: 90 K |
Details | Images were collected as 25-frame movies with a 2-second exposure |
Date | Jun 11, 2014 |
Image recording | Category: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Digitization - Sampling interval: 14 µm / Number real images: 1359 / Average electron dose: 35.5 e/Å2 Details: Every image is the average of all 25 aligned movie frames |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 100000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 4.793 µm / Nominal defocus min: 1.627 µm / Nominal magnification: 78000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | ![]() Model: Tecnai F30 / Image courtesy: FEI Company |
-
Image processing
Details | Manual particle selection with e2boxer (EMAN2), 2D classification with ISAC, initial map generation with e2initialmodel (EMAN2), 3D refinement and classification with Frealign v9.11 |
---|---|
CTF correction | Details: Each particle |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 11.0 Å / Resolution method: OTHER / Software - Name: Frealign, v9 Details: Final map was the best class, out of size 3D classes Number images used: 10956 |
Final two d classification | Number classes: 6 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D / Chain - #4 - Chain ID: I / Chain - #5 - Chain ID: J / Chain - #6 - Chain ID: K / Chain - #7 - Chain ID: L |
---|---|
Software | Name: CNS 1.3 |
Details | Manual docking followed by highly restrained DEN-refinement in CNS |
Refinement | Space: RECIPROCAL / Protocol: FLEXIBLE FIT / Overall B value: 500 / Target criteria: HLML |
Output model | ![]() PDB-5j0n: |
-Atomic model buiding 2
Initial model | PDB ID: Chain - #0 - Chain ID: 1 / Chain - #1 - Chain ID: 2 / Chain - #2 - Chain ID: 3 |
---|---|
Software | Name: CNS 1.3 |
Details | Manual docking followed by highly restrained DEN-refinement in CNS |
Refinement | Space: RECIPROCAL / Protocol: FLEXIBLE FIT / Overall B value: 500 / Target criteria: HLML |
Output model | ![]() PDB-5j0n: |
-Atomic model buiding 3
Initial model | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D / Chain - #4 - Chain ID: E / Chain - #5 - Chain ID: F |
---|---|
Software | Name: CNS 1.3 |
Details | Manual docking followed by highly restrained DEN-refinement in CNS |
Refinement | Space: RECIPROCAL / Protocol: FLEXIBLE FIT / Overall B value: 500 / Target criteria: HLML |
Output model | ![]() PDB-5j0n: |