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Open data
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Basic information
Entry | Database: PDB / ID: 6fia | ||||||
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Title | Structure of the human LINE-1 ORF1p coiled coil domain | ||||||
![]() | LINE-1 retrotransposable element ORF1 protein | ||||||
![]() | RNA BINDING PROTEIN / coiled coil / genome evolution / nucleic acid chaperone / retrotransposition / RNP | ||||||
Function / homology | ![]() retrotransposition / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / single-stranded DNA binding / single-stranded RNA binding / ribonucleoprotein complex / nucleotide binding / nucleolus / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Khazina, E. / Weichenrieder, O. | ||||||
![]() | ![]() Title: Human LINE-1 retrotransposition requires a metastable coiled coil and a positively charged N-terminus in L1ORF1p. Authors: Khazina, E. / Weichenrieder, O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 257.9 KB | Display | ![]() |
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PDB format | ![]() | 212.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 463.8 KB | Display | ![]() |
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Full document | ![]() | 466 KB | Display | |
Data in XML | ![]() | 19.6 KB | Display | |
Data in CIF | ![]() | 28.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ykpS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 12597.237 Da / Num. of mol.: 6 / Mutation: M121A, M125I, M128I Source method: isolated from a genetically manipulated source Details: The first four amino acids GPHM remain from the purification tag. Engineered mutations, M121A, M125I, M128I. Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CL / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.41 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M HEPES, 0.15M AMMONIUM SULFATE, 12% PEG 2000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 14, 2013 / Details: dynamically bendable mirrors |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→125.31 Å / Num. obs: 23830 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 71.15 Å2 / Rsym value: 0.073 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 2.65→2.72 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1688 / Rsym value: 0.813 / % possible all: 98.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2ykp Resolution: 2.65→125.31 Å / Cor.coef. Fo:Fc: 0.9372 / Cor.coef. Fo:Fc free: 0.9248 / SU R Cruickshank DPI: 0.599 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.662 / SU Rfree Blow DPI: 0.286 / SU Rfree Cruickshank DPI: 0.285
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Displacement parameters | Biso mean: 87.23 Å2
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Refine analyze | Luzzati coordinate error obs: 0.374 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.65→125.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.65→2.77 Å / Total num. of bins used: 12
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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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