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- PDB-6fia: Structure of the human LINE-1 ORF1p coiled coil domain -

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Basic information

Entry
Database: PDB / ID: 6fia
TitleStructure of the human LINE-1 ORF1p coiled coil domain
ComponentsLINE-1 retrotransposable element ORF1 protein
KeywordsRNA BINDING PROTEIN / coiled coil / genome evolution / nucleic acid chaperone / retrotransposition / RNP
Function / homology
Function and homology information


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
L1 transposable element, trimerization domain / L1 transposable element trimerization domain / Transposase, L1 / L1 transposable element, dsRBD-like domain / L1 transposable element, C-terminal domain / L1 transposable element, RRM domain / L1 transposable element RBD-like domain / L1 transposable element dsRBD-like domain
Similarity search - Domain/homology
LINE-1 retrotransposable element ORF1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsKhazina, E. / Weichenrieder, O.
CitationJournal: Elife / Year: 2018
Title: Human LINE-1 retrotransposition requires a metastable coiled coil and a positively charged N-terminus in L1ORF1p.
Authors: Khazina, E. / Weichenrieder, O.
History
DepositionJan 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.page_first / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LINE-1 retrotransposable element ORF1 protein
B: LINE-1 retrotransposable element ORF1 protein
C: LINE-1 retrotransposable element ORF1 protein
D: LINE-1 retrotransposable element ORF1 protein
E: LINE-1 retrotransposable element ORF1 protein
F: LINE-1 retrotransposable element ORF1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,72510
Polymers75,5836
Non-polymers1424
Water1,15364
1
A: LINE-1 retrotransposable element ORF1 protein
B: LINE-1 retrotransposable element ORF1 protein
C: LINE-1 retrotransposable element ORF1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8635
Polymers37,7923
Non-polymers712
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: LINE-1 retrotransposable element ORF1 protein
E: LINE-1 retrotransposable element ORF1 protein
F: LINE-1 retrotransposable element ORF1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8635
Polymers37,7923
Non-polymers712
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.160, 250.610, 33.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
LINE-1 retrotransposable element ORF1 protein / L1ORF1p / LINE retrotransposable element 1 / LINE1 retrotransposable element 1


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.) Homo sapiens (human) / Gene: L1RE1, LRE1 / Plasmid: pnEA / Details (production host): pH / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: Q9UN81
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M HEPES, 0.15M AMMONIUM SULFATE, 12% PEG 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 14, 2013 / Details: dynamically bendable mirrors
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ykp

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
RfactorNum. reflection% reflectionSelection details
Rfree0.2377 1225 5.14 %RANDOM
Rwork0.2082 ---
obs0.2096 23830 99.76 %-
Displacement parametersBiso mean: 87.23 Å2
Baniso -1Baniso -2Baniso -3
1--15.359 Å20 Å20 Å2
2--16.403 Å20 Å2
3----1.044 Å2
Refine analyzeLuzzati coordinate error obs: 0.374 Å
Refinement stepCycle: 1 / Resolution: 2.65→125.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4851 0 4 64 4919
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014878HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.826476HARMONIC3
X-RAY DIFFRACTIONt_dihedral_angle_d2042SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes203HARMONIC2
X-RAY DIFFRACTIONt_gen_planes660HARMONIC5
X-RAY DIFFRACTIONt_it4878HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.51
X-RAY DIFFRACTIONt_other_torsion18.53
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion627SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5385SEMIHARMONIC4
LS refinement shellResolution: 2.65→2.77 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2882 147 5.26 %
Rwork0.2475 2649 -
all0.2496 2796 -
obs--98.84 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.86111.9179-0.94749.6333-4.97135.5084-0.03380.11810.12590.4005-0.4345-1.2326-0.20110.70010.46830.2816-0.024-0.06350.09840.13820.299717.373422.5391-5.9734
20.60581.0966-0.84886.1118-4.91265.0791-0.03190.0314-0.111-0.14060.35360.26230.1414-0.4305-0.3217-0.0518-0.06710.0017-0.05770.0446-0.02820.946876.9714-55.37
33.9165-1.48040.60744.73251.0474.7520.1103-0.20930.32080.3519-0.06470.4852-0.1034-0.3873-0.04560.12770.0560.29760.34080.44720.5908-0.485186.9833-51.7932
41.4440.1865-0.50834.6346-2.76892.93680.02070.41010.33920.1719-0.1201-0.4817-0.03930.04430.0994-0.05360.0591-0.0434-0.02690.0442-0.1167-5.061833.2339-13.4104
52.2994-3.47771.39630.00364.07493.44520.01730.1591-0.0961-0.04440.09730.36750.0125-0.4669-0.11460.4775-0.157-0.04390.13350.16090.093520.2577111.684-53.8518
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|50 - A|91 B|53 - B|91 C|63 - C|91 }
2X-RAY DIFFRACTION2{ A|92 - A|152 B|92 - B|152 C|92 - C|151 }
3X-RAY DIFFRACTION3{ D|65 - D|91 E|65 - E|91 F|65 - F|91 }
4X-RAY DIFFRACTION4{ D|92 - D|152 E|92 - E|152 F|92 - F|152 }
5X-RAY DIFFRACTION5{ D|49 - D|64 }

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