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- PDB-7n8s: LINE-1 endonuclease domain complex with DNA -

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Basic information

Entry
Database: PDB / ID: 7n8s
TitleLINE-1 endonuclease domain complex with DNA
Components
  • DNA (5'-D(*CP*CP*TP*TP*AP*AP*AP*AP*AP*GP*GP*AP*GP*CP*T)-3')
  • DNA (5'-D(*GP*CP*TP*CP*CP*TP*TP*TP*TP*TP*AP*AP*GP*GP*A)-3')
  • LINE-1 retrotransposable element ORF2 protein
KeywordsHYDROLASE/DNA / endonuclease / non-LTR retrotransposon / HYDROLASE-DNA complex
Function / homology
Function and homology information


retrotransposition / nucleic acid metabolic process / type II site-specific deoxyribonuclease activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / DNA recombination / RNA binding / metal ion binding
Similarity search - Function
Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / LINE-1 retrotransposable element ORF2 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsKorolev, S. / Miller, I.
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Structural dissection of sequence recognition and catalytic mechanism of human LINE-1 endonuclease.
Authors: Miller, I. / Totrov, M. / Korotchkina, L. / Kazyulkin, D.N. / Gudkov, A.V. / Korolev, S.
History
DepositionJun 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LINE-1 retrotransposable element ORF2 protein
D: DNA (5'-D(*CP*CP*TP*TP*AP*AP*AP*AP*AP*GP*GP*AP*GP*CP*T)-3')
C: DNA (5'-D(*GP*CP*TP*CP*CP*TP*TP*TP*TP*TP*AP*AP*GP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)36,2503
Polymers36,2503
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-22 kcal/mol
Surface area15150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.613, 91.613, 229.822
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein LINE-1 retrotransposable element ORF2 protein / ORF2p


Mass: 27073.240 Da / Num. of mol.: 1 / Mutation: D145A, Y226K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: O00370, RNA-directed DNA polymerase, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters
#2: DNA chain DNA (5'-D(*CP*CP*TP*TP*AP*AP*AP*AP*AP*GP*GP*AP*GP*CP*T)-3')


Mass: 4602.024 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*GP*CP*TP*CP*CP*TP*TP*TP*TP*TP*AP*AP*GP*GP*A)-3')


Mass: 4574.983 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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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: 3.84 Å3/Da / Density % sol: 67.97 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 4.5 / Details: 0.2M NH4 CH3 CO2; 15% PEG 4000

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.79→30 Å / Num. obs: 14939 / % possible obs: 100 % / Redundancy: 8.6 % / Biso Wilson estimate: 63.46 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.05 / Rrim(I) all: 0.148 / Χ2: 1.414 / Net I/σ(I): 18.5
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 9 % / Rmerge(I) obs: 1.565 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 728 / CC1/2: 0.675 / CC star: 0.898 / Rpim(I) all: 0.548 / Rrim(I) all: 1.66 / Χ2: 1.388 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1vyb

1vyb


Resolution: 2.79→29.74 Å / SU ML: 0.5295 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.4956
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3218 1486 10.01 %
Rwork0.2635 13352 -
obs0.2693 14838 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.29 Å2
Refinement stepCycle: LAST / Resolution: 2.79→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1854 611 0 0 2465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00572642
X-RAY DIFFRACTIONf_angle_d0.81843709
X-RAY DIFFRACTIONf_chiral_restr0.0466428
X-RAY DIFFRACTIONf_plane_restr0.0038351
X-RAY DIFFRACTIONf_dihedral_angle_d16.89771489
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.79-2.880.48571300.40581170X-RAY DIFFRACTION98.78
2.88-2.990.49981310.40551170X-RAY DIFFRACTION99.92
2.99-3.110.35771320.34651187X-RAY DIFFRACTION100
3.11-3.250.44731330.31091193X-RAY DIFFRACTION99.92
3.25-3.420.37141310.30021186X-RAY DIFFRACTION99.85
3.42-3.630.33341350.29611208X-RAY DIFFRACTION99.93
3.63-3.910.32541330.27451192X-RAY DIFFRACTION99.92
3.91-4.310.32261350.251213X-RAY DIFFRACTION99.63
4.31-4.930.29811350.21921221X-RAY DIFFRACTION99.27
4.93-6.20.30651400.23631258X-RAY DIFFRACTION99.57
6.2-29.740.23471510.21411354X-RAY DIFFRACTION99.67

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