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- PDB-7n94: LINE-1 endonuclease domain complex with DNA -

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Basic information

Entry
Database: PDB / ID: 7n94
TitleLINE-1 endonuclease domain complex with DNA
Components
  • DNA (5'-D(*AP*GP*CP*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*GP*CP*TP*A)-3')
  • LINE-1 retrotransposable element ORF2 protein
KeywordsHYDROLASE/DNA / endonuclease / non-LTR retrotransposon / HYDROLASE-DNA complex
Function / homology
Function and homology information


nucleic acid metabolic process / retrotransposition / 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 domain / Reverse transcriptase (RNA-dependent DNA polymerase) / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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 16, 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)76,2096
Polymers76,2096
Non-polymers00
Water00
1
A: LINE-1 retrotransposable element ORF2 protein
D: DNA (5'-D(*GP*CP*TP*CP*CP*TP*TP*TP*TP*TP*AP*AP*GP*GP*GP*CP*TP*A)-3')
E: DNA (5'-D(*AP*GP*CP*CP*CP*TP*TP*AP*AP*AP*AP*AP*GP*GP*AP*GP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)38,1043
Polymers38,1043
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-26 kcal/mol
Surface area16190 Å2
MethodPISA
2
B: LINE-1 retrotransposable element ORF2 protein
F: DNA (5'-D(*GP*CP*TP*CP*CP*TP*TP*TP*TP*TP*AP*AP*GP*GP*GP*CP*TP*A)-3')
G: DNA (5'-D(*AP*GP*CP*CP*CP*TP*TP*AP*AP*AP*AP*AP*GP*GP*AP*GP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)38,1043
Polymers38,1043
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-29 kcal/mol
Surface area16340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.774, 100.774, 140.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111HISHISARGARGchain 'A'AA7 - 2387 - 238
221HISHISARGARGchain 'B'BD7 - 2387 - 238
132DGDGDTDT(chain 'D' and resid 1 through 17)DB1 - 171 - 17
242DGDGDTDTchain 'F'FE1 - 171 - 17
153DADADCDCchain 'E'EC1 - 171 - 17
263DADADCDC(chain 'G' and resid 1 through 17)GF1 - 171 - 17

NCS ensembles :
ID
1
2
3

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Components

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


Mass: 27073.240 Da / Num. of mol.: 2 / 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(*GP*CP*TP*CP*CP*TP*TP*TP*TP*TP*AP*AP*GP*GP*GP*CP*TP*A)-3')


Mass: 5497.563 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*AP*GP*CP*CP*CP*TP*TP*AP*AP*AP*AP*AP*GP*GP*AP*GP*CP*T)-3')


Mass: 5533.619 Da / Num. of mol.: 2 / 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: 2.34 Å3/Da / Density % sol: 47.54 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 6 / Details: 0.1M MES pH 6.0, 0.2M NaCl, 30% Jeffamine ED-2003

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 17800 / % possible obs: 100 % / Redundancy: 14.7 % / Biso Wilson estimate: 46.43 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.017 / Χ2: 0.93 / Net I/σ(I): 40.5
Reflection shellResolution: 2.85→2.9 Å / Redundancy: 14.8 % / Rmerge(I) obs: 1.75 / Num. unique obs: 888 / CC1/2: 0.759 / Rpim(I) all: 0.464 / Χ2: 0.715 / % possible all: 100

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Processing

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

1vyb


Resolution: 2.85→42.92 Å / SU ML: 0.3927 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.0256
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2803 1744 10 %
Rwork0.2143 15695 -
obs0.2209 17439 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.29 Å2
Refinement stepCycle: LAST / Resolution: 2.85→42.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3720 1429 0 0 5149
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085386
X-RAY DIFFRACTIONf_angle_d1.26297565
X-RAY DIFFRACTIONf_chiral_restr0.0609872
X-RAY DIFFRACTIONf_plane_restr0.0067708
X-RAY DIFFRACTIONf_dihedral_angle_d17.78443024
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.930.41481320.33251191X-RAY DIFFRACTION92.52
2.93-3.030.38321430.29021283X-RAY DIFFRACTION99.93
3.03-3.140.36391440.28011287X-RAY DIFFRACTION100
3.14-3.260.33031430.26631288X-RAY DIFFRACTION100
3.26-3.410.32561440.22611301X-RAY DIFFRACTION100
3.41-3.590.29631440.22571301X-RAY DIFFRACTION100
3.59-3.820.31251430.22161290X-RAY DIFFRACTION100
3.82-4.110.27331460.21031310X-RAY DIFFRACTION100
4.11-4.520.24831460.17651322X-RAY DIFFRACTION100
4.52-5.180.22151480.17361324X-RAY DIFFRACTION99.86
5.18-6.520.24481500.19371355X-RAY DIFFRACTION99.93
6.52-42.920.2241610.18661443X-RAY DIFFRACTION99.69

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