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- PDB-8sp7: LINE-1 retrotransposon endonuclease domain complex with tranexami... -

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Basic information

Entry
Database: PDB / ID: 8sp7
TitleLINE-1 retrotransposon endonuclease domain complex with tranexamic acid
ComponentsLINE-1 retrotransposon endonuclease
KeywordsHYDROLASE / LINE-1 retrotransposon / endonuclease / fragment screening / small molecule complex
Function / homology
Function and homology information


catalytic activity / RNA-directed DNA polymerase
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
TRANS-4-AMINOMETHYLCYCLOHEXANE-1-CARBOXYLIC ACID / RNA-directed DNA polymerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsD'Ordine, A.M. / Jogl, G. / Sedivy, J.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA) United States
Citation
Journal: Nat Commun / Year: 2024
Title: Identification and characterization of small molecule inhibitors of the LINE-1 retrotransposon endonuclease.
Authors: D'Ordine, A.M. / Jogl, G. / Sedivy, J.M.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionMay 2, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LINE-1 retrotransposon endonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5053
Polymers27,2511
Non-polymers2532
Water1,09961
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.222, 64.671, 132.358
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein LINE-1 retrotransposon endonuclease


Mass: 27251.404 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: V9H0D0
#2: Chemical ChemComp-AMH / TRANS-4-AMINOMETHYLCYCLOHEXANE-1-CARBOXYLIC ACID


Mass: 157.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.13 Å3/Da / Density % sol: 42.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris acetate pH 6.0, 0.2 M lithium sulfate, 30% PEG 2000 monomethyl ether

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.83→29.05 Å / Num. obs: 20957 / % possible obs: 100 % / Redundancy: 13.6 % / Biso Wilson estimate: 31.87 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.9
Reflection shellResolution: 1.83→1.87 Å / Num. unique obs: 1271 / CC1/2: 0.897

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_4895refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
EM softwareName: PHENIX / Version: 1.21rc1_4895 / Category: model refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→29.05 Å / SU ML: 0.2419 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.0864
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2563 999 4.78 %
Rwork0.2198 19884 -
obs0.2216 20883 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.75 Å2
Refinement stepCycle: LAST / Resolution: 1.83→29.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1811 0 16 61 1888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00641867
X-RAY DIFFRACTIONf_angle_d0.90112529
X-RAY DIFFRACTIONf_chiral_restr0.0573299
X-RAY DIFFRACTIONf_plane_restr0.006317
X-RAY DIFFRACTIONf_dihedral_angle_d15.6493690
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.930.36651210.30072808X-RAY DIFFRACTION99.83
1.93-2.050.25591310.25092786X-RAY DIFFRACTION99.73
2.05-2.210.2761510.23172809X-RAY DIFFRACTION99.63
2.21-2.430.28531370.23952804X-RAY DIFFRACTION99.66
2.43-2.780.31821670.24162829X-RAY DIFFRACTION99.97
2.78-3.50.26791410.23092881X-RAY DIFFRACTION100
3.5-29.050.21851510.19492967X-RAY DIFFRACTION99.84
Refinement TLS params.Method: refined / Origin x: -20.5345407946 Å / Origin y: -9.11476518031 Å / Origin z: 15.1896368323 Å
111213212223313233
T0.225731746938 Å20.040539427355 Å20.0191254966908 Å2-0.314754731849 Å20.001399375435 Å2--0.293646743326 Å2
L2.71943821858 °20.678851861103 °2-1.8966142918 °2-1.94279023492 °2-0.446844989941 °2--6.3937673429 °2
S0.0205654506291 Å °-0.349369255663 Å °-0.0163458844282 Å °-0.105785361024 Å °-0.22388917506 Å °-0.103109532997 Å °0.090314493933 Å °0.625782862488 Å °-0.0303106946996 Å °
Refinement TLS groupSelection details: all

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