[English] 日本語
Yorodumi
- PDB-8sp5: LINE-1 retrotransposon endonuclease domain complex with Mn2+ -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8sp5
TitleLINE-1 retrotransposon endonuclease domain complex with Mn2+
ComponentsLINE-1 retrotransposon endonuclease
KeywordsHYDROLASE / LINE-1 retrotransposon / endonuclease / metal ion 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 domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
: / RNA-directed DNA polymerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 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
CitationJournal: 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.
History
DepositionMay 2, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LINE-1 retrotransposon endonuclease
B: LINE-1 retrotransposon endonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0939
Polymers54,5032
Non-polymers5907
Water4,252236
1
A: LINE-1 retrotransposon endonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5955
Polymers27,2511
Non-polymers3434
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LINE-1 retrotransposon endonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4984
Polymers27,2511
Non-polymers2473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.096, 122.378, 43.412
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein LINE-1 retrotransposon endonuclease


Mass: 27251.404 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: V9H0D0, RNA-directed DNA polymerase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.14 M ammonium sulfate, 24% polyethylene glycol 5000 monomethyl ether, 5 mM magnesium chloride

-
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: Mar 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.23→46.55 Å / Num. obs: 25007 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 0.996 / Net I/σ(I): 9.2
Reflection shellResolution: 2.23→2.3 Å / Num. unique obs: 2244 / CC1/2: 0.853

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.23→46.55 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.25 1298 4.84 %
Rwork0.203 --
obs-24961 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.23→46.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3758 0 27 236 4021
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073846
X-RAY DIFFRACTIONf_angle_d0.8885192
X-RAY DIFFRACTIONf_dihedral_angle_d14.3651457
X-RAY DIFFRACTIONf_chiral_restr0.053599
X-RAY DIFFRACTIONf_plane_restr0.007647
LS refinement shellResolution: 2.23→2.28 Å
RfactorNum. reflection% reflection
Rfree0.3601 137 -
Rwork0.2759 2782 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 17.9534 Å / Origin y: 16.4569 Å / Origin z: -14.6609 Å
111213212223313233
T0.2364 Å2-0.0306 Å20.0242 Å2-0.2957 Å2-0.0434 Å2--0.2221 Å2
L1.1715 °2-0.7379 °20.3109 °2-2.3974 °2-0.5859 °2--0.8565 °2
S-0.024 Å °-0.0116 Å °0.0081 Å °0.0025 Å °0.0948 Å °0.087 Å °-0.0423 Å °0.0488 Å °0.0012 Å °
Refinement TLS groupSelection details: all

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more