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- PDB-9erf: SLFN11 dimer bound to tRNA-Met-CAT -

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Basic information

Entry
Database: PDB / ID: 9erf
TitleSLFN11 dimer bound to tRNA-Met-CAT
Components
  • RNA (5'-R(P*UP*CP*UP*GP*CP*UP*AP*CP*CP*A)-3')
  • RNA (65-MER)
  • Schlafen family member 11
KeywordsHYDROLASE / tRNA / endoribonuclease activity / dimeric
Function / homology
Function and homology information


replication fork arrest / negative regulation of G1/S transition of mitotic cell cycle / negative regulation of DNA replication / immune system process / site of DNA damage / helicase activity / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / tRNA binding ...replication fork arrest / negative regulation of G1/S transition of mitotic cell cycle / negative regulation of DNA replication / immune system process / site of DNA damage / helicase activity / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / tRNA binding / chromatin remodeling / DNA damage response / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
Schlafen group 3-like, DNA/RNA helicase domain / Schlafen group 3, DNA/RNA helicase domain / : / Schlafen, GTPase-like domain / Schlafen family / Orthopoxvirus B3 protein / Poxviridae B3 protein / Schlafen, AlbA_2 domain / Schlafen, AlbA_2 domain superfamily / Schlafen, AlbA_2 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / Schlafen family member 11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.64 Å
AuthorsKugler, M. / Metzner, F.J. / Lammens, K.
Funding support Germany, European Union, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)1054 Germany
European Research Council (ERC)INO3DEuropean Union
CitationJournal: Nat Commun / Year: 2024
Title: Phosphorylation-mediated conformational change regulates human SLFN11.
Authors: Michael Kugler / Felix J Metzner / Gregor Witte / Karl-Peter Hopfner / Katja Lammens /
Abstract: Human Schlafen 11 (SLFN11) is sensitizing cells to DNA damaging agents by irreversibly blocking stalled replication forks, making it a potential predictive biomarker in chemotherapy. Furthermore, ...Human Schlafen 11 (SLFN11) is sensitizing cells to DNA damaging agents by irreversibly blocking stalled replication forks, making it a potential predictive biomarker in chemotherapy. Furthermore, SLFN11 acts as a pattern recognition receptor for single-stranded DNA (ssDNA) and functions as an antiviral restriction factor, targeting translation in a codon-usage-dependent manner through its endoribonuclease activity. However, the regulation of the various SLFN11 functions and enzymatic activities remains enigmatic. Here, we present cryo-electron microscopy (cryo-EM) structures of SLFN11 bound to tRNA-Leu and tRNA-Met that give insights into tRNA binding and cleavage, as well as its regulation by phosphorylation at S219 and T230. SLFN11 phosphomimetic mutant S753D adopts a monomeric conformation, shows ATP binding, but loses its ability to bind ssDNA and shows reduced ribonuclease activity. Thus, the phosphorylation site S753 serves as a conformational switch, regulating SLFN11 dimerization, as well as ATP and ssDNA binding, while S219 and T230 regulate tRNA recognition and nuclease activity.
History
DepositionMar 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Schlafen family member 11
B: Schlafen family member 11
T: RNA (65-MER)
U: RNA (5'-R(P*UP*CP*UP*GP*CP*UP*AP*CP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,97112
Polymers236,6024
Non-polymers3698
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization, mass photometry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Schlafen family member 11


Mass: 106207.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLFN11 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q7Z7L1, Hydrolases; Acting on acid anhydrides

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RNA chain , 2 types, 2 molecules TU

#2: RNA chain RNA (65-MER)


Mass: 21088.666 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: GenBank: 1769890393
#3: RNA chain RNA (5'-R(P*UP*CP*UP*GP*CP*UP*AP*CP*CP*A)-3')


Mass: 3097.885 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 8 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: SLFN11 bound to tRNA-Met / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2600 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 213920 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00414879
ELECTRON MICROSCOPYf_angle_d0.53420349
ELECTRON MICROSCOPYf_dihedral_angle_d9.5562447
ELECTRON MICROSCOPYf_chiral_restr0.042278
ELECTRON MICROSCOPYf_plane_restr0.0052422

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