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- EMDB-51456: SLFN11 WT dimer bound to tRNA-Leu-TAA (pre-cleavage state) -

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Basic information

Entry
Database: EMDB / ID: EMD-51456
TitleSLFN11 WT dimer bound to tRNA-Leu-TAA (pre-cleavage state)
Map data
Sample
  • Organelle or cellular component: SLFN11 WT dimer bound to tRNA-Leu-TAA (pre-cleavage state)
    • Protein or peptide: Schlafen family member 11
    • RNA: RNA (86-MER)
  • Ligand: ZINC ION
  • Ligand: MANGANESE (II) ION
  • Ligand: MAGNESIUM ION
KeywordstRNA / endoribonuclease activity / dimeric / HYDROLASE
Function / homology
Function and homology information


replication fork arrest / negative regulation of G1/S transition of mitotic cell cycle / negative regulation of DNA replication / site of DNA damage / immune system process / 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 / site of DNA damage / immune system process / 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
Schlafen family member 11
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsKugler M / Metzner FJ / Lammens K
Funding support Germany, European Union, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)210592381 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
DepositionAug 29, 2024-
Header (metadata) releaseDec 11, 2024-
Map releaseDec 11, 2024-
UpdateDec 18, 2024-
Current statusDec 18, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51456.png

Downloads & links

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Map

FileDownload / File: emd_51456.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 400 pix.
= 290.8 Å		0.73 Å/pix.
x 400 pix.
= 290.8 Å		0.73 Å/pix.
x 400 pix.
= 290.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.727 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.33
Minimum - Maximum-1.5189514 - 2.3802228
Average (Standard dev.)-0.00045730697 (±0.061126936)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 290.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51456_msk_1.map
Projections & Slices
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Half map: #1

Fileemd_51456_half_map_1.map
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Half map: #2

Fileemd_51456_half_map_2.map
Projections & Slices
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Sample components

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Entire : SLFN11 WT dimer bound to tRNA-Leu-TAA (pre-cleavage state)

EntireName: SLFN11 WT dimer bound to tRNA-Leu-TAA (pre-cleavage state)
Components
  • Organelle or cellular component: SLFN11 WT dimer bound to tRNA-Leu-TAA (pre-cleavage state)
    • Protein or peptide: Schlafen family member 11
    • RNA: RNA (86-MER)
  • Ligand: ZINC ION
  • Ligand: MANGANESE (II) ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: SLFN11 WT dimer bound to tRNA-Leu-TAA (pre-cleavage state)

SupramoleculeName: SLFN11 WT dimer bound to tRNA-Leu-TAA (pre-cleavage state)
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Schlafen family member 11

MacromoleculeName: Schlafen family member 11 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: Hydrolases; Acting on acid anhydrides
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 106.207914 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MADYKDDDDK GTDYKDDDDK LEVLFQGPME ANQCPLVVEP SYPDLVINVG EVTLGEENRK KLQKIQRDQE KERVMRAACA LLNSGGGVI RMAKKVEHPV EMGLDLEQSL RELIQSSDLQ AFFETKQQGR CFYIFVKSWS SGPFPEDRSV KPRLCSLSSS L YRRSETSV ...String:
MADYKDDDDK GTDYKDDDDK LEVLFQGPME ANQCPLVVEP SYPDLVINVG EVTLGEENRK KLQKIQRDQE KERVMRAACA LLNSGGGVI RMAKKVEHPV EMGLDLEQSL RELIQSSDLQ AFFETKQQGR CFYIFVKSWS SGPFPEDRSV KPRLCSLSSS L YRRSETSV RSMDSREAFC FLKTKRKPKI LEEGPFHKIH KGVYQELPNS DPADPNSDPA DLIFQKDYLE YGEILPFPES QL VEFKQFS TKHFQEYVKR TIPEYVPAFA NTGGGYLFIG VDDKSREVLG CAKENVDPDS LRRKIEQAIY KLPCVHFCQP QRP ITFTLK IVNVLKRGEL YGYACMIRVN PFCCAVFSEA PNSWIVEDKY VCSLTTEKWV GMMTDTDPDL LQLSEDFECQ LSLS SGPPL SRPVYSKKGL EHKKELQQLL FSVPPGYLRY TPESLWRDLI SEHRGLEELI NKQMQPFFRG ILIFSRSWAV DLNLQ EKPG VICDALLIAQ NSTPILYTIL REQDAEGQDY CTRTAFTLKQ KLVNMGGYTG KVCVRAKVLC LSPESSAEAL EAAVSP MDY PASYSLAGTQ HMEALLQSLV IVLLGFRSLL SDQLGCEVLN LLTAQQYEIF SRSLRKNREL FVHGLPGSGK TIMAMKI ME KIRNVFHCEA HRILYVCENQ PLRNFISDRN ICRAETRKTF LRENFEHIQH IVIDEAQNFR TEDGDWYGKA KSITRRAK G GPGILWIFLD YFQTSHLDCS GLPPLSDQYP REELTRIVRN ADPIAKYLQK EMQVIRSNPS FNIPTGCLEV FPEAEWSQG VQGTLRIKKY LTVEQIMTCV ADTCRRFFDR GYSPKDVAVL VSTAKEVEHY KYELLKAMRK KRVVQLSDAC DMLGDHIVLD SVRRFSGLE RSIVFGIHPR TADPAILPNV LICLASRAKQ HLYIFPWGGH

UniProtKB: Schlafen family member 11

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Macromolecule #2: RNA (86-MER)

MacromoleculeName: RNA (86-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.700455 KDa
SequenceString:
ACCAGGAUGG CCGAGUGGUU AAGGCGUUGG ACUUAAGAUC CAAUGGACAU AUGUCCGCGU GGGUUCGAAC CCCACUCCUG GUACCA

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #4: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 4 / Number of copies: 3 / Formula: MN
Molecular weightTheoretical: 54.938 Da

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7zel

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 57414
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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