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- EMDB-14693: SLFN11 E209A monomer -

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Basic information

Entry
Database: EMDB / ID: EMD-14693
TitleSLFN11 E209A monomer
Map datasharpened map
Sample
  • Organelle or cellular component: SLFN11 E209A monomer
    • Protein or peptide: SLFN11 E209A
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsMetzner FJ / Kugler M / Wenzl SJ / Lammens K
Funding support Germany, European Union, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)1054 Germany
European Research Council (ERC)INO3DEuropean Union
CitationJournal: Nat Commun / Year: 2022
Title: Mechanistic understanding of human SLFN11.
Authors: Felix J Metzner / Simon J Wenzl / Michael Kugler / Stefan Krebs / Karl-Peter Hopfner / Katja Lammens /
Abstract: Schlafen 11 (SLFN11) is an interferon-inducible antiviral restriction factor with tRNA endoribonuclease and DNA binding functions. It is recruited to stalled replication forks in response to ...Schlafen 11 (SLFN11) is an interferon-inducible antiviral restriction factor with tRNA endoribonuclease and DNA binding functions. It is recruited to stalled replication forks in response to replication stress and inhibits replication of certain viruses such as the human immunodeficiency virus 1 (HIV-1) by modulating the tRNA pool. SLFN11 has been identified as a predictive biomarker in cancer, as its expression correlates with a beneficial response to DNA damage inducing anticancer drugs. However, the mechanism and interdependence of these two functions are largely unknown. Here, we present cryo-electron microscopy (cryo-EM) structures of human SLFN11 in its dimeric apoenzyme state, bound to tRNA and in complex with single-strand DNA. Full-length SLFN11 neither hydrolyses nor binds ATP and the helicase domain appears in an autoinhibited state. Together with biochemical and structure guided mutagenesis studies, our data give detailed insights into the mechanism of endoribonuclease activity as well as suggestions on how SLFN11 may block stressed replication forks.
History
DepositionMar 31, 2022-
Header (metadata) releaseSep 28, 2022-
Map releaseSep 28, 2022-
UpdateOct 5, 2022-
Current statusOct 5, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14693.png

Downloads & links

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Map

FileDownload / File: emd_14693.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 256 pix.
= 267.776 Å		1.05 Å/pix.
x 256 pix.
= 267.776 Å		1.05 Å/pix.
x 256 pix.
= 267.776 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.046 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.75
Minimum - Maximum-3.351862 - 4.288844
Average (Standard dev.)0.0004236456 (±0.067900434)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 267.776 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14693_msk_1.map
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Half map: half map A

Fileemd_14693_half_map_1.map
Annotationhalf map A
Projections & Slices
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Half map: half map B

Fileemd_14693_half_map_2.map
Annotationhalf map B
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Sample components

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Entire : SLFN11 E209A monomer

EntireName: SLFN11 E209A monomer
Components
  • Organelle or cellular component: SLFN11 E209A monomer
    • Protein or peptide: SLFN11 E209A

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Supramolecule #1: SLFN11 E209A monomer

SupramoleculeName: SLFN11 E209A monomer / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

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Macromolecule #1: SLFN11 E209A

MacromoleculeName: SLFN11 E209A / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MADYKDDDDK GTDYKDDDDK LEVLFQGPME ANQCPLVVEP SYPDLVINVG EVTLGEENRK KLQKIQRDQE KERVMRAACA LLNSGGGVIR MAKKVEHPVE MGLDLEQSLR ELIQSSDLQA FFETKQQGRC FYIFVKSWSS GPFPEDRSVK PRLCSLSSSL YRRSETSVRS ...String:
MADYKDDDDK GTDYKDDDDK LEVLFQGPME ANQCPLVVEP SYPDLVINVG EVTLGEENRK KLQKIQRDQE KERVMRAACA LLNSGGGVIR MAKKVEHPVE MGLDLEQSLR ELIQSSDLQA FFETKQQGRC FYIFVKSWSS GPFPEDRSVK PRLCSLSSSL YRRSETSVRS MDSREAFCFL KTKRKPKILE EGPFHKIHKG VYQELPNSDP ADPNSDPADL IFQKDYLEYG EILPFPASQL VEFKQFSTKH FQEYVKRTIP EYVPAFANTG GGYLFIGVDD KSREVLGCAK ENVDPDSLRR KIEQAIYKLP CVHFCQPQRP ITFTLKIVNV LKRGELYGYA CMIRVNPFCC AVFSEAPNSW IVEDKYVCSL TTEKWVGMMT DTDPDLLQLS EDFECQLSLS SGPPLSRPVY SKKGLEHKKE LQQLLFSVPP GYLRYTPESL WRDLISEHRG LEELINKQMQ PFFRGILIFS RSWAVDLNLQ EKPGVICDAL LIAQNSTPIL YTILREQDAE GQDYCTRTAF TLKQKLVNMG GYTGKVCVRA KVLCLSPESS AEALEAAVSP MDYPASYSLA GTQHMEALLQ SLVIVLLGFR SLLSDQLGCE VLNLLTAQQY EIFSRSLRKN RELFVHGLPG SGKTIMAMKI MEKIRNVFHC EAHRILYVCE NQPLRNFISD RNICRAETRK TFLRENFEHI QHIVIDEAQN FRTEDGDWYG KAKSITRRAK GGPGILWIFL DYFQTSHLDC SGLPPLSDQY PREELTRIVR NADPIAKYLQ KEMQVIRSNP SFNIPTGCLE VFPEAEWSQG VQGTLRIKKY LTVEQIMTCV ADTCRRFFDR GYSPKDVAVL VSTAKEVEHY KYELLKAMRK KRVVQLSDAC DMLGDHIVLD SVRRFSGLER SIVFGIHPRT ADPAILPNVL ICLASRAKQH LYIFPWGGH

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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: 9
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 43.58 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.9 µm / Nominal defocus min: 1.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 223491
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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