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- EMDB-14692: Human SLFN11 dimer bound to ssDNA -

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Basic information

Entry
Database: EMDB / ID: EMD-14692
TitleHuman SLFN11 dimer bound to ssDNA
Map datasharpened map
Sample
  • Organelle or cellular component: SLFN11 dimer bound to ssDNA
    • Complex: Schlafen family member 11
      • Protein or peptide: Schlafen family member 11
    • Complex: DNA (5'-D(P*CP*GP*CP*GP*T)-3')
      • DNA: DNA (5'-D(P*CP*GP*CP*GP*T)-3')
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
KeywordstRNA endonuclease / single-strand DNA binding protein / HYDROLASE
Function / homology
Function and homology information


replication fork arrest / negative regulation of G1/S transition of mitotic cell cycle / immune system process / negative regulation of DNA replication / site of DNA damage / helicase activity / endonuclease activity / defense response to virus / tRNA binding / Hydrolases; Acting on ester bonds ...replication fork arrest / negative regulation of G1/S transition of mitotic cell cycle / immune system process / negative regulation of DNA replication / site of DNA damage / helicase activity / endonuclease activity / defense response to virus / tRNA binding / Hydrolases; Acting on ester bonds / 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) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14692.png

Downloads & links

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Map

FileDownload / File: emd_14692.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 320 pix.
= 334.72 Å		1.05 Å/pix.
x 320 pix.
= 334.72 Å		1.05 Å/pix.
x 320 pix.
= 334.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.046 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-3.6525028 - 5.669668
Average (Standard dev.)0.0021759553 (±0.10588442)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 334.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14692_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_14692_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_14692_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SLFN11 dimer bound to ssDNA

EntireName: SLFN11 dimer bound to ssDNA
Components
  • Organelle or cellular component: SLFN11 dimer bound to ssDNA
    • Complex: Schlafen family member 11
      • Protein or peptide: Schlafen family member 11
    • Complex: DNA (5'-D(P*CP*GP*CP*GP*T)-3')
      • DNA: DNA (5'-D(P*CP*GP*CP*GP*T)-3')
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: SLFN11 dimer bound to ssDNA

SupramoleculeName: SLFN11 dimer bound to ssDNA / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Supramolecule #2: Schlafen family member 11

SupramoleculeName: Schlafen family member 11 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: DNA (5'-D(P*CP*GP*CP*GP*T)-3')

SupramoleculeName: DNA (5'-D(P*CP*GP*CP*GP*T)-3') / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: synthetic construct (others) / Synthetically produced: Yes

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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: DNA (5'-D(P*CP*GP*CP*GP*T)-3')

MacromoleculeName: DNA (5'-D(P*CP*GP*CP*GP*T)-3') / type: dna / ID: 2 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 1.496011 KDa
SequenceString:
(DC)(DG)(DC)(DG)(DT)

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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: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / 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: 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: 43.33 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

Startup modelType of model: OTHER / Details: AlphaFold
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 247654
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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