[English] 日本語
Yorodumi
- EMDB-19914: SLFN11 dimer bound to tRNA-Met-CAT -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-19914
TitleSLFN11 dimer bound to tRNA-Met-CAT
Map data
Sample
  • Organelle or cellular component: SLFN11 bound to tRNA-Met
    • Protein or peptide: Schlafen family member 11
    • RNA: RNA (65-MER)
    • RNA: RNA (5'-R(P*UP*CP*UP*GP*CP*UP*AP*CP*CP*A)-3')
  • 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: 2.64 Å
AuthorsKugler M / Metzner FJ / 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: 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, 2024-
Header (metadata) releaseDec 11, 2024-
Map releaseDec 11, 2024-
UpdateDec 18, 2024-
Current statusDec 18, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_19914.png

Downloads & links

-
Map

FileDownload / File: emd_19914.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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.727 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-2.6333523 - 3.8559887
Average (Standard dev.)-0.00030151685 (±0.088624835)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Mask #1

Fileemd_19914_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: cryoSPARC DeepEMhance map

Fileemd_19914_additional_1.map
AnnotationcryoSPARC DeepEMhance map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_19914_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_19914_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : SLFN11 bound to tRNA-Met

EntireName: SLFN11 bound to tRNA-Met
Components
  • Organelle or cellular component: SLFN11 bound to tRNA-Met
    • Protein or peptide: Schlafen family member 11
    • RNA: RNA (65-MER)
    • RNA: RNA (5'-R(P*UP*CP*UP*GP*CP*UP*AP*CP*CP*A)-3')
  • Ligand: ZINC ION
  • Ligand: MANGANESE (II) ION
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: SLFN11 bound to tRNA-Met

SupramoleculeName: SLFN11 bound to tRNA-Met / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

-
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

-
Macromolecule #2: RNA (65-MER)

MacromoleculeName: RNA (65-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.088666 KDa
SequenceString:
AGCAGAGUGG CGCAGCGGAA GCGUGCUGGG CCCAUAACCC AGAGGUCGAU GGAUCGAAAC CAUCC

GENBANK: GENBANK: NG_066782.1

-
Macromolecule #3: RNA (5'-R(P*UP*CP*UP*GP*CP*UP*AP*CP*CP*A)-3')

MacromoleculeName: RNA (5'-R(P*UP*CP*UP*GP*CP*UP*AP*CP*CP*A)-3') / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 3.097885 KDa
SequenceString:
UCUGCUACCA

-
Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Macromolecule #5: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 5 / Number of copies: 3 / Formula: MN
Molecular weightTheoretical: 54.938 Da

-
Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
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

+
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 213920
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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