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- EMDB-13581: human SLFN5 -

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Basic information

Entry
Database: EMDB / ID: EMD-13581
Titlehuman SLFN5
Map data
Sample
  • Organelle or cellular component: full length human Schlafen 5
    • Protein or peptide: Schlafen family member 5
  • Ligand: ZINC ION
Keywordsnucleotide binding protein antiviral linked to tumorigenesis transcription regulation / DNA BINDING PROTEIN
Function / homology
Function and homology information


cell differentiation / ATP binding / nucleus
Similarity search - Function
: / 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 5
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.44 Å
AuthorsLammens K / Metzner FJ
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)CRC1054 Germany
CitationJournal: Nucleic Acids Res / Year: 2022
Title: Structural and biochemical characterization of human Schlafen 5.
Authors: Felix J Metzner / Elisabeth Huber / Karl-Peter Hopfner / Katja Lammens /
Abstract: The Schlafen family belongs to the interferon-stimulated genes and its members are involved in cell cycle regulation, T cell quiescence, inhibition of viral replication, DNA-repair and tRNA ...The Schlafen family belongs to the interferon-stimulated genes and its members are involved in cell cycle regulation, T cell quiescence, inhibition of viral replication, DNA-repair and tRNA processing. Here, we present the cryo-EM structure of full-length human Schlafen 5 (SLFN5) and the high-resolution crystal structure of the highly conserved N-terminal core domain. We show that the core domain does not resemble an ATPase-like fold and neither binds nor hydrolyzes ATP. SLFN5 binds tRNA as well as single- and double-stranded DNA, suggesting a potential role in transcriptional regulation. Unlike rat Slfn13 or human SLFN11, human SLFN5 did not cleave tRNA. Based on the structure, we identified two residues in proximity to the zinc finger motif that decreased DNA binding when mutated. These results indicate that Schlafen proteins have divergent enzymatic functions and provide a structural platform for future biochemical and genetic studies.
History
DepositionSep 14, 2021-
Header (metadata) releaseJan 26, 2022-
Map releaseJan 26, 2022-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.707
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.707
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ppj
  • Surface level: 0.707
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13581.png

Downloads & links

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Map

FileDownload / File: emd_13581.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
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)

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: 0.707 / Movie #1: 0.707
Minimum - Maximum-3.2573326 - 5.7037306
Average (Standard dev.)-0.0008210466 (±0.08136485)
SymmetrySpace group: 1
Details

EMDB XML:

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

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0461.0461.046
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z267.776267.776267.776
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-3.2575.704-0.001

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Supplemental data

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Half map: #2

Fileemd_13581_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_13581_half_map_2.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : full length human Schlafen 5

EntireName: full length human Schlafen 5
Components
  • Organelle or cellular component: full length human Schlafen 5
    • Protein or peptide: Schlafen family member 5
  • Ligand: ZINC ION

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Supramolecule #1: full length human Schlafen 5

SupramoleculeName: full length human Schlafen 5 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Schlafen family member 5

MacromoleculeName: Schlafen family member 5 / type: protein_or_peptide / ID: 1
Details: N-terminal 2 x Flag tag HRV 3C site flexible C-terminus
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 104.420016 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MADYKDDDDK GTDYKDDDDK LEVLFQGPMS LRIDVDTNFP ECVVDAGKVT LGTQQRQEMD PRLREKQNEI ILRAVCALLN SGGGIIKAE IENKGYNYER HGVGLDVPPI FRSHLDKMQK ENHFLIFVKS WNTEAGVPLA TLCSNLYHRE RTSTDVMDSQ E ALAFLKCR ...String:
MADYKDDDDK GTDYKDDDDK LEVLFQGPMS LRIDVDTNFP ECVVDAGKVT LGTQQRQEMD PRLREKQNEI ILRAVCALLN SGGGIIKAE IENKGYNYER HGVGLDVPPI FRSHLDKMQK ENHFLIFVKS WNTEAGVPLA TLCSNLYHRE RTSTDVMDSQ E ALAFLKCR TQTPTNINVS NSLGPQAAQG SVQYEGNINV SAAALFDRKR LQYLEKLNLP ESTHVEFVMF STDVSHCVKD RL PKCVSAF ANTEGGYVFF GVHDETCQVI GCEKEKIDLT SLRASIDGCI KKLPVHHFCT QRPEIKYVLN FLEVHDKGAL RGY VCAIKV EKFCCAVFAK VPSSWQVKDN RVRQLPTREW TAWMMEADPD LSRCPEMVLQ LSLSSATPRS KPVCIHKNSE CLKE QQKRY FPVFSDRVVY TPESLYKELF SQHKGLRDLI NTEMRPFSQG ILIFSQSWAV DLGLQEKQGV ICDALLISQN NTPIL YTIF SKWDAGCKGY SMIVAYSLKQ KLVNKGGYTG RLCITPLVCV LNSDRKAQSV YSSYLQIYPE SYNFMTPQHM EALLQS LVI VLLGFKSFLS EELGSEVLNL LTNKQYELLS KNLRKTRELF VHGLPGSGKT ILALRIMEKI RNVFHCEPAN ILYICEN QP LKKLVSFSKK NICQPVTRKT FMKNNFEHIQ HIIIDDAQNF RTEDGDWYGK AKFITQTARD GPGVLWIFLD YFQTYHLS C SGLPPPSDQY PREEINRVVR NAGPIANYLQ QVMQEARQNP PPNLPPGSLV MLYEPKWAQG VPGNLEIIED LNLEEILIY VANKCRFLLR NGYSPKDIAV LFTKASEVEK YKDRLLTAMR KRKLSQLHEE SDLLLQIGDA SDVLTDHIVL DSVCRFSGLE RNIVFGINP GVAPPAGAYN LLLCLASRAK RHLYILKASV

UniProtKB: Schlafen family member 5

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 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: 41.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 140715
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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