7ZEP | pdb_00007zep

Human SLFN11 E209A dimer

• PDB DOI: https://doi.org/10.2210/pdb7ZEP/pdb
• EM Map EMD-14691: EMDB EMDataResource

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2022-03-31 Released: 2022-09-28 
• Deposition Author(s): Metzner, F.J., Kugler, M., Wenzl, S.J., Lammens, K.
• Funding Organization(s): German Research Foundation (DFG), European Research Council (ERC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Mechanistic understanding of human SLFN11.

Metzner, F.J., Wenzl, S.J., Kugler, M., Krebs, S., Hopfner, K.P., Lammens, K.

(2022) Nat Commun 13: 5464-5464

• PubMed: 36115853 
• DOI: https://doi.org/10.1038/s41467-022-33123-0


• PubMed 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 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.

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Organizational Affiliation: 
• Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen Straße 25, 81377, Munich, Germany.
Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen Straße 25, 81377, Munich, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: assay for oligomerization

Macromolecule Content 

• Total Structure Weight: 212.43 kDa 
• Atom Count: 13,324 
• Modeled Residue Count: 1,654 
• Deposited Residue Count: 1,858 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Schlafen family member 11	A, B	929	Homo sapiens	Mutation(s): 0  Gene Names: SLFN11 EC: 3.6 (PDB Primary Data), 3.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z7L1 (Homo sapiens) Explore Q7Z7L1  Go to UniProtKB:  Q7Z7L1
PHAROS:  Q7Z7L1 GTEx:  ENSG00000172716

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-09-28 
Deposition Author(s): Metzner, F.J., Kugler, M., Wenzl, S.J., Lammens, K.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	1054
European Research Council (ERC)	European Union	INO3D

Revision History  

• Version 1.0: 2022-09-28
  Type: Initial release
  
• Version 1.1: 2024-07-24
  Changes: Data collection