7CUX | pdb_00007cux

Crystal structure of human Schlafen 5 N'-terminal domain (SLFN5-N) involved in ssRNA cleaving and DNA binding

• PDB DOI: https://doi.org/10.2210/pdb7CUX/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2020-08-25 Released: 2021-08-25 
• Deposition Author(s): Yang, J.Y., Luo, M., Ou, J.Y., Wang, Z.W., Gao, S.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.29 Å
• R-Value Free: 
  0.247 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human Schlafen 5 N'-terminal domain (SLFN5-N) involved in ssRNA cleaving and DNA binding

Yang, J.Y., Luo, M., Ou, J.Y., Wang, Z.W., Gao, S.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 221.21 kDa 
• Atom Count: 14,075 
• Modeled Residue Count: 1,764 
• Deposited Residue Count: 1,956 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Schlafen family member 5	A, B, C, D, E, F	326	Homo sapiens	Mutation(s): 0  Gene Names: SLFN5
UniProt & NIH Common Fund Data Resources
Find proteins for Q08AF3 (Homo sapiens) Explore Q08AF3  Go to UniProtKB:  Q08AF3
PHAROS:  Q08AF3 GTEx:  ENSG00000166750

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.29 Å
• R-Value Free:  0.247 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 211.86	α = 90
b = 156.442	β = 110.382
c = 131.459	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
REFMAC	refinement
XDS	data reduction
STARANISO	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-08-25 
Deposition Author(s): Yang, J.Y., Luo, M., Ou, J.Y., Wang, Z.W., Gao, S.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81772977
National Natural Science Foundation of China (NSFC)	China	81902841
Chinese Academy of Sciences	China	2018M640852

Revision History  

• Version 1.0: 2021-08-25
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description