Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content

• Total Structure Weight: 9.94 kDa 
• Atom Count: 683 
• Modelled Residue Count: 78 
• Deposited Residue Count: 83 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

 6KTC

Crystal structure of YBX1 CSD with m5C RNA

• PDB DOI:  https://doi.org/10.2210/pdb6KTC/pdb
• NDB: 6KTC

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-08-27 Released: 2020-02-05 
• Deposition Author(s): Zou, F., Li, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.274 
• R-Value Work: 0.237 
• R-Value Observed: 0.239 

Literature

DrosophilaYBX1 homolog YPS promotes ovarian germ line stem cell development by preferentially recognizing 5-methylcytosine RNAs.

Zou, F., Tu, R., Duan, B., Yang, Z., Ping, Z., Song, X., Chen, S., Price, A., Li, H., Scott, A., Perera, A., Li, S., Xie, T.

(2020) Proc Natl Acad Sci U S A 117: 3603-3609

• PubMed: 32015133 
• DOI: https://doi.org/10.1073/pnas.1910862117
• Primary Citation of Related Structures:  
  6KTC, 6KUG


• PubMed Abstract: 
  

5-Methylcytosine (m ⁵ C) is a RNA modification that exists in tRNAs and rRNAs and was recently found in mRNAs. Although it has been suggested to regulate diverse biological functions, whether m ⁵ C RNA modification influences adult stem cell development remains undetermined. In this study, we show that Ypsilon schachtel (YPS), a homolog of human Y box binding protein 1 (YBX1), promotes germ line stem cell (GSC) maintenance, proliferation, and differentiation in the Drosophila ovary by preferentially binding to m ⁵ C-containing RNAs. YPS is genetically demonstrated to function intrinsically for GSC maintenance, proliferation, and progeny differentiation in the Drosophila ovary, and human YBX1 can functionally replace YPS to support normal GSC development. Highly conserved cold-shock domains (CSDs) of YPS and YBX1 preferentially bind to m ⁵ C RNA in vitro. Moreover, YPS also preferentially binds to m ⁵ C-containing RNAs, including mRNAs, in germ cells. The crystal structure of the YBX1 CSD-RNA complex reveals that both hydrophobic stacking and hydrogen bonds are critical for m ⁵ C binding. Overexpression of RNA-binding-defective YPS and YBX1 proteins disrupts GSC development. Taken together, our findings show that m ⁵ C RNA modification plays an important role in adult stem cell development.

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Organizational Affiliation: 

Department of Anatomy and Cell Biology, University of Kansas School of Medicine, Kansas City, KS 66160.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclease-sensitive element-binding protein 1	A	79	Homo sapiens	Mutation(s): 0  Gene Names: YBX1, NSEP1, YB1
UniProt & NIH Common Fund Data Resources
Find proteins for P67809 (Homo sapiens) Explore P67809  Go to UniProtKB:  P67809
PHAROS:  P67809

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*GP*(5MC)P*CP*U)-3')	B [auth V]	4	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.274 
• R-Value Work: 0.237 
• R-Value Observed: 0.239 
• Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.706	α = 90
b = 66.706	β = 90
c = 34.224	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-02-05 
Deposition Author(s): Zou, F., Li, S.

Revision History  

• Version 1.0: 2020-02-05
  Type: Initial release
  
• Version 1.1: 2020-02-19
  Changes: Database references
• Version 1.2: 2020-03-04
  Changes: Database references