7F3I

Crystal structure of human YBX2 CSD in complex with m5C RNA in space group P212121

• PDB DOI: https://doi.org/10.2210/pdb7F3I/pdb
• NAKB: 7F3I

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2021-06-16 Released: 2022-06-22 
• Deposition Author(s): Zhang, Y., Huang, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.246 
• R-Value Work: 0.185 
• R-Value Observed: 0.191 

Literature

Crystal structure of human YBX2 CSD in complex with m5C RNA in space group P212121

Zhang, Y., Huang, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content

• Total Structure Weight: 33.72 kDa 
• Atom Count: 2,482 
• Modelled Residue Count: 285 
• Deposited Residue Count: 289 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Y-box-binding protein 2	A, C, E	93	Homo sapiens	Mutation(s): 2  Gene Names: YBX2, CSDA3, MSY2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2T7 (Homo sapiens) Explore Q9Y2T7  Go to UniProtKB:  Q9Y2T7
PHAROS:  Q9Y2T7 GTEx:  ENSG00000006047

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*UP*(5MC)P*CP*(5MC))-3')	B, D	5	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.246 
• R-Value Work: 0.185 
• R-Value Observed: 0.191 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.532	α = 90
b = 59.348	β = 90
c = 118.623	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-06-22 
Deposition Author(s): Zhang, Y., Huang, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31870741

Revision History  

• Version 1.0: 2022-06-22
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description