7F3J | pdb_00007f3j

Crystal structure of human YBX2 CSD in complex with m5C RNA in space group P1

• PDB DOI: https://doi.org/10.2210/pdb7F3J/pdb
• NAKB: 7F3J

• 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: 1.95 Å
• R-Value Free: 
  0.229 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human YBX2 CSD in complex with m5C RNA in space group P1

Zhang, Y., Huang, Y.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: isothermal titration calorimetry

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 49.35 kDa 
• Atom Count: 3,530 
• Modeled Residue Count: 378 
• Deposited Residue Count: 400 
• 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, G	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(*UP*CP*AP*UP*(5MC))-3')	B, D, F, H	7	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.229 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.616	α = 69.264
b = 46.364	β = 85.601
c = 57.704	γ = 90.015

Software Package:

Software Name	Purpose
Coot	model building
PHENIX	refinement
Coot	model building
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