Biological Assembly 1  

 3D View: Structure | Electron Density

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Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: immunoprecipitation

Macromolecule Content

• Total Structure Weight: 10810.13 
• Atom Count: 664 
• Residue Count: 89 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

5YTV

Crystal structure of YB1 cold-shock domain in complex with UCAUCU

• DOI: 10.2210/pdb5YTV/pdb

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli


• Deposited: 2017-11-20 Released: 2018-12-05 
• Deposition Author(s): Yang, X., Huang, Y.
• Funding Organization(s): National Natural Science Foundation of China; Strategic Priority Research Program of the Chinese Academy of Sciences 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.7 Å
• R-Value Free: 0.228 
• R-Value Work: 0.196 

Literature

Crystal structure of YB1 cold-shock domain in complex with CAUC

Yang, X., Huang, Y.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Nuclease-sensitive element-binding protein 1	A	83	Homo sapiens	Mutation(s): 0  Gene Names: YBX1 (NSEP1, YB1)
Find proteins for P67809 (Homo sapiens) Go to Gene View: YBX1 Go to UniProtKB:  P67809

Entity ID: 2
Molecule	Chains	Length	Organism
RNA (5'-R(P*UP*CP*AP*UP*CP*U)-3')	B	6	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.7 Å
• R-Value Free: 0.228 
• R-Value Work: 0.196 
• Space Group: P 6₂

Unit Cell:

Length (Å)	Angle (°)
a = 66.275	α = 90.00
b = 66.275	β = 90.00
c = 35.195	γ = 120.00

Software Package:

Software Name	Purpose
HKL-2000	data reduction
PHENIX	phasing
HKL-2000	data scaling
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-11-20 
• Released Date: 2018-12-05 
• Deposition Author(s): Yang, X., Huang, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	91640102
Strategic Priority Research Program of the Chinese Academy of Sciences	China	XDB08010202

Revision History 

• Version 1.0: 2018-12-05
  Type: Initial release