6A6L | pdb_00006a6l

Crystal structure of the cold shock domain of YB-1 in complex with m5C RNA

• PDB DOI: https://doi.org/10.2210/pdb6A6L/pdb
• NAKB: 6A6L

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


• Deposited: 2018-06-28 Released: 2019-06-19 
• Deposition Author(s): Huang, Y.
• Funding Organization(s): National Natural Science Foundation of China, Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.207 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the cold shock domain of YB-1 in complex with m5C RNA

Huang, Y.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: fluorescence resonance energy transfer

Macromolecule Content 

• Total Structure Weight: 10.82 kDa 
• Atom Count: 734 
• Modeled Residue Count: 80 
• Deposited Residue Count: 89 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclease-sensitive element-binding protein 1	A	83	Homo sapiens	Mutation(s): 0  Gene Names: YB1
UniProt & NIH Common Fund Data Resources
Find proteins for P67809 (Homo sapiens) Explore P67809  Go to UniProtKB:  P67809
PHAROS:  P67809 GTEx:  ENSG00000065978

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*CP*AP*UP*(5MC))-3')	B [auth D]	6	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.207 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.38	α = 90
b = 66.38	β = 90
c = 34.702	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-06-19 
Deposition Author(s): Huang, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	91640102
Chinese Academy of Sciences	China	XDB08010202

Revision History  

• Version 1.0: 2019-06-19
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description