6A6L

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

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

Huang, Y.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nuclease-sensitive element-binding protein 1
A
83Homo sapiensMutation(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
MoleculeChainsLengthOrganism
RNA (5'-R(P*CP*AP*UP*(5MC))-3')D6Homo sapiens
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5MC
Query on 5MC
D
RNA LINKINGC10 H16 N3 O8 PC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.180 
  • Space Group: P 62
Unit Cell:
Length (Å)Angle (°)
a = 66.380α = 90.00
b = 66.380β = 90.00
c = 34.702γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-06-28 
  • Released Date: 2019-06-19 
  • Deposition Author(s): Huang, Y.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina91640102
Chinese Academy of SciencesChinaXDB08010202

Revision History 

  • Version 1.0: 2019-06-19
    Type: Initial release