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 
  • R-Value Observed: 0.183 

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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclease-sensitive element-binding protein 1A83Homo sapiensMutation(s): 0 
Gene Names: YB1YBX1NSEP1
UniProt & NIH Common Fund Data Resources
Find proteins for P67809 (Homo sapiens)
Explore P67809 
Go to UniProtKB:  P67809
PHAROS:  P67809
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP67809
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
RNA (5'-R(P*CP*AP*UP*(5MC))-3')B [auth D]6Homo sapiens
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.183 
  • Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.38α = 90
b = 66.38β = 90
c = 34.702γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • 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  (Full details and data files)

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