1E7K | pdb_00001e7k

Crystal structure of the spliceosomal 15.5kD protein bound to a U4 snRNA fragment

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.302 (Depositor) 
  • R-Value Work: 
    0.216 (Depositor) 
  • R-Value Observed: 
    0.216 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history. 

Literature

Crystal Structure of the Spliceosomal 15.5Kd Protein Bound to a U4 Snrna Fragment

Vidovic, I., Nottrott, S., Hartmuth, K., Luhrmann, R., Ficner, R.

(2000) Mol Cell 6: 1331

  • DOI: https://doi.org/10.1016/s1097-2765(00)00131-3
  • Primary Citation Related Structures: 
    1E7K

  • PubMed Abstract: 

    We have determined the crystal structure of a spliceosomal RNP complex comprising the 15.5kD protein of the human U4/U6.U5 tri-snRNP and the 5' stem-loop of U4 snRNA. The protein interacts almost exclusively with a purine-rich (5+2) internal loop within the 5' stem-loop, giving an unusual RNA fold characterized by two tandem sheared G-A base pairs, a high degree of purine stacking, and the accommodation of a single RNA base, rotated out of the RNA chain, in a pocket of the protein. Apart from yielding the structure of an important entity in the pre-mRNA splicing apparatus, this work also implies a model for the complex of the 15.5kD protein with box C/D snoRNAs. It additionally suggests a general recognition principle in a novel family of RNA binding proteins.

    • Organizational Affiliation: 
    • Institut für Molekularbiologie und Tumorforschung, Philipps-Universität Marburg, Emil-Mannkopff-Strasse 2, 35037 Marburg, Germany.

Macromolecule Content 

  • Total Structure Weight: 42.53 kDa 
  • Atom Count: 2,655 
  • Modeled Residue Count: 282 
  • Deposited Residue Count: 300 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
15.5 KD RNA BINDING PROTEIN
A, B
128Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P55769 (Homo sapiens)
Explore P55769 
Go to UniProtKB:  P55769
PHAROS:  P55769
GTEx:  ENSG00000100138 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55769
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(*GP*CP*CP*AP*AP*UP*GP*AP*GP*GP*UP*UP*UP* AP*UP*CP*CP*GP*AP*GP*G*C(-3')
C, D
22Homo sapiens
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.302 (Depositor) 
  • R-Value Work:  0.216 (Depositor) 
  • R-Value Observed: 0.216 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.756α = 90
b = 55.287β = 90
c = 146.735γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement
SHARPphasing
SOLOMONphasing
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-02-19
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references