4CQ1

Crystal structure of the neuronal isoform of PTB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Solution and Crystal Structures of a C Terminal Fragment of the Neuronal Isoform of the Polypyrimidine Tract Binding Protein (Nptb)

Joshi, A.Esteve, V.Buckroyd, A.N.Blatter, M.Allain, F.H.-T.Curry, S.

(2014) PeerJ 2: E305

  • DOI: https://doi.org/10.7717/peerj.305
  • Primary Citation of Related Structures:  
    2MJU, 4CQ1

  • PubMed Abstract: 

    The eukaryotic polypyrimidine tract binding protein (PTB) serves primarily as a regulator of alternative splicing of messenger RNA, but is also co-opted to other roles such as RNA localisation and translation initiation from internal ribosome entry sites. The neuronal paralogue of PTB (nPTB) is 75% identical in amino acid sequence with PTB. Although the two proteins have broadly similar RNA binding specificities and effects on RNA splicing, differential expression of PTB and nPTB can lead to the generation of alternatively spliced mRNAs. RNA binding by PTB and nPTB is mediated by four RNA recognition motifs (RRMs). We present here the crystal and solution structures of the C-terminal domain of nPTB (nPTB34) which contains RRMs 3 and 4. As expected the structures are similar to each other and to the solution structure of the equivalent fragment from PTB (PTB34). The result confirms that, as found for PTB, RRMs 3 and 4 of nPTB interact with one another to form a stable unit that presents the RNA-binding surfaces of the component RRMs on opposite sides that face away from each other. The major differences between PTB34 and nPTB34 arise from amino acid side chain substitutions on the exposed β-sheet surfaces and adjoining loops of each RRM, which are likely to modulate interactions with RNA.


  • Organizational Affiliation

    Department of Life Sciences, Imperial College, London, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
POLYPYRIMIDINE TRACT-BINDING PROTEIN 2
A, B, C, D, E
A, B, C, D, E, F, G, H
196Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKA9 (Homo sapiens)
Explore Q9UKA9 
Go to UniProtKB:  Q9UKA9
PHAROS:  Q9UKA9
GTEx:  ENSG00000117569 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UKA9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth G]
I [auth A]
K [auth A]
L [auth B]
N [auth B]
AA [auth G],
I [auth A],
K [auth A],
L [auth B],
N [auth B],
O [auth B],
P [auth C],
S [auth E],
U [auth E],
V [auth F],
X [auth F],
Z [auth F]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
BA [auth G]
J [auth A]
M [auth B]
Q [auth C]
R [auth D]
BA [auth G],
J [auth A],
M [auth B],
Q [auth C],
R [auth D],
T [auth E],
W [auth F],
Y [auth F]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61α = 89.99
b = 65.81β = 90
c = 99.58γ = 89.99
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
autoSHARPphasing
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-19
    Type: Initial release
  • Version 1.1: 2014-03-26
    Changes: Database references
  • Version 1.2: 2014-04-09
    Changes: Database references
  • Version 1.3: 2014-04-16
    Changes: Database references
  • Version 1.4: 2016-01-13
    Changes: Database references
  • Version 1.5: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other