5IFM

Human NONO (p54nrb) Homodimer

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

A crystallographic study of human NONO (p54(nrb)): overcoming pathological problems with purification, data collection and noncrystallographic symmetry.

Knott, G.J., Panjikar, S., Thorn, A., Fox, A.H., Conte, M.R., Lee, M., Bond, C.S.

(2016) Acta Crystallogr D Struct Biol 72: 761-769

  • DOI: 10.1107/S2059798316005830
  • Primary Citation of Related Structures:  
    5IFM

  • PubMed Abstract: 

    • Non-POU domain-containing octamer-binding protein (NONO, a.k.a. p54(nrb)) is a central player in nuclear gene regulation with rapidly emerging medical significance. NONO is a member of the highly conserved Drosophila behaviour/human splicing (DBHS) protein family, a dynamic family of obligatory dimeric nuclear regulatory mediators ...

    Non-POU domain-containing octamer-binding protein (NONO, a.k.a. p54(nrb)) is a central player in nuclear gene regulation with rapidly emerging medical significance. NONO is a member of the highly conserved Drosophila behaviour/human splicing (DBHS) protein family, a dynamic family of obligatory dimeric nuclear regulatory mediators. However, work with the NONO homodimer has been limited by rapid irreversible sample aggregation. Here, it is reported that L-proline stabilizes purified NONO homodimers, enabling good-quality solution small-angle X-ray structure determination and crystallization. NONO crystallized in the apparent space group P21 with a unique axis (b) of 408.9 Å and with evidence of twinning, as indicated by the cumulative intensity distribution L statistic, suggesting the possibility of space group P1. Structure solution by molecular replacement shows a superhelical arrangement of six NONO homodimers (or 12 in P1) oriented parallel to the long axis, resulting in extensive noncrystallographic symmetry. Further analysis revealed that the crystal was not twinned, but the collected data suffered from highly overlapping reflections that obscured the L-test. Optimized data collection on a new crystal using higher energy X-rays, a smaller beam width and an increased sample-to-detector distance produced non-overlapping reflections to 2.6 Å resolution. The steps taken to analyse and overcome this series of practical difficulties and to produce a biologically informative structure are discussed.

    Organizational Affiliation: 

    School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA 6009, Australia.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Non-POU domain-containing octamer-binding protein
A, B, C, D, E, F, G, H, I, J, K, L
A, B, C, D, E, F, G, H, I, J, K, L
261Homo sapiensMutation(s): 0 
Gene Names: NONO, NRB54
UniProt & NIH Common Fund Data Resources
Find proteins for Q15233 (Homo sapiens)
Explore Q15233 
Go to UniProtKB:  Q15233
PHAROS:  Q15233
GTEx:  ENSG00000147140 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15233
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PRO
Query on PRO
Download Ideal Coordinates CCD File 
N [auth A],
U [auth C]		PROLINE
C5 H9 N O2
ONIBWKKTOPOVIA-BYPYZUCNSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
P [auth B],
Q [auth B],
V [auth C],
W [auth C],
Z [auth D]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
K
Query on K
Download Ideal Coordinates CCD File 
AA [auth D],
O [auth A],
R [auth B],
X [auth C]		POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
BA [auth E],
CA [auth F],
DA [auth F],
EA [auth G],
FA [auth H],
BA [auth E],
CA [auth F],
DA [auth F],
EA [auth G],
FA [auth H],
GA [auth L],
M [auth A],
S [auth C],
T [auth C],
Y [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.15α = 90
b = 407.177β = 97.75
c = 68.961γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
MOLREPphasing
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia1048659
National Health and Medical Research Council (NHMRC, Australia)Australia1050585
ARCDPAustraliaDP160102435

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-09
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Author supporting evidence, Data collection, Derived calculations
  • Version 1.2: 2020-01-08
    Changes: Author supporting evidence