5XN3

Crystal structure of SPSB2 in complex with a rational designed RGD containing cyclic peptide inhibitor of SPSB2-iNOS interaction


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of SPSB2 in complex with a rational designed RGD-containing cyclic peptide inhibitor of SPSB2-iNOS interaction.

You, T.Wang, Y.Li, K.Zhang, D.Wei, H.Luo, Y.Li, H.Lu, Y.Su, X.Kuang, Z.

(2017) Biochem Biophys Res Commun 489: 346-352

  • DOI: 10.1016/j.bbrc.2017.05.122
  • Primary Citation of Related Structures:  
    5XN3

  • PubMed Abstract: 
  • SPRY domain-containing SOCS box protein 2 (SPSB2) is a negative regulator of inducible nitric oxide synthase (iNOS) that modulates the lifetime of iNOS and thus the levels of nitric oxide (NO) production. Inhibitors that can disrupt the endogenous SP ...

    SPRY domain-containing SOCS box protein 2 (SPSB2) is a negative regulator of inducible nitric oxide synthase (iNOS) that modulates the lifetime of iNOS and thus the levels of nitric oxide (NO) production. Inhibitors that can disrupt the endogenous SPSB2-iNOS interaction and augment NO production have potential as novel antimicrobial and anticancer drugs. In this study, we have designed a cyclic peptide (cR8), containing an RGD motif and the SPSB2 binding motif (DINNNV). ITC and chemical shift perturbation showed that cR8 binds to the iNOS binding site on SPSB2 with a K d of 671 nM, and saturation transfer difference NMR showed that cR8 binds to α v β 3 integrin-expressing cells. Moreover, we determined the crystal structure of SPSB2 in complex with cR8, at a resolution of 1.34 Å. cR8 forms extensive hydrogen bonding with SPSB2 residues, but loss of an intramolecular hydrogen bond that is present in SPSB2-bound iNOS peptide may destabilize the bound conformation of cR8 and lead to a gentle reduction in SPSB2 binding affinity. These results serve as a useful basis for designing site-directed SPSB2 inhibitors in the future.


    Organizational Affiliation

    Department of Cell Biology and Institute of Biomedicine, Jinan University, Guangzhou 510632, China; Guangdong Provincial Key Laboratory of Bioengineering Medicine, National Engineering Research Center of Genetic Medicine, Guangzhou 510632, China. Electronic address: zhihe.kuang@jnu.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SPRY domain-containing SOCS box protein 2A209Homo sapiensMutation(s): 0 
Gene Names: SPSB2GRCC9SSB2
Find proteins for Q99619 (Homo sapiens)
Explore Q99619 
Go to UniProtKB:  Q99619
NIH Common Fund Data Resources
PHAROS  Q99619
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
cR8 peptide from NOS2B8Homo sapiensMutation(s): 0 
Gene Names: NOS2NOS2A
EC: 1.14.13.39
Find proteins for P35228 (Homo sapiens)
Explore P35228 
Go to UniProtKB:  P35228
NIH Common Fund Data Resources
PHAROS  P35228
Protein Feature View
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  • Reference Sequence
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_002275
Query on PRD_002275
BcR8 peptide from NOS2Cyclic peptide /  Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.49α = 90
b = 64.6β = 102.95
c = 47.59γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-05-17 
  • Released Date: 2017-06-14 
  • Deposition Author(s): You, T., Kuang, Z.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31270817
National Natural Science Foundation of ChinaChina81571539

Revision History 

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2017-07-05
    Changes: Database references