6JKJ

Crystal structure of human SPSB2 in the apo-state

  • Classification: PROTEIN BINDING
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2019-03-01 Released: 2019-07-03 
  • Deposition Author(s): Luo, Y., Kuang, Z.
  • Funding Organization(s): National Natural Science Foundation of China, Ministry of Education (China)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


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Literature

Crystal structure of the SPRY domain of human SPSB2 in the apo state.

Luo, Y.Li, K.Yang, J.Zhang, D.Zhou, Y.Kuang, Z.

(2019) Acta Crystallogr F Struct Biol Commun 75: 412-418

  • DOI: 10.1107/S2053230X1900623X
  • Primary Citation of Related Structures:  
    6JKJ

  • PubMed Abstract: 
  • The SPRY domain-containing SOCS box protein 2 (SPSB2) is one of four mammalian SPSB proteins that are characterized by a C-terminal SOCS box and a central SPRY/B30.2 domain. SPSB2 interacts with inducible nitric oxide synthase (iNOS) via the SPRY domain and polyubiquitinates iNOS, resulting in its proteasomal degradation ...

    The SPRY domain-containing SOCS box protein 2 (SPSB2) is one of four mammalian SPSB proteins that are characterized by a C-terminal SOCS box and a central SPRY/B30.2 domain. SPSB2 interacts with inducible nitric oxide synthase (iNOS) via the SPRY domain and polyubiquitinates iNOS, resulting in its proteasomal degradation. Inhibitors that can disrupt SPSB2-iNOS interaction and augment NO production may serve as novel anti-infective and anticancer agents. The previously determined murine SPSB2 structure may not reflect the true apo conformation of the iNOS-binding site. Here, the crystal structure of human SPSB2 SPRY domain in the apo state is reported at a resolution of 1.9 Å. Comparison of the apo and ligand-bound structures reveals that the iNOS-binding site is highly preformed and that major conformational changes do not occur upon ligand binding. Moreover, the C-terminal His 6 tag of the recombinant protein binds to a shallow pocket adjacent to the iNOS-binding site on a crystallographically related SPSB2 molecule. These findings may help in structure-based and fragment-based SPSB2 inhibitor design in the future.


    Organizational Affiliation

    Department of Cell Biology and Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, People's Republic of China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SPRY domain-containing SOCS box protein 2A, B209Homo sapiensMutation(s): 0 
Gene Names: SPSB2GRCC9SSB2
UniProt & NIH Common Fund Data Resources
Find proteins for Q99619 (Homo sapiens)
Explore Q99619 
Go to UniProtKB:  Q99619
PHAROS:  Q99619
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99619
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.45α = 90
b = 75.1β = 101.38
c = 79.2γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina81571539
National Natural Science Foundation of ChinaChina31270817
Ministry of Education (China)China21617443

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-03
    Type: Initial release