7VMB

Crystal structure of IQSEC1-IQ motif, Sec7PH tandem in complex with calmodulin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Ca2+-induced release of IQSEC2/BRAG1 autoinhibition under physiological and pathological conditions.

Bai, G.Li, H.Qin, P.Guo, Y.Yang, W.Lian, Y.Ye, F.Chen, J.Wu, M.Huang, R.Li, J.Lu, Y.Zhang, M.

(2023) J Cell Biol 222

  • DOI: https://doi.org/10.1083/jcb.202307117
  • Primary Citation of Related Structures:  
    7VMB

  • PubMed Abstract: 

    IQSEC2 (aka BRAG1) is a guanine nucleotide exchange factor (GEF) highly enriched in synapses. As a top neurodevelopmental disorder risk gene, numerous mutations are identified in Iqsec2 in patients with intellectual disabilities accompanied by other developmental, neurological, and psychiatric symptoms, though with poorly understood underlying molecular mechanisms. The atomic structures of IQSECs, together with biochemical analysis, presented in this study reveal an autoinhibition and Ca2+-dependent allosteric activation mechanism for all IQSECs and rationalize how each identified Iqsec2 mutation can alter the structure and function of the enzyme. Transgenic mice modeling two pathogenic variants of Iqsec2 (R359C and Q801P), with one activating and the other inhibiting the GEF activity of the enzyme, recapitulate distinct clinical phenotypes in patients. Our study demonstrates that different mutations on one gene such as Iqsec2 can have distinct neurological phenotypes and accordingly will require different therapeutic strategies.


  • Organizational Affiliation

    School of Life Sciences, Southern University of Science and Technology , Shenzhen, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
IQ motif and SEC7 domain-containing protein 1372Homo sapiensMutation(s): 0 
Gene Names: IQSEC1ARFGEP100BRAG2KIAA0763
UniProt & NIH Common Fund Data Resources
Find proteins for Q6DN90 (Homo sapiens)
Explore Q6DN90 
Go to UniProtKB:  Q6DN90
PHAROS:  Q6DN90
GTEx:  ENSG00000144711 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6DN90
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
IQ motif and SEC7 domain-containing protein 174Homo sapiensMutation(s): 0 
Gene Names: IQSEC1ARFGEP100BRAG2KIAA0763
UniProt & NIH Common Fund Data Resources
Find proteins for Q6DN90 (Homo sapiens)
Explore Q6DN90 
Go to UniProtKB:  Q6DN90
PHAROS:  Q6DN90
GTEx:  ENSG00000144711 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6DN90
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Calmodulin-1153Homo sapiensMutation(s): 0 
Gene Names: CALM1CALMCAMCAM1
UniProt & NIH Common Fund Data Resources
Find proteins for P0DP23 (Homo sapiens)
Explore P0DP23 
Go to UniProtKB:  P0DP23
PHAROS:  P0DP23
GTEx:  ENSG00000198668 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DP23
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.01α = 90
b = 81.436β = 90
c = 124.762γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The University Grants Committee, Research Grants Council (RGC)Hong Kong--

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-12
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-29
    Changes: Refinement description