4XU4

Crystal structure of a mycobacterial Insig homolog MvINS from Mycobacterium vanbaalenii at 1.9A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.203 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.186 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted BNGClick on this verticalbar to view detailsBest fitted DDQClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

PROTEIN STRUCTURE. Crystal structure of a mycobacterial Insig homolog provides insight into how these sensors monitor sterol levels

Ren, R.Zhou, X.He, Y.Ke, M.Wu, J.Liu, X.Yan, C.Wu, Y.Gong, X.Lei, X.Yan, S.F.Radhakrishnan, A.Yan, N.

(2015) Science 349: 187-191

  • DOI: https://doi.org/10.1126/science.aab1091
  • Primary Citation of Related Structures:  
    4XU4, 4XU5, 4XU6

  • PubMed Abstract: 

    Insulin-induced gene 1 (Insig-1) and Insig-2 are endoplasmic reticulum membrane-embedded sterol sensors that regulate the cellular accumulation of sterols. Despite their physiological importance, the structural information on Insigs remains limited. Here we report the high-resolution structures of MvINS, an Insig homolog from Mycobacterium vanbaalenii. MvINS exists as a homotrimer. Each protomer comprises six transmembrane segments (TMs), with TM3 and TM4 contributing to homotrimerization. The six TMs enclose a V-shaped cavity that can accommodate a diacylglycerol molecule. A homology-based structural model of human Insig-2, together with biochemical characterizations, suggest that the central cavity of Insig-2 accommodates 25-hydroxycholesterol, whereas TM3 and TM4 engage in Scap binding. These analyses provide an important framework for further functional and mechanistic understanding of Insig proteins and the sterol regulatory element-binding protein pathway.


  • Organizational Affiliation

    State Key Laboratory of Membrane Biology, Tsinghua University, Beijing 100084, China. Center for Structural Biology, School of Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China. Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein210Mycolicibacterium vanbaalenii PYR-1Mutation(s): 0 
Gene Names: Mvan_1475
Membrane Entity: Yes 
UniProt
Find proteins for A1T557 (Mycolicibacterium vanbaalenii (strain DSM 7251 / JCM 13017 / BCRC 16820 / KCTC 9966 / NRRL B-24157 / PYR-1))
Explore A1T557 
Go to UniProtKB:  A1T557
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1T557
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.203 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.498α = 90
b = 85.498β = 90
c = 125.851γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted BNGClick on this verticalbar to view detailsBest fitted DDQClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-14
    Type: Initial release
  • Version 1.1: 2020-02-05
    Changes: Data collection, Derived calculations
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2024-03-20
    Changes: Data collection, Database references, Structure summary