5NV6

Structure of human transforming growth factor beta-induced protein (TGFBIp).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.93 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

Structural and Functional Implications of Human Transforming Growth Factor beta-Induced Protein, TGFBIp, in Corneal Dystrophies.

Garcia-Castellanos, R.Nielsen, N.S.Runager, K.Thgersen, I.B.Lukassen, M.V.Poulsen, E.T.Goulas, T.Enghild, J.J.Gomis-Ruth, F.X.

(2017) Structure 25: 1740-1750.e2

  • DOI: 10.1016/j.str.2017.09.001
  • Primary Citation of Related Structures:  
    5NV6

  • PubMed Abstract: 
  • A major cause of visual impairment, corneal dystrophies result from accumulation of protein deposits in the cornea. One of the proteins involved is transforming growth factor β-induced protein (TGFBIp), an extracellular matrix component that interacts with integrins but also produces corneal deposits when mutated ...

    A major cause of visual impairment, corneal dystrophies result from accumulation of protein deposits in the cornea. One of the proteins involved is transforming growth factor β-induced protein (TGFBIp), an extracellular matrix component that interacts with integrins but also produces corneal deposits when mutated. Human TGFBIp is a multi-domain 683-residue protein, which contains one CROPT domain and four FAS1 domains. Its structure spans ∼120 Å and reveals that vicinal domains FAS1-1/FAS1-2 and FAS1-3/FAS1-4 tightly interact in an equivalent manner. The FAS1 domains are sandwiches of two orthogonal four-stranded β sheets decorated with two three-helix insertions. The N-terminal FAS1 dimer forms a compact moiety with the structurally novel CROPT domain, which is a five-stranded all-β cysteine-knot solely found in TGFBIp and periostin. The overall TGFBIp architecture discloses regions for integrin binding and that most dystrophic mutations cluster at both molecule ends, within domains FAS1-1 and FAS1-4.


    Organizational Affiliation

    Proteolysis Laboratory, Structural Biology Unit ("María-de-Maeztu" Unit of Excellence), Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park, c/Baldiri Reixac 15-21, 08028 Barcelona, Catalonia, Spain. Electronic address: xgrcri@ibmb.csic.es.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transforming growth factor-beta-induced protein ig-h3A, B683Homo sapiensMutation(s): 0 
Gene Names: TGFBIBIGH3
UniProt & NIH Common Fund Data Resources
Find proteins for Q15582 (Homo sapiens)
Explore Q15582 
Go to UniProtKB:  Q15582
PHAROS:  Q15582
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15582
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download Ideal Coordinates CCD File 
C [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.93 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.220 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.84α = 90
b = 114.84β = 90
c = 181.24γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
BUSTER-TNTrefinement
Cootmodel building

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpainBFU2015-64487-R
Spanish Ministry of Economy and CompetitivenessSpainMDM-2014-0435
Catalan Department of EconomySpain2014SGR9
Spanish Ministry of Economy and CompetitivenessSpainJCI-2012-13573

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-09
    Type: Initial release
  • Version 2.0: 2017-09-06
    Changes: Atomic model, Author supporting evidence
  • Version 2.1: 2017-10-25
    Changes: Database references
  • Version 2.2: 2017-11-15
    Changes: Database references