6GFF

Structure of GARP (LRRC32) in complex with latent TGF-beta1 and MHG-8 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structural basis of latent TGF-beta 1 presentation and activation by GARP on human regulatory T cells.

Lienart, S.Merceron, R.Vanderaa, C.Lambert, F.Colau, D.Stockis, J.van der Woning, B.De Haard, H.Saunders, M.Coulie, P.G.Savvides, S.N.Lucas, S.

(2018) Science 362: 952-956

  • DOI: 10.1126/science.aau2909
  • Primary Citation of Related Structures:  
    6GFF

  • PubMed Abstract: 
  • Transforming growth factor-β1 (TGF-β1) is one of very few cytokines produced in a latent form, requiring activation to exert any of its vastly diverse effects on development, immunity, and cancer. Regulatory T cells (T regs ) suppress immune cells within close proximity by activating latent TGF-β1 presented by GARP (glycoprotein A repetitions predominant) to integrin αVβ8 on their surface ...

    Transforming growth factor-β1 (TGF-β1) is one of very few cytokines produced in a latent form, requiring activation to exert any of its vastly diverse effects on development, immunity, and cancer. Regulatory T cells (T regs ) suppress immune cells within close proximity by activating latent TGF-β1 presented by GARP (glycoprotein A repetitions predominant) to integrin αVβ8 on their surface. We solved the crystal structure of GARP:latent TGF-β1 bound to an antibody that stabilizes the complex and blocks release of active TGF-β1. This finding reveals how GARP exploits an unusual medley of interactions, including fold complementation by the amino terminus of TGF-β1, to chaperone and orient the cytokine for binding and activation by αVβ8. Thus, this work further elucidates the mechanism of antibody-mediated blockade of TGF-β1 activation and immunosuppression by T regs .


    Organizational Affiliation

    Walloon Excellence in Lifesciences and Biotechnology, 1300 Wavre, Belgium.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transforming growth factor beta-1A, C, E, G249Homo sapiensMutation(s): 0 
Gene Names: TGFB1TGFB
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Find proteins for P01137 (Homo sapiens)
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Go to UniProtKB:  P01137
PHAROS:  P01137
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Transforming growth factor beta-1B, D, F, H112Homo sapiensMutation(s): 0 
Gene Names: TGFB1TGFB
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Explore P01137 
Go to UniProtKB:  P01137
PHAROS:  P01137
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Leucine-rich repeat-containing protein 32I, J618Homo sapiensMutation(s): 0 
Gene Names: LRRC32D11S833EGARP
UniProt & NIH Common Fund Data Resources
Find proteins for Q14392 (Homo sapiens)
Explore Q14392 
Go to UniProtKB:  Q14392
PHAROS:  Q14392
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
MHG-8 Fab light chainK, M212Mus musculusMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
MHG-8 Fab heavy chainL, N221Mus musculusMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

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Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseO, P, Q, S, T3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 7
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseR2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 8
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseU4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G22573RC
GlyCosmos:  G22573RC
GlyGen:  G22573RC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.86α = 90
b = 175.01β = 92.23
c = 145.77γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Walloon Excellence in Lifesciences & BIOtechnologyBelgiumBF-2014-01
European Research CouncilBelgiumTARG-SUP 682818

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 1.1: 2018-12-05
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary