8VSD | pdb_00008vsd

avb8/L-TGF-b1/GARP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8VSD

This is version 1.3 of the entry. See complete history

Literature

Dynamic allostery drives autocrine and paracrine TGF-beta signaling.

Jin, M.Seed, R.I.Cai, G.Shing, T.Wang, L.Ito, S.Cormier, A.Wankowicz, S.A.Jespersen, J.M.Baron, J.L.Carey, N.D.Campbell, M.G.Yu, Z.Tang, P.K.Cossio, P.Wen, W.Lou, J.Marks, J.Nishimura, S.L.Cheng, Y.

(2024) Cell 187: 6200

  • DOI: https://doi.org/10.1016/j.cell.2024.08.036
  • Primary Citation Related Structures: 
    8VS6, 8VSB, 8VSC, 8VSD

  • PubMed Abstract: 

    TGF-β, essential for development and immunity, is expressed as a latent complex (L-TGF-β) non-covalently associated with its prodomain and presented on immune cell surfaces by covalent association with GARP. Binding to integrin αvβ8 activates L-TGF-β1/GARP. The dogma is that mature TGF-β must physically dissociate from L-TGF-β1 for signaling to occur. Our previous studies discovered that αvβ8-mediated TGF-β autocrine signaling can occur without TGF-β1 release from its latent form. Here, we show that mice engineered to express TGF-β1 that cannot release from L-TGF-β1 survive without early lethal tissue inflammation, unlike those with TGF-β1 deficiency. Combining cryogenic electron microscopy with cell-based assays, we reveal a dynamic allosteric mechanism of autocrine TGF-β1 signaling without release where αvβ8 binding redistributes the intrinsic flexibility of L-TGF-β1 to expose TGF-β1 to its receptors. Dynamic allostery explains the TGF-β3 latency/activation mechanism and why TGF-β3 functions distinctly from TGF-β1, suggesting that it broadly applies to other flexible cell surface receptor/ligand systems.


  • Organizational Affiliation
    • Department of Biochemistry and Biophysics, University of California, San Francisco (UCSF), San Francisco, CA, USA.

Macromolecule Content 

  • Total Structure Weight: 252.49 kDa 
  • Atom Count: 16,276 
  • Modeled Residue Count: 2,109 
  • Deposited Residue Count: 2,235 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Transforming growth factor beta activator LRRC32A [auth I]566Homo sapiensMutation(s): 0 
Gene Names: LRRC32D11S833E
UniProt & NIH Common Fund Data Resources
Find proteins for Q14392 (Homo sapiens)
Explore Q14392 
Go to UniProtKB:  Q14392
PHAROS:  Q14392
GTEx:  ENSG00000137507 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14392
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Integrin alpha-V heavy chainB [auth A]593Homo sapiensMutation(s): 0 
Gene Names: ITGAVMSK8VNRAVTNR
UniProt & NIH Common Fund Data Resources
Find proteins for P06756 (Homo sapiens)
Explore P06756 
Go to UniProtKB:  P06756
PHAROS:  P06756
GTEx:  ENSG00000138448 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06756
Glycosylation
Glycosylation Sites: 3Go to GlyGen: P06756-1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Integrin beta-8C [auth B]354Homo sapiensMutation(s): 0 
Gene Names: ITGB8
UniProt & NIH Common Fund Data Resources
Find proteins for P26012 (Homo sapiens)
Explore P26012 
Go to UniProtKB:  P26012
PHAROS:  P26012
GTEx:  ENSG00000105855 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26012
Glycosylation
Glycosylation Sites: 5Go to GlyGen: P26012-1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Transforming growth factor beta-1 proproteinD [auth E],
E [auth F]
361Homo sapiensMutation(s): 0 
Gene Names: TGFB1TGFB
UniProt & NIH Common Fund Data Resources
Find proteins for P01137 (Homo sapiens)
Explore P01137 
Go to UniProtKB:  P01137
PHAROS:  P01137
GTEx:  ENSG00000105329 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01137
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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-glucopyranoseF [auth C]6N-Glycosylation
Glycosylation Resources
GlyTouCan: G56014GC
GlyCosmos: G56014GC
GlyGen: G56014GC
Entity ID: 6
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth D],
H [auth G],
I [auth H],
J
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
K [auth A],
P [auth B],
Q [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
L [auth A],
M [auth A],
N [auth A],
O [auth A],
R [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
S [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL134183

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-11
    Type: Initial release
  • Version 1.1: 2024-10-02
    Changes: Data collection, Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection, Database references, Structure summary
  • Version 1.3: 2024-11-20
    Changes: Data collection, Database references