6VXK

Cryo-EM Structure of the full-length A39R/PlexinC1 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Cryo-EM structure of the PlexinC1/A39R complex reveals inter-domain interactions critical for ligand-induced activation.

Kuo, Y.C.Chen, H.Shang, G.Uchikawa, E.Tian, H.Bai, X.C.Zhang, X.

(2020) Nat Commun 11: 1953-1953

  • DOI: https://doi.org/10.1038/s41467-020-15862-0
  • Primary Citation of Related Structures:  
    6VXK

  • PubMed Abstract: 

    Plexins are receptors for semaphorins that transduce signals for regulating neuronal development and other processes. Plexins are single-pass transmembrane proteins with multiple domains in both the extracellular and intracellular regions. Semaphorin activates plexin by binding to its extracellular N-terminal Sema domain, inducing the active dimer of the plexin intracellular region. The mechanism underlying this activation process of plexin is incompletely understood. We present cryo-electron microscopic structure of full-length human PlexinC1 in complex with the viral semaphorin mimic A39R. The structure shows that A39R induces a specific dimer of PlexinC1 where the membrane-proximal domains from the two PlexinC1 protomers are placed close to each other, poised to promote the active dimer of the intracellular region. This configuration is imposed by a distinct conformation of the PlexinC1 extracellular region, stabilized by inter-domain interactions among the Sema and membrane-proximal domains. Our mutational analyses support the critical role of this conformation in PlexinC1 activation.


  • Organizational Affiliation

    Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Semaphorin-like protein 139
A, C
398Ectromelia virus MoscowMutation(s): 0 
Gene Names: EVM139SEMA
UniProt
Find proteins for Q8JL80 (Ectromelia virus (strain Moscow))
Explore Q8JL80 
Go to UniProtKB:  Q8JL80
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8JL80
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Plexin-C1
B, D
1,545Homo sapiensMutation(s): 0 
Gene Names: PLXNC1VESPR
UniProt & NIH Common Fund Data Resources
Find proteins for O60486 (Homo sapiens)
Explore O60486 
Go to UniProtKB:  O60486
PHAROS:  O60486
GTEx:  ENSG00000136040 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60486
Glycosylation
Glycosylation Sites: 8Go to GlyGen: O60486-1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
E [auth A]
F [auth B]
G [auth B]
H [auth B]
I [auth B]
E [auth A],
F [auth B],
G [auth B],
H [auth B],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth C],
O [auth D],
P [auth D],
Q [auth D],
R [auth D],
S [auth D],
T [auth D],
U [auth D],
V [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM130289
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesRP160082
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesRP170644
Welch FoundationUnited StatesI-1702
Welch FoundationUnited StatesI-1944

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-29
    Type: Initial release
  • Version 1.1: 2020-05-06
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2024-11-13
    Changes: Data collection, Database references, Refinement description, Structure summary