3NVN | pdb_00003nvn

Molecular mechanism of guidance cue recognition


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 
    0.276 (Depositor) 
  • R-Value Work: 
    0.239 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 
    0.239 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3NVN

Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history

Literature

Structural Basis of Semaphorin-Plexin Recognition and Viral Mimicry from Sema7A and A39R Complexes with PlexinC1.

Liu, H.Juo, Z.S.Shim, A.H.Focia, P.J.Chen, X.Garcia, K.C.He, X.

(2010) Cell 142: 749-761

  • DOI: https://doi.org/10.1016/j.cell.2010.07.040
  • Primary Citation Related Structures: 
    3NVN, 3NVQ, 3NVX

  • PubMed Abstract: 

    Repulsive signaling by Semaphorins and Plexins is crucial for the development and homeostasis of the nervous, immune, and cardiovascular systems. Sema7A acts as both an immune and a neural Semaphorin through PlexinC1, and A39R is a Sema7A mimic secreted by smallpox virus. We report the structures of Sema7A and A39R complexed with the Semaphorin-binding module of PlexinC1. Both structures show two PlexinC1 molecules symmetrically bridged by Semaphorin dimers, in which the Semaphorin and PlexinC1 beta propellers interact in an edge-on, orthogonal orientation. Both binding interfaces are dominated by the insertion of the Semaphorin's 4c-4d loop into a deep groove in blade 3 of the PlexinC1 propeller. A39R appears to achieve Sema7A mimicry by preserving key Plexin-binding determinants seen in the mammalian Sema7A complex that have evolved to achieve higher affinity binding to the host-derived PlexinC1. The complex structures support a conserved Semaphorin-Plexin recognition mode and suggest that Plexins are activated by dimerization.


  • Organizational Affiliation
    • Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.

Macromolecule Content 

  • Total Structure Weight: 97.65 kDa 
  • Atom Count: 7,296 
  • Modeled Residue Count: 857 
  • Deposited Residue Count: 865 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
EVM139389Ectromelia virusMutation(s): 0 
Gene Names: SEMA
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
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Plexin-C1476Homo 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: 4Go to GlyGen: O60486-1
Sequence Annotations
Expand
Reference Sequence

Small Molecules

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

Query on NAG



Download:Ideal Coordinates CCD File
E [auth B],
G [auth B],
H [auth B],
I [auth B],
J [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
NDG

Query on NDG



Download:Ideal Coordinates CCD File
C [auth A],
F [auth B],
K [auth B]
2-acetamido-2-deoxy-alpha-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
D [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free:  0.276 (Depositor) 
  • R-Value Work:  0.239 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 0.239 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.749α = 90
b = 133.494β = 90
c = 172.231γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2024-10-30
    Changes: Data collection, Database references, Structure summary