3NVQ

Molecular mechanism of guidance cue recognition


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.248 

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Ligand Structure Quality Assessment 


This is version 2.0 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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Semaphorin-7AA,
C [auth E]
590Homo sapiensMutation(s): 0 
Gene Names: SEMA7ACD108SEMAL
UniProt & NIH Common Fund Data Resources
Find proteins for O75326 (Homo sapiens)
Explore O75326 
Go to UniProtKB:  O75326
PHAROS:  O75326
GTEx:  ENSG00000138623 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75326
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Plexin-C1B,
D [auth F]
476Homo 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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDG
Query on NDG

Download Ideal Coordinates CCD File 
H [auth A]2-acetamido-2-deoxy-alpha-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.248 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.645α = 90
b = 126.078β = 90
c = 236.419γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SOLVEphasing
RESOLVEmodel building
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RESOLVEphasing

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