Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 290.31 kDa 
• Atom Count: 15,600 
• Modelled Residue Count: 1,974 
• Deposited Residue Count: 2,586 
• Unique protein chains: 2

 6FKN

Drosophila Plexin A in complex with Semaphorin 1b

• PDB DOI:  https://doi.org/10.2210/pdb6FKN/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Drosophila melanogaster
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2018-01-24 Released: 2019-02-06 
• Deposition Author(s): Rozbesky, D., Harlos, K., Jones, E.Y.
• Funding Organization(s): Cancer Research UK

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.80 Å
• R-Value Free: 0.297 
• R-Value Work: 0.285 
• R-Value Observed: 0.285 

Literature

Structural basis of semaphorin-plexin cis interaction.

Rozbesky, D., Verhagen, M.G., Karia, D., Nagy, G.N., Alvarez, L., Robinson, R.A., Harlos, K., Padilla-Parra, S., Pasterkamp, R.J., Jones, E.Y.

(2020) EMBO J : e102926-e102926

• PubMed: 32500924 
• DOI: https://doi.org/10.15252/embj.2019102926
• Primary Citation of Related Structures:  
  6FKM, 6FKN


• PubMed Abstract: 
  

Semaphorin ligands interact with plexin receptors to contribute to functions in the development of myriad tissues including neurite guidance and synaptic organisation within the nervous system. Cell-attached semaphorins interact in trans with plexins on opposing cells, but also in cis on the same cell. The interplay between trans and cis interactions is crucial for the regulated development of complex neural circuitry, but the underlying molecular mechanisms are uncharacterised. We have discovered a distinct mode of interaction through which the Drosophila semaphorin Sema1b and mouse Sema6A mediate binding in cis to their cognate plexin receptors. Our high-resolution structural, biophysical and in vitro analyses demonstrate that monomeric semaphorins can mediate a distinctive plexin binding mode. These findings suggest the interplay between monomeric vs dimeric states has a hereto unappreciated role in semaphorin biology, providing a mechanism by which Sema6s may balance cis and trans functionalities.

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Organizational Affiliation: 

Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Plexin A, isoform A	A, C	715	Drosophila melanogaster	Mutation(s): 0  Gene Names:  plexA, BcDNA:GM05237, D-Plex A, Dmel\CG11081, DPlexA, lincRNA.927, plex, plex A, Plex1, PlexA1, CG11081, Dmel_CG11081, PlexA, PlexinA
UniProt
Find proteins for Q9V491 (Drosophila melanogaster) Explore Q9V491  Go to UniProtKB:  Q9V491

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MIP07328p	B, D	578	Drosophila melanogaster	Mutation(s): 0  Gene Names:  sema1b, Sema-1b, Sema-1b-RB, semaphorin-like, CG6446, Dmel_CG6446, Sema1b, BcDNA:GH03186, D-semaIII, Dmel\CG6446, Sema 1b, Sema III, sema-III
UniProt
Find proteins for Q7KK54 (Drosophila melanogaster) Explore Q7KK54  Go to UniProtKB:  Q7KK54

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
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-glucopyranose	G, H	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	I [auth A], J [auth A], K [auth A], L [auth C], M [auth C], N [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.80 Å
• R-Value Free: 0.297 
• R-Value Work: 0.285 
• R-Value Observed: 0.285 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.63	α = 90
b = 153.63	β = 90
c = 425.37	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-02-06 
Deposition Author(s): Rozbesky, D., Harlos, K., Jones, E.Y.

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Funding Organization	Location	Grant Number
Cancer Research UK	United Kingdom	B5R00120

Revision History  

• Version 1.0: 2019-02-06
  Type: Initial release
  
• Version 1.1: 2020-06-17
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary