2V5E

The structure of the GDNF:Coreceptor complex: Insights into RET signalling and heparin binding.

• PDB DOI: https://doi.org/10.2210/pdb2V5E/pdb

• Classification: RECEPTOR/GLYCOPROTEIN COMPLEX
• Organism(s): Rattus norvegicus, Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2008-10-03 Released: 2008-10-21 
• Deposition Author(s): Parkash, V., Leppanen, V.-M., Virtanen, H., Jurvansuu, J.-M., Bespalov, M.M., Sidorova, Y.A., Runeberg-Roos, P., Saarma, M., Goldman, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.237 
• R-Value Work: 0.184 
• R-Value Observed: 0.187 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35.42 kDa 
• Atom Count: 2,664 
• Modelled Residue Count: 301 
• Deposited Residue Count: 301 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GDNF FAMILY RECEPTOR ALPHA-1	A	200	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for Q62997 (Rattus norvegicus) Explore Q62997  Go to UniProtKB:  Q62997

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GLIAL CELL LINE-DERIVED NEUROTROPHIC FACTOR	B	101	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P39905 (Homo sapiens) Explore P39905  Go to UniProtKB:  P39905
PHAROS:  P39905 GTEx:  ENSG00000168621

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose-(2-1)-2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose	C	2		N/A
Glycosylation Resources
GlyTouCan:  G97555GV GlyCosmos:  G97555GV

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	H [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO	D [auth A], E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900013	C	sucrose octasulfate	Oligosaccharide / Substrate analog

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.237 
• R-Value Work: 0.184 
• R-Value Observed: 0.187 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.9	α = 90
b = 75.7	β = 91.9
c = 105.5	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-21 
Deposition Author(s): Parkash, V., Leppanen, V.-M., Virtanen, H., Jurvansuu, J.-M., Bespalov, M.M., Sidorova, Y.A., Runeberg-Roos, P., Saarma, M., Goldman, A.

Revision History  

• Version 1.0: 2008-10-21
  Type: Initial release
  
• Version 1.1: 2014-02-05
  Changes: Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary
• Version 2.1: 2023-12-13
  Changes: Data collection, Database references, Refinement description, Structure summary