2VM8 | pdb_00002vm8

Human CRMP-2 crystallised in the presence of Mg

• PDB DOI: https://doi.org/10.2210/pdb2VM8/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-01-24 Released: 2008-08-26 
• Deposition Author(s): Kursula, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.325 (Depositor), 0.315 (DCC) 
• R-Value Work: 
  0.256 (Depositor) 
• R-Value Observed: 
  0.259 (Depositor) 

Starting Model: experimental

Literature

Crystal and Solution Structure, Stability and Post- Translational Modifications of Collapsin Response Mediator Protein 2.

Majava, V., Loytynoja, N., Chen, W.Q., Lubec, G., Kursula, P.

(2008) FEBS J 275: 4583

• PubMed: 18699782 
• DOI: https://doi.org/10.1111/j.1742-4658.2008.06601.x
• Primary Citation Related Structures: 
  2VM8


• PubMed Abstract: 
  

  The collapsin response mediator protein 2 (CRMP-2) is a central molecule regulating axonal growth cone guidance. It interacts with the cytoskeleton and mediates signals related to myelin-induced axonal growth inhibition. CRMP-2 has also been characterized as a constituent of neurofibrillary tangles in Alzheimer's disease. CD spectroscopy and thermal stability assays using the Thermofluor method indicated that Ca2+ and Mg2+ affect the stability of CRMP-2 and prevent the formation of beta-aggregates upon heating. Gel filtration showed that the presence of Ca2+ or Mg2+ promoted the formation of CRMP-2 homotetramers, and this was further proven by small-angle X-ray scattering experiments, where a 3D solution structure for CRMP-2 was obtained. Previously, we described a crystal structure of human CRMP-2 complexed with calcium. In the present study, we determined the structure of CRMP-2 in the absence of calcium at 1.9 A resolution. When Ca2+ was omitted, crystals could only be grown in the presence of Mg2+ ions. By a proteomic approach, we further identified a number of post-translational modifications in CRMP-2 from rat brain hippocampus and mapped them onto the crystal structure.

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Organizational Affiliation: 
• Department of Biochemistry, University of Oulu, Finland.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 220.46 kDa 
• Atom Count: 16,539 
• Modeled Residue Count: 1,905 
• Deposited Residue Count: 2,004 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DIHYDROPYRIMIDINASE-RELATED PROTEIN 2	A, B, C, D	501	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q16555 (Homo sapiens) Explore Q16555  Go to UniProtKB:  Q16555
PHAROS:  Q16555 GTEx:  ENSG00000092964

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	E [auth A], F [auth B], G [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.325 (Depositor), 0.315 (DCC) 
• R-Value Work:  0.256 (Depositor) 
• R-Value Observed: 0.259 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.51	α = 90
b = 126.24	β = 90
c = 209.75	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-26 
Deposition Author(s): Kursula, P.

Revision History  

• Version 1.0: 2008-08-26
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-17
  Changes: Data collection
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description