4B90 | pdb_00004b90

Crystal structure of WT human CRMP-5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.221 (Depositor), 0.225 (DCC) 
  • R-Value Work: 
    0.180 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.182 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Insights Into the Oligomerization of Crmps: Crystal Structure of Human Collapsin Response Mediator Protein 5.

Ponnusamy, R.Lohkamp, B.

(2013) J Neurochem 125: 855

  • DOI: https://doi.org/10.1111/jnc.12188
  • Primary Citation Related Structures: 
    4B90, 4B91, 4B92

  • PubMed Abstract: 

    Collapsin response mediator protein-5 (CRMP-5) is the latest identified member of the CRMP cytosolic phosphoprotein family, which is crucial for neuronal development and repair. CRMPs exist as homo- and/or hetero-tetramers in vivo and participate in signaling transduction, cytoskeleton rearrangements, and endocytosis. CRMP-5 antagonizes many of the other CRMPs' functions either by directly interacting with them or by competing for their binding partners. We determined the crystal structures of a full length and a truncated version of human CRMP-5, both of which form a homo-tetramer similar to those observed in CRMP-1 and CRMP-2. However, solution studies indicate that CRMP-5 and CRMP-1 form weaker homo-tetramers compared with CRMP-2, and that divalent cations, Ca(2+) and Mg(2+), destabilize oligomers of CRMP-5 and CRMP-1, but promote CRMP-2 oligomerization. On the basis of comparative analysis of the CRMP-5 crystal structure, we identified residues that are crucial for determining the preference for hetero-oligomer or homo-oligomer formation. We also show that in spite of being the CRMP family member most closely related to dihydropyrimidinase, CRMP-5 does not have any detectable amidohydrolase activity. The presented findings provide new detailed insights into the structure, oligomerization, and regulation of CRMPs.


  • Organizational Affiliation
    • Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.

Macromolecule Content 

  • Total Structure Weight: 128.25 kDa 
  • Atom Count: 7,716 
  • Modeled Residue Count: 970 
  • Deposited Residue Count: 1,172 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DIHYDROPYRIMIDINASE-RELATED PROTEIN 5
A, B
586Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BPU6 (Homo sapiens)
Explore Q9BPU6 
Go to UniProtKB:  Q9BPU6
PHAROS:  Q9BPU6
GTEx:  ENSG00000157851 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BPU6
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.221 (Depositor), 0.225 (DCC) 
  • R-Value Work:  0.180 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.182 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.15α = 90
b = 90.15β = 90
c = 247.76γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-13
    Type: Initial release
  • Version 1.1: 2013-06-19
    Changes: Database references
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description