5IKC

X-RAY STRUCTURE OF THE N-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN in complex with FAB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 

wwPDB Validation 3D Report Full Report



Literature

Crystal Structures of the Human Doublecortin C- and N-terminal Domains in Complex with Specific Antibodies.

Burger, D.Stihle, M.Sharma, A.Di Lello, P.Benz, J.D'Arcy, B.Debulpaep, M.Fry, D.Huber, W.Kremer, T.Laeremans, T.Matile, H.Ross, A.Rufer, A.C.Schoch, G.Steinmetz, M.O.Steyaert, J.Rudolph, M.G.Thoma, R.Ruf, A.

(2016) J Biol Chem 291: 16292-16306

  • DOI: 10.1074/jbc.M116.726547
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Doublecortin is a microtubule-associated protein produced during neurogenesis. The protein stabilizes microtubules and stimulates their polymerization, which allows migration of immature neurons to their designated location in the brain. Mutations in ...

    Doublecortin is a microtubule-associated protein produced during neurogenesis. The protein stabilizes microtubules and stimulates their polymerization, which allows migration of immature neurons to their designated location in the brain. Mutations in the gene that impair doublecortin function and cause severe brain formation disorders are located on a tandem repeat of two doublecortin domains. The molecular mechanism of action of doublecortin is only incompletely understood. Anti-doublecortin antibodies, such as the rabbit polyclonal Abcam 18732, are widely used as neurogenesis markers. Here, we report the generation and characterization of antibodies that bind to single doublecortin domains. The antibodies were used as tools to obtain structures of both domains. Four independent crystal structures of the N-terminal domain reveal several distinct open and closed conformations of the peptide linking N- and C-terminal domains, which can be related to doublecortin function. An NMR assignment and a crystal structure in complex with a camelid antibody fragment show that the doublecortin C-terminal domain adopts the same well defined ubiquitin-like fold as the N-terminal domain, despite its reported aggregation and molten globule-like properties. The antibodies' unique domain specificity also renders them ideal research tools to better understand the role of individual domains in doublecortin function. A single chain camelid antibody fragment specific for the C-terminal doublecortin domain affected microtubule binding, whereas a monoclonal mouse antibody specific for the N-terminal domain did not. Together with steric considerations, this suggests that the microtubule-interacting doublecortin domain observed in cryo-electron micrographs is the C-terminal domain rather than the N-terminal one.


    Organizational Affiliation

    From the pRED Pharma Research and Early Development, Therapeutic Modalities, and armin.ruf@roche.com.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MAb 6H10 light chainA, L213Mus musculusMutation(s): 0 
Gene Names: LC
Find proteins for A0A0U5BC76 (Mus musculus)
Explore A0A0U5BC76 
Go to UniProtKB:  A0A0U5BC76
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Neuronal migration protein doublecortinM, N90Homo sapiensMutation(s): 0 
Gene Names: DCXDBCNLISX
Find proteins for O43602 (Homo sapiens)
Explore O43602 
Go to UniProtKB:  O43602
NIH Common Fund Data Resources
PHAROS  O43602
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ighg proteinB, H215Mus musculusMutation(s): 0 
Gene Names: Ighg
Find proteins for Q569X1 (Mus musculus)
Explore Q569X1 
Go to UniProtKB:  Q569X1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download CCD File 
B, H
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
B,HL-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.858α = 90
b = 110.399β = 106.54
c = 75.092γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-05-18
    Type: Initial release
  • Version 1.1: 2016-06-08
    Changes: Database references
  • Version 1.2: 2016-12-14
    Changes: Structure summary
  • Version 2.0: 2020-03-11
    Changes: Polymer sequence