5NAX

Crystal structures of homooligomers of the non-collagenous domains of collagen type IV. alpha121NC1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.143 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structures of collagen IV globular domains: insight into associated pathologies, folding and network assembly.

Casino, P.Gozalbo-Rovira, R.Rodriguez-Diaz, J.Banerjee, S.Boutaud, A.Rubio, V.Hudson, B.G.Saus, J.Cervera, J.Marina, A.

(2018) IUCrJ 5: 765-779

  • DOI: 10.1107/S2052252518012459
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Basement membranes are extracellular structures of epithelia and endothelia that have collagen IV scaffolds of triple α-chain helical protomers that associate end-to-end, forming networks. The molecular mechanisms by which the noncollagenous C-termin ...

    Basement membranes are extracellular structures of epithelia and endothelia that have collagen IV scaffolds of triple α-chain helical protomers that associate end-to-end, forming networks. The molecular mechanisms by which the noncollagenous C-terminal domains of α-chains direct the selection and assembly of the α1α2α1 and α3α4α5 hetero-oligomers found in vivo remain obscure. Autoantibodies against the noncollagenous domains of the α3α4α5 hexamer or mutations therein cause Goodpasture's or Alport's syndromes, respectively. To gain further insight into oligomer-assembly mechanisms as well as into Goodpasture's and Alport's syndromes, crystal structures of non-collagenous domains produced by recombinant methods were determined. The spontaneous formation of canonical homohexamers (dimers of trimers) of these domains of the α1, α3 and α5 chains was shown and the components of the Goodpasture's disease epitopes were viewed. Crystal structures of the α2 and α4 non-collagenous domains generated by recombinant methods were also determined. These domains spontaneously form homo-oligomers that deviate from the canonical architectures since they have a higher number of subunits (dimers of tetramers and of hexamers, respectively). Six flexible structural motifs largely explain the architectural variations. These findings provide insight into noncollagenous domain folding, while supporting the in vivo operation of extrinsic mechanisms for restricting the self-assembly of noncollagenous domains. Intriguingly, Alport's syndrome missense mutations concentrate within the core that nucleates the folding of the noncollagenous domain, suggesting that this syndrome, when owing to missense changes, is a folding disorder that is potentially amenable to pharmacochaperone therapy.


    Organizational Affiliation

    CIBER de Enfermedades Raras (CIBERER-ISCIII), Spain.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Collagen alpha-1(IV) chainA, B, D, F229Homo sapiensMutation(s): 0 
Gene Names: COL4A1
Find proteins for P02462 (Homo sapiens)
Explore P02462 
Go to UniProtKB:  P02462
NIH Common Fund Data Resources
PHAROS  P02462
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Collagen alpha-2(IV) chainC, E228Homo sapiensMutation(s): 0 
Gene Names: COL4A2
Find proteins for P08572 (Homo sapiens)
Explore P08572 
Go to UniProtKB:  P08572
NIH Common Fund Data Resources
PHAROS  P08572
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 
A, B, C, D, E, F
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.143 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.148α = 90
b = 126.148β = 90
c = 216.211γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-02-28 
  • Released Date: 2018-09-12 
  • Deposition Author(s): Casino, P., Marina, A.

Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpainBIO2013-42619-P
Spanish Ministry of Economy and CompetitivenessSpainBFU2016-78606-P
European UnionSpainFP7/2007-2013

Revision History 

  • Version 1.0: 2018-09-12
    Type: Initial release
  • Version 1.1: 2018-10-24
    Changes: Data collection, Database references
  • Version 1.2: 2018-11-28
    Changes: Data collection, Database references