Crystal structures of homooligomers of collagen type IV. alpha1NC1

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

Starting Model: experimental
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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: https://doi.org/10.1107/S2052252518012459
  • Primary Citation of Related Structures:  
    5NAX, 5NAY, 5NAZ, 5NB0, 5NB1, 5NB2

  • 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-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

    Department of Biochemistry and Molecular Biology/ERI BIOTECMED, Universitat de València, Dr Moliner 50, Burjassot, 46100 Valencia, Spain.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Collagen alpha-1(IV) chain
A, B, C, D, E
A, B, C, D, E, F
229Homo sapiensMutation(s): 0 
Gene Names: COL4A1
UniProt & NIH Common Fund Data Resources
Find proteins for P02462 (Homo sapiens)
Explore P02462 
Go to UniProtKB:  P02462
GTEx:  ENSG00000187498 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02462
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SO4

Download Ideal Coordinates CCD File 
K [auth A]
O [auth B]
R [auth C]
T [auth D]
U [auth D]
K [auth A],
O [auth B],
R [auth C],
T [auth D],
U [auth D],
W [auth E],
X [auth E],
Z [auth F]
O4 S
Query on CL

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
L [auth B]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
L [auth B],
M [auth B],
N [auth B],
P [auth C],
Q [auth C],
S [auth D],
V [auth E],
Y [auth F]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.851α = 90
b = 127.045β = 90
c = 130.543γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpainBIO2013-42619-P
Spanish Ministry of Economy and CompetitivenessSpainBFU2016-78606-P

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2019-10-09
    Changes: Data collection
  • Version 1.4: 2024-01-17
    Changes: Data collection, Database references, Refinement description