5NAZ

Crystal structures of homooligomers of collagen type IV. alpha5NC1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.3 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
  • Primary Citation of Related Structures:  

  • 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

    Department of Medicine at Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,CIBER de Enfermedades Raras (CIBERER-ISCIII), Spain.,Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Vanderbilt Institute of Chemical Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Department of Biochemistry and Molecular Biology/ERI BIOTECMED, Universitat de València, Dr Moliner 50, Burjassot, 46100 Valencia, Spain.,Department of Defense, Center for Prostate Disease Research, Bethesda, Maryland, USA.,Laboratorio de Reconocimiento Molecular, Centro de Investigación Príncipe Felipe, Eduardo Primo Yúfera 3, 46012 Valencia, Spain.,Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), Jaume Roig 11, 46010 Valencia, Spain.,Department of Biochemistry, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,BioStratum Inc., Durham, North Carolina, USA.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Departamento de Bioquímica y Biología Molecular at Facultad de Medicina y Odontología, Universitat de València, Blasco Ibáñez 15-17, 46010 Valencia, Spain.,Departamento de Microbiología, Facultad de Medicina at Universitat de València, Blasco Ibáñez 17, 46010 Valencia, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Collagen alpha-5(IV) chain
A
229Homo sapiensMutation(s): 0 
Gene Names: COL4A5
Find proteins for P29400 (Homo sapiens)
Go to Gene View: COL4A5
Go to UniProtKB:  P29400
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
PG4
Query on PG4

Download SDF File 
Download CCD File 
A
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.185 
  • Space Group: P 41 3 2
Unit Cell:
Length (Å)Angle (°)
a = 121.283α = 90.00
b = 121.283β = 90.00
c = 121.283γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHASERphasing
REFMACrefinement
SCALAdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



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

Revision History 

  • Version 1.0: 2018-09-12
    Type: Initial release
  • Version 1.1: 2018-10-24
    Type: Data collection, Database references
  • Version 1.2: 2018-11-28
    Type: Data collection, Database references
  • Version 1.3: 2019-10-09
    Type: Data collection