Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: homology

Macromolecule Content

• Total Structure Weight: 153.34 kDa 
• Atom Count: 11453 
• Residue Count: 1370 
• Unique protein chains: 1

5NAY

Crystal structures of homooligomers of collagen type IV. alpha1NC1

• DOI: 10.2210/pdb5NAY/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2017-02-28 Released: 2018-09-12 
• Deposition Author(s): Casino, P., Marina, A.
• Funding Organization(s): Spanish Ministry of Economy and Competitiveness

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.199 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 

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

• PubMed: 30443360 
• DOI: 10.1107/S2052252518012459
• Primary Citation of Related Structures:  
  5NAY, 5NAX, 5NAZ, 5NB2, 5NB1, 5NB0


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Collagen alpha-1(IV) chain	A, B, C, D, E, F	229	Homo sapiens	Mutation(s): 0  Gene Names: COL4A1
Find proteins for P02462 (Homo sapiens) Explore P02462  Go to UniProtKB:  P02462
NIH Common Fund Data Resources
PHAROS:  P02462 GTEx:  ENSG00000187498

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	A, B, C, D, E, F	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	A, B, C, D, E, F	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 94.851	α = 90
b = 127.045	β = 90
c = 130.543	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

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

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Funding Organization	Location	Grant Number
Spanish Ministry of Economy and Competitiveness	Spain	BIO2013-42619-P
Spanish Ministry of Economy and Competitiveness	Spain	BFU2016-78606-P

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
• Version 1.3: 2019-10-09
  Changes: Data collection