6S4C | pdb_00006s4c

Crystal Structure of the vWFA2 subdomain of type VII collagen

• PDB DOI: https://doi.org/10.2210/pdb6S4C/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-06-27 Released: 2020-02-19 
• Deposition Author(s): Gebauer, J.M., Flachsenberg, F., Baumann, U., Seeger, K.
• Funding Organization(s): German Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Structural and biophysical characterization of the type VII collagen vWFA2 subdomain leads to identification of two binding sites.

Gebauer, J.M., Flachsenberg, F., Windler, C., Richer, B., Baumann, U., Seeger, K.

(2020) FEBS Open Bio 10: 580-592

• PubMed: 32031736 
• DOI: https://doi.org/10.1002/2211-5463.12807
• Primary Citation Related Structures: 
  6S4C


• PubMed Abstract: 
  

  Type VII collagen is an extracellular matrix protein, which is important for skin stability; however, detailed information at the molecular level is scarce. The second vWFA (von Willebrand factor type A) domain of type VII collagen mediates important interactions, and immunization of mice induces skin blistering in certain strains. To understand vWFA2 function and the pathophysiological mechanisms leading to skin blistering, we structurally characterized this domain by X-ray crystallography and NMR spectroscopy. Cell adhesion assays identified two new interactions: one with β1 integrin via its RGD motif and one with laminin-332. The latter interaction was confirmed by surface plasmon resonance with a K _D of about 1 mm. These data show that vWFA2 has additional functions in the extracellular matrix besides interacting with type I collagen.

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Organizational Affiliation: 
• Institute of Biochemistry, University of Cologne, Germany.
Institute of Chemistry and Metabolomics, University of Lübeck, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 21.24 kDa 
• Atom Count: 1,572 
• Modeled Residue Count: 185 
• Deposited Residue Count: 196 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Collagen alpha-1(VII) chain	A	196	Mus musculus	Mutation(s): 0  Gene Names: Col7a1
UniProt
Find proteins for Q63870 (Mus musculus) Explore Q63870  Go to UniProtKB:  Q63870

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDT	C [auth A]	{[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID C10 H16 N2 O8 KCXVZYZYPLLWCC-UHFFFAOYSA-N
PO4	E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG	B [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.207 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.034	α = 90
b = 123.034	β = 90
c = 63.749	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
ARP/wARP	model building
PDB_EXTRACT	data extraction
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-02-19 
Deposition Author(s): Gebauer, J.M., Flachsenberg, F., Baumann, U., Seeger, K.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	SFB829
German Research Foundation	Germany	EXC 306
German Research Foundation	Germany	RTG1727

Revision History  

• Version 1.0: 2020-02-19
  Type: Initial release
  
• Version 1.1: 2020-04-15
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description