6MPX

Twelve chloride ions induce formation and stabilize the NC1 hexamer of collagen IV assembled from transition state trimers


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A chloride ring is an ancient evolutionary innovation mediating the assembly of the collagen IV scaffold of basement membranes.

Pedchenko, V.Bauer, R.Pokidysheva, E.N.Al-Shaer, A.Forde, N.R.Fidler, A.L.Hudson, B.G.Boudko, S.P.

(2019) J.Biol.Chem. 294: 7968-7981

  • DOI: 10.1074/jbc.RA119.007426

  • PubMed Abstract: 
  • Collagen IV scaffold is a principal component of the basement membrane (BM), a specialized extracellular matrix that is essential for animal multicellularity and tissue evolution. Scaffold assembly begins with the trimerization of α-chains into proto ...

    Collagen IV scaffold is a principal component of the basement membrane (BM), a specialized extracellular matrix that is essential for animal multicellularity and tissue evolution. Scaffold assembly begins with the trimerization of α-chains into protomers inside the cell, which then are secreted and undergo oligomerization outside the cell. For the ubiquitous scaffold composed of α1- and α2-chains, both intracellular and extracellular stages are mediated by the noncollagenous domain (NC1). The association of protomers is chloride-dependent, whereby chloride ions induce interactions of the protomers' trimeric NC1 domains leading to NC1 hexamer formation. Here, we investigated the mechanisms, kinetics, and functionality of the chloride ion-mediated protomer assembly by using a single-chain technology to produce a stable NC1 trimer comprising α1, α2, and α1 NC1 monomers. We observed that in the presence of chloride, the single-chain NC1-trimer self-assembles into a hexamer, for which the crystal structure was determined. We discovered that a chloride ring, comprising 12 ions, induces the assembly of and stabilizes the NC1 hexamer. Furthermore, we found that the chloride ring is evolutionarily conserved across all animals, first appearing in cnidarians. These findings reveal a fundamental role for the chloride ring in the assembly of collagen IV scaffolds of BMs, a critical event enabling tissue evolution and development. Moreover, the single-chain technology is foundational for generating trimeric NC1 domains of other α-chain compositions to investigate the α121, α345, and α565 collagen IV scaffolds and to develop therapies for managing Alport syndrome, Goodpasture's disease, and cancerous tumor growth.


    Organizational Affiliation

    From the Department of Medicine, Division of Nephrology and Hypertension.,Vanderbilt Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, Tennessee 37232.,Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232.,Physics, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.,Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, and.,the Aspirnaut Program.,Vanderbilt-Ingram Cancer Center.,Departments of Pathology, Microbiology, and Immunology and.,From the Department of Medicine, Division of Nephrology and Hypertension, sergey.budko@vanderbilt.edu.,the Departments of Molecular Biology and Biochemistry and.,the Department of Biochemistry.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
fusion protein of non-collagenous domains of collagen type IV
A
693Homo sapiensMutation(s): 0 
Gene Names: COL4A1, COL4A2
Find proteins for P02462 (Homo sapiens)
Go to Gene View: COL4A1
Go to UniProtKB:  P02462
Find proteins for P08572 (Homo sapiens)
Go to Gene View: COL4A2
Go to UniProtKB:  P08572
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
P6G
Query on P6G

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A
HEXAETHYLENE GLYCOL
POLYETHYLENE GLYCOL PEG400
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

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A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.148 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 121.160α = 90.00
b = 121.160β = 90.00
c = 106.020γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesRDK18381-45
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United States5T32DK007569-30

Revision History 

  • Version 1.0: 2019-04-03
    Type: Initial release
  • Version 1.1: 2019-04-10
    Type: Data collection, Database references
  • Version 1.2: 2019-05-29
    Type: Data collection, Database references
  • Version 1.3: 2019-12-25
    Type: Author supporting evidence