1M3D

Structure of Type IV Collagen NC1 Domains


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of NC1 Domains. Structural Basis for Type IV Collagen Assembly in Basement Membranes

Sundaramoorthy, M.Meiyappan, M.Todd, P.Hudson, B.G.

(2002) J.Biol.Chem. 277: 31142-31153

  • DOI: 10.1074/jbc.M201740200

  • PubMed Abstract: 
  • Type IV collagen, which is present in all metazoan, exists as a family of six homologous alpha(IV) chains, alpha1-alpha6, in mammals. The six chains assemble into three different triple helical protomers and self-associate as three distinct networks. ...

    Type IV collagen, which is present in all metazoan, exists as a family of six homologous alpha(IV) chains, alpha1-alpha6, in mammals. The six chains assemble into three different triple helical protomers and self-associate as three distinct networks. The network underlies all epithelia as a component of basement membranes, which play important roles in cell adhesion, growth, differentiation, tissue repair and molecular ultrafiltration. The specificity of both protomer and network assembly is governed by amino acid sequences of the C-terminal noncollagenous (NC1) domain of each chain. In this study, the structural basis for protomer and network assembly was investigated by determining the crystal structure of the ubiquitous [(alpha1)(2).alpha2](2) NC1 hexamer of bovine lens capsule basement membrane at 2.0 A resolution. The NC1 monomer folds into a novel tertiary structure. The (alpha1)(2).alpha2 trimer is organized through the unique three-dimensional domain swapping interactions. The differences in the primary sequences of the hypervariable region manifest in different secondary structures, which determine the chain specificity at the monomer-monomer interfaces. The trimer-trimer interface is stabilized by the extensive hydrophobic and hydrophilic interactions without a need for disulfide cross-linking.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160-7421, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Type IV Collagen Noncollagenous Domain- Alpha1
A, B, D, E, G, H, J, K
229Bos taurusGene Names: COL4A1
Find proteins for Q7SIB2 (Bos taurus)
Go to Gene View: COL4A1
Go to UniProtKB:  Q7SIB2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Type IV Collagen Noncollagenous Domain- Alpha2
C, F, I, L
227Bos taurusGene Names: COL4A2
Find proteins for Q7SIB3 (Bos taurus)
Go to Gene View: COL4A2
Go to UniProtKB:  Q7SIB3
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, D, E, G, H, J, K
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BR
Query on BR

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
LU
Query on LU

Download SDF File 
Download CCD File 
C, F, I, L
LUTETIUM (III) ION
LU
Lu
PSDMOPINLDTFSZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.169 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 80.069α = 90.00
b = 137.963β = 90.31
c = 127.131γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-01-07
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance