2UUR

N-terminal NC4 domain of collagen IX

Summary for 2UUR

• Entry DOI: 10.2210/pdb2uur/pdb
• Descriptor: COLLAGEN ALPHA-1(IX) CHAIN, ZINC ION, SULFATE ION, ... (5 entities in total)
• Functional Keywords: glycoprotein, hydroxylation, structural protein, nc4, collagen, collagen ix, polymorphism, extracellular matrix, alternative splicing
• Biological source: HOMO SAPIENS (HUMAN)
• Cellular location: Secreted, extracellular space, extracellular matrix (By similarity): P20849
• Total number of polymer chains: 1
• Total formula weight: 27955.04

Authors

Leppanen, V.-M.,Tossavainen, H.,Permi, P.,Lehtio, L.,Ronnholm, G.,Goldman, A.,Kilpelainen, I.,Pihlajamaa, T. (deposition date: 2007-03-07, release date: 2007-06-05, Last modification date: 2024-11-20)

Primary citation

Leppanen, V.-M.,Tossavainen, H.,Permi, P.,Lehtio, L.,Ronnholm, G.,Goldman, A.,Kilpelainen, I.,Pihlajamaa, T.
Crystal Structure of the N-Terminal Nc4 Domain of Collagen Ix, a Zinc Binding Member of the Laminin-Neurexin-Sex Hormone Binding Globulin (Lns) Domain Family.
J.Biol.Chem., 282:23219-, 2007

PubMed Abstract: Collagen IX, located on the surface of collagen fibrils, is crucial for cartilage integrity and stability. The N-terminal NC4 domain of the alpha1(IX) chain is probably important in this because it interacts with various macromolecules such as proteoglycans and cartilage oligomeric matrix protein. At least 17 distinct collagen polypeptides carry an NC4-like unit near their N terminus, but this report, describing the crystal structure of NC4 at 1.8-A resolution, represents the first atomic level structure for these domains. The structure is similar to previously characterized laminin-neurexin-sex hormone binding globulin (LNS) structures, dominated by an antiparallel beta-sheet sandwich. In addition, a zinc ion was found in a position similar to that of the metal binding site of other LNS domains. A partial backbone NMR assignment of NC4 was obtained and utilized in NMR titration studies to investigate the zinc binding in solution state and to quantitate the affinity of metal binding. The K(d) of 11.5 mM suggests a regulatory rather than a structural role for zinc in solution. NMR titration with a heparin tetrasaccharide revealed the presence of a secondary binding site for heparin on NC4, showing structural and functional conservation with thrombospondin-1, but a markedly reduced affinity for the ligand. Also the overall arrangement of the N and C termini of NC4 resembles most closely the N-terminal domain of thrombospondin-1, distinguishing the two from the majority of the published LNS structures.

PubMed: 17553797
DOI: 10.1074/JBC.M702514200

Experimental method

X-RAY DIFFRACTION (1.8 Å)