PDBsum entry 1ndx

Structural protein

PDB id: 1ndx

Contents

Protein chain

266 a.a.

Theoretical model

PDB id:

1ndx

Name:

Structural protein

Title:

Theoretical model of human nidogen ywtd beta-propeller domain

Structure:

Nidogen. Chain: a. Fragment: ywtd domain. Synonym: entactin

Source:

Homo sapiens. Human. Cellular_location: extracellular

Authors:

T.A.Springer

Key ref:

T.A.Springer (1998). An extracellular beta-propeller module predicted in lipoprotein and scavenger receptors, tyrosine kinases, epidermal growth factor precursor, and extracellular matrix components. J Mol Biol, 283, 837-862. PubMed id: 9790844 DOI: 10.1006/jmbi.1998.2115

Date:

15-Sep-98 Release date: 16-Dec-98

Protein chain

P14543  (NID1_HUMAN) -  Nidogen-1

Seq: 1247 a.a.

Struc: 266 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1006/jmbi.1998.2115

J Mol Biol 283:837-862 (1998)

PubMed id: 9790844

An extracellular beta-propeller module predicted in lipoprotein and scavenger receptors, tyrosine kinases, epidermal growth factor precursor, and extracellular matrix components.

T.A.Springer.

ABSTRACT

An abundant, widely dispersed, extracellular sequence repeat that contains a consensus YWTD motif is shown here to occur in groups of six contiguous repeats. Thirteen lines of evidence, including experimental and computational data, predict with p<3x10(-9) that the repeats do not form tandem domains, but rather each group of six repeats folds into a compact beta-propeller structure. The six beta-sheets are arranged about a 6-fold pseudosymmetry axis, and each repeat contributes loops to the faces surrounding the pseudosymmetry axis. Seven different endocytic receptors that contain from one to eight YWTD beta-propeller domains act as lipoprotein, vitellogenin, and scavenger receptors. In the low density lipoprotein receptor (LDLR), the many mutations in familial hypercholesterolaemia that map to the YWTD domain can now be interpreted. In the extracellular matrix component nidogen, the YWTD domain functions to bind laminin. Three YWTD domains and interspersed fibronectin type III (FN3) domains constitute almost the entire extracellular domain of the sevenless and c-ros receptor tyrosine kinases. YWTD domains often are bounded by epidermal growth factor (EGF) modules, including in the EGF precursor itself. YWTD beta-propellers have a circular folding pattern that brings neighboring modules into close proximity, and may have important consequences for the architecture of multi-domain proteins.

Selected figure(s)

Figure 4.
Figure 4. Topology and ribbon diagrams of the six-bladed β-propeller domain predicted for the YWTD domain of nidogen. A, Topology diagram, with each β-sheet given a different color. Sequence repeats are separated by vertical broken lines. Note the offset between sequence repeats and β-sheets. Each sheet is termed a W, with each β-strand representing one leg of the W. β-Strands are represented by arrows. The disulfide bonds in nidogen between strands 2 and 3 of W4 and between the 1-2 loop of W1 and the C-terminal segment in W6 are shown as gold lines. B, Stereo view ribbon representation, with each β-sheet or blade of the nidogen β-propeller model given the same color code as in A. The 4-1 loops that connect each sheet are grey. The view is up the 6-fold pseudosymmetry axis, with the “bottom” of the propeller containing the strand 1 to 2 loops, the strand 3 to 4 loops, and the N and C termini of the propeller domain in the foreground. C, Side view, with the 1-2, 3-4, and N and C termini upward. The side-chain bonds for the cysteine residues in the two disulfide bonds of the nidogen β-propeller domain are shown in gold. The β-strands shown as ribbons are as defined by DSSP [Kabsch and Sander 1983] from the nido model (see Figure 7 and Table 6). Prepared with MOLMOL [Koradi et al 1996].

Figure 6.
Figure 6. Threading scores for YWTD domains. A and B, Average Z-scores for 89 YWTD domains related to LDLR (A) and 18 YWTD domains from sevenless and c-ros (B). Z-scores for each structure were averaged for the 89 or 18 sequences using a program written by Kemin Tan, and plotted with the histogram tool of Microsoft Excel. The arrows mark 1gotB1. C, The distribution of Z-scores for all 107 YWTD domain sequences for the second highest hit, 2aaiB0, ricin β-trefoil domain; and the top hit, 1gotB1, G protein β-propeller domain.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 283, 837-862) copyright 1998.

Figures were selected by an automated process.