PDBsum entry: 1kex

Protein binding

PDB id: 1kex

Contents

Protein chain

155 a.a. *

Waters ×201

* Residue conservation analysis

PDB id:

1kex

Name:

Protein binding

Title:

Crystal structure of the b1 domain of human neuropilin-1

Structure:

Neuropilin-1. Chain: a. Fragment: b1 domain. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: nrp1. Expressed in: trichoplusia ni. Expression_system_taxid: 7111.

Resolution:

1.90Å R-factor: 0.189 R-free: 0.266

Authors:

C.C.Lee,A.Kreusch,D.Mcmullan,K.Ng,G.Spraggon

Key ref:

C.C.Lee et al. (2003). Crystal structure of the human neuropilin-1 b1 domain. Structure, 11, 99. PubMed id: 12517344 DOI: 10.1016/S0969-2126(02)00941-3

Date:

18-Nov-01 Release date: 28-Jan-03

Protein chain

O14786  (NRP1_HUMAN) -  Neuropilin-1

Seq: 923 a.a.

Struc: 155 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: cell adhesion (1 term)

DOI no: 10.1016/S0969-2126(02)00941-3

Structure 11:99 (2003)

PubMed id: 12517344

Crystal structure of the human neuropilin-1 b1 domain.

C.C.Lee, A.Kreusch, D.McMullan, K.Ng, G.Spraggon.

ABSTRACT

Neuropilin-1 (Npn-1) is a type I cell surface receptor involved in a broad range of developmental processes, including axon guidance, angiogenesis, and heterophilic cell adhesion. We have determined the crystal structure of the human Npn-1 b1 domain to 1.9 A. The overall structure resembles coagulation factor V and VIII (F5/8) C1 and C2 domains, exhibiting a distorted jellyroll fold. Details of the structure provide insight to b1 domain regions responsible for ligand binding and facilitate rationalization of existing biochemical binding data. A polar cleft formed by adjacent loops at one end of the molecule in conjunction with flanking electronegative surfaces may represent the binding site for the positively charged tails of semaphorins and VEGF(165). The nature of the cell adhesion binding site of the b1 domain can be visualized in context of the structure.

Selected figure(s)

Figure 4.
Figure 4. C-a Backbone Diagram Showing Six Loop Regions that form the Putative Binding GrooveThe molecule is viewed in an orientation rotated 180 degrees along the long central axis from that in Figure 3A, with the loop and cleft region tilted outward from the plane of the paper toward the viewer. Loop 1, blue; loop 2, yellow; loop 3, red; loop 4, orange; loop 5, brown; loop 6, purple. Representative side chains are displayed and described in the text. The figure was created with the program Setor.

The above figure is reprinted by permission from Cell Press: Structure (2003, 11, 99-0) copyright 2003.

Figure was selected by an automated process.