PDBsum entry 3mjg

Hormone/transferase

PDB id: 3mjg

Contents

Protein chains

97 a.a. *

274 a.a. *

Ligands

NDG

NAG ×13

Waters ×1170

* Residue conservation analysis

PDB id:

3mjg

Name:

Hormone/transferase

Title:

The structure of a platelet derived growth factor receptor complex

Structure:

Platelet-derived growth factor subunit b. Chain: a, b. Fragment: unp residues 21-185. Synonym: pdgf subunit b, platelet-derived growth factor b chain, platelet-derived growth factor beta polypeptide, pdgf-2, proto- oncogenE C-sis. Engineered: yes. Beta-type platelet-derived growth factor receptor. Chain: x, y.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: pdgf2, pdgfb, sis. Expressed in: homo sapiens. Expression_system_taxid: 9606. Expression_system_cell_line: embryonic kidney-293 cells. Gene: pdgfrb. Expression_system_cell_line: embryonic kidney-293 cells

Resolution:

2.30Å R-factor: 0.237 R-free: 0.277

Authors:

A.H.R.Shim,X.He

Key ref:

A.H.Shim et al. (2010). Structures of a platelet-derived growth factor/propeptide complex and a platelet-derived growth factor/receptor complex. Proc Natl Acad Sci U S A, 107, 11307-11312. PubMed id: 20534510

Date:

12-Apr-10 Release date: 16-Jun-10

Protein chains

P01127  (PDGFB_HUMAN) -  Platelet-derived growth factor subunit B from Homo sapiens

Seq: 241 a.a.

Struc: 97 a.a.

Protein chains

P09619  (PGFRB_HUMAN) -  Platelet-derived growth factor receptor beta from Homo sapiens

Seq: 1106 a.a.

Struc: 274 a.a.

Enzyme reactions

• Enzyme class: Chains X, Y: E.C.2.7.10.1 - receptor protein-tyrosine kinase.
• Reaction: L-tyrosyl-[protein] + ATP = O-phospho-L-tyrosyl-[protein] + ADP + H⁺

L-tyrosyl-[protein] + ATP = O-phospho-L-tyrosyl-[protein] (Bound ligand (Het Group name = NDG) matches with 41.38% similarity) + ADP + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

Proc Natl Acad Sci U S A 107:11307-11312 (2010)

PubMed id: 20534510

Structures of a platelet-derived growth factor/propeptide complex and a platelet-derived growth factor/receptor complex.

A.H.Shim, H.Liu, P.J.Focia, X.Chen, P.C.Lin, X.He.

ABSTRACT

Platelet-derived growth factors (PDGFs) and their receptors (PDGFRs) are prototypic growth factors and receptor tyrosine kinases which have critical functions in development. We show that PDGFs share a conserved region in their prodomain sequences which can remain noncovalently associated with the mature cystine-knot growth factor domain after processing. The structure of the PDGF-A/propeptide complex reveals this conserved, hydrophobic association mode. We also present the structure of the complex between PDGF-B and the first three Ig domains of PDGFRbeta, showing that two PDGF-B protomers clamp PDGFRbeta at their dimerization seam. The PDGF-B:PDGFRbeta interface is predominantly hydrophobic, and PDGFRs and the PDGF propeptides occupy overlapping positions on mature PDGFs, rationalizing the need of propeptides by PDGFs to cover functionally important hydrophobic surfaces during secretion. A large-scale structural organization and rearrangement is observed for PDGF-B upon receptor binding, in which the PDGF-B L1 loop, disordered in the structure of the free form, adopts a highly specific conformation to form hydrophobic interactions with the third Ig domain of PDGFRbeta. Calorimetric data also shows that the membrane-proximal homotypic PDGFRalpha interaction, albeit required for activation, contributes negatively to ligand binding. The structural and biochemical data together offer insights into PDGF-PDGFR signaling, as well as strategies for PDGF-antagonism.