PDBsum entry 3es6

Cell adhesion

PDB id: 3es6

Contents

Protein chains

277 a.a. *

118 a.a. *

Ligands

NAG-NAG-BMA-MAN-NDG

NAG-NAG-BMA-MAN

CO3

P6G

* Residue conservation analysis

PDB id:

3es6

Name:

Cell adhesion

Title:

Crystal structure of the novel complex formed between zinc 2- glycoprotein (zag) and prolactin inducible protein (pip) from human seminal plasma

Structure:

Zinc-alpha-2-glycoprotein. Chain: a. Synonym: zn-alpha-2-glycoprotein, zn-alpha-2-gp. Prolactin-inducible protein. Chain: b. Synonym: prolactin-induced protein, secretory actin-binding protein, sabp, gross cystic disease fluid protein 15, gcdfp-15, gp17

Source:

Homo sapiens. Human. Organism_taxid: 9606. Other_details: seminal fluid. Other_details: seminal fluid

Resolution:

3.23Å R-factor: 0.200 R-free: 0.240

Authors:

M.I.Hassan,S.Bilgrami,V.Kumar,N.Singh,S.Yadav,P.Kaur,T.P.Singh

Key ref:

M.I.Hassan et al. (2008). Crystal structure of the novel complex formed between zinc alpha2-glycoprotein (ZAG) and prolactin-inducible protein (PIP) from human seminal plasma. J Mol Biol, 384, 663-672. PubMed id: 18930737 DOI: 10.1016/j.jmb.2008.09.072

Date:

04-Oct-08 Release date: 28-Oct-08

Supersedes:

2icn

Protein chain

P25311  (ZA2G_HUMAN) -  Zinc-alpha-2-glycoprotein from Homo sapiens

Seq: 298 a.a.

Struc: 277 a.a.*

Protein chain

P12273  (PIP_HUMAN) -  Prolactin-inducible protein from Homo sapiens

Seq: 146 a.a.

Struc: 118 a.a.

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

DOI no: 10.1016/j.jmb.2008.09.072

J Mol Biol 384:663-672 (2008)

PubMed id: 18930737

Crystal structure of the novel complex formed between zinc alpha2-glycoprotein (ZAG) and prolactin-inducible protein (PIP) from human seminal plasma.

M.I.Hassan, S.Bilgrami, V.Kumar, N.Singh, S.Yadav, P.Kaur, T.P.Singh.

ABSTRACT

This is the first report on the formation of a complex between zinc alpha2-glycoprotein (ZAG) and prolactin-inducible protein (PIP). The complex was purified from human seminal plasma and crystallized using 20% polyethylene glycol 9000 and 5% hexaethylene glycol. The structure of the complex has been determined using X-ray crystallographic method and refined to an R(cryst) of 0.199 (R(free)=0.239). The structure of ZAG is broadly similar to the structure of serum ZAG. The scaffolding of PIP consists of seven beta-strands that are organized in the form of two antiparallel beta-pleated sheets, resulting in the formation of a sandwiched beta-sheet. The amino acid sequence of PIP contains one potential N-glycosylation site at Asn77, and the same is found glycosylated with four sugar residues. The structure of the complex shows that the beta-structure of PIP is ideally aligned with the beta-structure of domain alpha3 of ZAG to form a long interface between two proteins. The proximal beta-strands at the long interface are arranged in an antiparallel manner. There are 12 hydrogen bonds and three salt bridges between ZAG and PIP. At the two ends of vertical interface, two salt bridges are formed between pairs of Lys41-Asp233 and Lys68-Glu229. On the perpendicular interface involving alpha1-alpha2 domains of ZAG and a loop of PIP, another salt bridge is formed. The internal space at the corner of the L-shaped structure is filled with solvent molecules including a carbonate ion. The overall buried area in the complex is approximately 914 A(2), which is considerably higher than the 660 A(2) reported for the class I major histocompatibility complex structures.

Selected figure(s)

Figure 2.
Fig. 2. (a) Schematic representation of PIP.^46 (b) A cluster of hydrophobic residues present between two β-sheets of PIP. The interactions of the glycan chain residue NAG with protein residues are shown in ball-and-stick representation. The hydrogen bonds are presented in dotted line. (c) The superimposition of C^α traces of PIP (green) and FN-7 (magenta) is shown. The comparisons of loops L4 and L7 (blue) are significantly different.

Figure 5.
Fig. 5. The electron density for the PIP was observed in the cleft of domains α1–α2 and α3 of ZAG.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 384, 663-672) copyright 2008.

Figures were selected by an automated process.