5XZ3

The X-ray structure of Apis mellifera PGRP-SA

PDB DOI: https://doi.org/10.2210/pdb5XZ3/pdb

Classification: IMMUNE SYSTEM
Organism(s): Apis mellifera
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-07-11 Released: 2018-07-18
Deposition Author(s): Liu, Y.J., Huang, J.X., Zhao, X.M., An, J.D.
Funding Organization(s): Natural Science Foundation of China, Agricultural Science and Technology Innovation Program

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free: 0.217
R-Value Work: 0.190
R-Value Observed: 0.191

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of peptidoglycan recognition protein SA in Apis mellifera (Hymenoptera: Apidae).

Liu, Y., Zhao, X., Naeem, M., An, J.

(2018) Protein Sci 27: 893-897

PubMed: 29396863 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/pro.3383
Primary Citation of Related Structures:
5XZ3

PubMed Abstract:
Peptidoglycan recognition protein SA (PGRP-SA) is a key pattern recognition receptor in the insect innate immune system. PGRP-SA can bind to bacterial PGN and activate the Toll pathway, which triggers the expression and release of antimicrobial peptides to prevent bacterial infection. Here, we report the first structure of Apis mellifera PGRP-SA from Hymenoptera at 1.86 Å resolution. The overall architecture of Am-PGRP-SA was similar to the Drosophila PGRP-SA; however, the residues involved in PGN binding groove were not conserved, and the binding pocket was narrower. This structure gives insight into PGN binding characteristics in honeybees.

Organizational Affiliation

Key Laboratory for Insect-Pollinator Biology of the Ministry of Agriculture, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, 100093, China.

Macromolecule Content

Total Structure Weight: 79.08 kDa
Atom Count: 5,625
Modelled Residue Count: 671
Deposited Residue Count: 692
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidoglycan-recognition protein	A, B, C, D	173	Apis mellifera	Mutation(s): 0 Gene Names: PGRP-S3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free: 0.217
R-Value Work: 0.190
R-Value Observed: 0.191
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.898	α = 90
b = 68.607	β = 94.92
c = 71.699	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-07-18

Deposition Author(s):

Funding Organization	Location	Grant Number
Natural Science Foundation of China	China	NO.31672500
Agricultural Science and Technology Innovation Program	China	CAAS-ASTIP-2015-IAR

Revision History (Full details and data files)

Version 1.0: 2018-07-18
Type: Initial release
Version 1.1: 2019-01-30
Changes: Data collection, Database references
Version 1.2: 2023-11-22
Changes: Data collection, Database references, Refinement description