5XZ4 | pdb_00005xz4

The X-tay structure of Bumblebee PGRP-SA

PDB DOI: https://doi.org/10.2210/pdb5XZ4/pdb

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

Deposited: 2017-07-11 Released: 2018-09-19
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: 1.41 Å
R-Value Free:
0.209 (Depositor), 0.180 (DCC)
R-Value Work:
0.185 (Depositor), 0.150 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structural Insights into the Preferential Binding of PGRP-SAs from Bumblebees and Honeybees to Dap-Type Peptidoglycans Rather than Lys-Type Peptidoglycans.

Liu, Y.J., Zhao, X.M., Huang, J.X., Chen, M.M., An, J.D.

(2019) J Immunol 202: 249-259

PubMed: 30510067 Search on PubMed
DOI: https://doi.org/10.4049/jimmunol.1800439
Primary Citation of Related Structures:
5XZ4

PubMed Abstract:
The peptidoglycan recognition protein SAs (PGRP-SAs) from Bombus ignitus (Bi-PGRP-SA), Apis mellifera (Am-PGRP-SA), and Megachile rotundata PGRP-SA (Mr-PGRP-SA) exhibit an intrinsic ability to preferentially bind to Dap-type peptidoglycan (PGN) from Bacillus subtilis rather than Lys-type PGN from Micrococcus luteus This ability is more analogous to the binding exhibited by PGRP-LCx and PGRP-SD than to that exhibited by PGRP-SA in Drosophila Moreover, Bi-PGRP-SA and Am-PGRP-SA share greater sequence identity with Drosophila PGRP-LCx than with PGRP-SD and retain several conserved contact residues, including His ³⁷/His ³⁸, His ⁶⁰/His ⁶¹, Trp ⁶⁶/Trp ⁶⁷, Ala ¹⁵⁰/Ala ¹⁵¹, and Thr ¹⁵¹/Thr ¹⁵² However, the corresponding contact residue Arg ⁸⁵ is not a major anchor residue in bees (e.g., bumblebees, honeybees, and leaf-cutting bees), and an in silico analysis indicated that the residues Thr ¹⁵¹/Thr ¹⁵² and Ser ¹⁵³/Ser ¹⁵⁴ of Bi-PGRP-SA and Am-PGRP-SA are deduced to be anchor residues. In addition, the nonconserved residues Asp ⁶⁷ in Bi-PGRP-SA and Mr-PGRP-SA and His ⁶⁸ in Am-PGRP-SA are deduced to be involved in the binding to Dap-type PGNs in bumblebees, honeybees, and leaf-cutting bees. We conclude that the structures and specificities of PGRP-SAs in bees are more analogous to those of PGRP-LCx than to those of Drosophila PGRP-SA. This phenomenon might be explained by the fact that the evolutionary clade of Hymenoptera is more ancient than that of Diptera.

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: 38.96 kDa
Atom Count: 2,967
Modeled Residue Count: 334
Deposited Residue Count: 346
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bumblebee peptidoglycan recognition protein SA	A, B	173	Bombus	Mutation(s): 0
UniProt
Find proteins for A0A452CSL6 (Bombus) Explore A0A452CSL6 Go to UniProtKB: A0A452CSL6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A452CSL6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	C [auth A], D [auth A], F [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.41 Å
R-Value Free: 0.209 (Depositor), 0.180 (DCC)
R-Value Work: 0.185 (Depositor), 0.150 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.95	α = 90
b = 49.94	β = 120.37
c = 78.77	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: 2018-09-19

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: 2018-09-19
Type: Initial release
Version 1.1: 2019-10-02
Changes: Data collection, Database references
Version 1.2: 2023-11-22
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-11-06
Changes: Structure summary