2XZ4 | pdb_00002xz4

Crystal structure of the LFZ ectodomain of the peptidoglycan recognition protein LF

PDB DOI: https://doi.org/10.2210/pdb2XZ4/pdb

Classification: IMMUNE SYSTEM
Organism(s): Drosophila melanogaster
Expression System: Drosophila melanogaster
Mutation(s): No

Deposited: 2010-11-23 Released: 2011-04-13
Deposition Author(s): Basbous, N., Coste, F., Leone, P., Vincentelli, R., Royet, J., Kellenberger, C., Roussel, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free:
0.201 (Depositor), 0.190 (DCC)
R-Value Work:
0.164 (Depositor), 0.160 (DCC)
R-Value Observed:
0.166 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

The Drosophila Peptidoglycan-Recognition Protein Lf Interacts with Peptidoglycan-Recognition Protein Lc to Downregulate the Imd Pathway.

Basbous, N., Coste, F., Leone, P., Vincentelli, R., Royet, J., Kellenberger, C., Roussel, A.

(2011) EMBO Rep 12: 327

PubMed: 21372849 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/embor.2011.19
Primary Citation of Related Structures:
2XZ4, 2XZ8

PubMed Abstract:
The peptidoglycan (PGN)-recognition protein LF (PGRP-LF) is a specific negative regulator of the immune deficiency (Imd) pathway in Drosophila. We determine the crystal structure of the two PGRP domains constituting the ectodomain of PGRP-LF at 1.72 and 1.94 Å resolution. The structures show that the LFz and LFw domains do not have a PGN-docking groove that is found in other PGRP domains, and they cannot directly interact with PGN, as confirmed by biochemical-binding assays. By using surface plasmon resonance analysis, we show that the PGRP-LF ectodomain interacts with the PGRP-LCx ectodomain in the absence and presence of tracheal cytotoxin. Our results suggest a mechanism for downregulation of the Imd pathway on the basis of the competition between PRGP-LCa and PGRP-LF to bind to PGRP-LCx.

Organizational Affiliation

Centre de Biophysique Moléculaire, UPR 4301 CNRS, Rue Charles Sadron, Orléans 2 45071, France.

Macromolecule Content

Total Structure Weight: 41.7 kDa
Atom Count: 2,877
Modelled Residue Count: 326
Deposited Residue Count: 360
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 LF	A, B	180	Drosophila melanogaster	Mutation(s): 0
UniProt
Find proteins for Q8SXQ7 (Drosophila melanogaster) Explore Q8SXQ7 Go to UniProtKB: Q8SXQ7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8SXQ7
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PG Query on 1PG Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL C₁₁ H₂₄ O₆ SLNYBUIEAMRFSZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	D [auth A], E [auth A], G [auth B], H [auth B], I [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free: 0.201 (Depositor), 0.190 (DCC)
R-Value Work: 0.164 (Depositor), 0.160 (DCC)
R-Value Observed: 0.166 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.802	α = 90
b = 113.443	β = 90
c = 37.532	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-04-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-04-13
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.4: 2024-11-13
Changes: Structure summary