5GY2 | pdb_00005gy2

Crystal structure of a complex between Bacillus subtilis flagellin and zebrafish Toll-like receptor 5

PDB DOI: https://doi.org/10.2210/pdb5GY2/pdb

Classification: IMMUNE SYSTEM
Organism(s): Danio rerio, Eptatretus burgeri, Bacillus spizizenii str. W23
Expression System: Trichoplusia ni, Escherichia coli
Mutation(s): Yes

Deposited: 2016-09-21 Released: 2017-02-15
Deposition Author(s): Song, W.S., Yoon, S.I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.236 (Depositor), 0.238 (DCC)
R-Value Work:
0.195 (Depositor), 0.200 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

A conserved TLR5 binding and activation hot spot on flagellin

Song, W.S., Jeon, Y.J., Namgung, B., Hong, M., Yoon, S.I.

(2017) Sci Rep 7: 40878-40878

PubMed: 28106112 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/srep40878
Primary Citation Related Structures:
5GY2

PubMed Abstract:
Flagellin is a bacterial protein that polymerizes into the flagellar filament and is essential for bacterial motility. When flagellated bacteria invade the host, flagellin is recognized by Toll-like receptor 5 (TLR5) as a pathogen invasion signal and eventually evokes the innate immune response. Here, we provide a conserved structural mechanism by which flagellins from Gram-negative γ-proteobacteria and Gram-positive Firmicutes bacteria bind and activate TLR5. The comparative structural analysis using our crystal structure of a complex between Bacillus subtilis flagellin (bsflagellin) and TLR5 at 2.1 Å resolution, combined with the alanine scanning analysis of the binding interface, reveals a common hot spot in flagellin for TLR5 activation. An arginine residue (bsflagellin R89) of the flagellin D1 domain and its adjacent residues (bsflagellin E114 and L93) constitute a hot spot that provides shape and chemical complementarity to a cavity generated by the loop of leucine-rich repeat 9 in TLR5. In addition to the flagellin D1 domain, the D0 domain also contributes to TLR5 activity through structurally dispersed regions, but not a single focal area. These results establish the groundwork for the future design of flagellin-based therapeutics.

Organizational Affiliation

Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea.

Macromolecule Content

Total Structure Weight: 143.41 kDa
Atom Count: 10,156
Modeled Residue Count: 1,221
Deposited Residue Count: 1,276
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tlr5b protein,Variable lymphocyte receptor B	A, C [auth B]	455	Danio rerio, Eptatretus burgeri This entity is chimeric	Mutation(s): 6 Gene Names: tlr5b, VLRB
UniProt
Find proteins for B3DIN1 (Danio rerio) Explore B3DIN1 Go to UniProtKB: B3DIN1
Find proteins for Q4G1L2 (Eptatretus burgeri) Explore Q4G1L2 Go to UniProtKB: Q4G1L2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	B3DIN1 Q4G1L2
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A Focus chain C [auth B]
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellin	B [auth C], D	183	Bacillus spizizenii str. W23	Mutation(s): 0 Gene Names: hag, BSUW23_17335
UniProt
Find proteins for E0U497 (Bacillus spizizenii (strain ATCC 23059 / NRRL B-14472 / W23)) Explore E0U497 Go to UniProtKB: E0U497
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E0U497
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F	2		N-Glycosylation	Interactions Focus chain E Focus chain F Interactions & Density Focus chain E Focus chain F
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B]	G [auth A] H [auth A] I [auth A] K [auth B] L [auth B] G [auth A], H [auth A], I [auth A], K [auth B], L [auth B], M [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain J [auth A]	J [auth A], N [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain N [auth B] Interactions & Density Focus chain J [auth A] Focus chain N [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.236 (Depositor), 0.238 (DCC)
R-Value Work: 0.195 (Depositor), 0.200 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.146	α = 90
b = 54.281	β = 98.62
c = 165.98	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-02-15

Deposition Author(s):

Song, W.S.

Yoon, S.I.

Revision History (Full details and data files)

Version 1.0: 2017-02-15
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-11-06
Changes: Structure summary