PDB-5gy2: Crystal structure of a complex between Bacillus subtilis flagelli...

ID or keywords:

Entry

Database: PDB / ID: 5gy2

Title

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

Components

Flagellin
Tlr5b protein,Variable lymphocyte receptor B

Keywords

IMMUNE SYSTEM / Bacterial protein Immune receptor

Function / homology

Function and homology information

toll-like receptor 5 signaling pathway / activation of immune response / bacterial-type flagellum / toll-like receptor signaling pathway / bacterial-type flagellum-dependent cell motility / transmembrane signaling receptor activity / signaling receptor activity / inflammatory response / innate immune response / structural molecule activity ...
Similarity search - Function

Biological species

Danio rerio (zebrafish)

Eptatretus burgeri (inshore hagfish)

Bacillus subtilis subsp. spizizenii strain W23 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Song, W.S. / Yoon, S.I.

Citation

Journal: Sci Rep / Year: 2017
Title: A conserved TLR5 binding and activation hot spot on flagellin
Authors: Song, W.S. / Jeon, Y.J. / Namgung, B. / Hong, M. / Yoon, S.I.

History

Deposition	Sep 21, 2016	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Feb 15, 2017	Provider: repository / Type: Initial release
Revision 2.0	Jul 29, 2020	Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / struct_asym / struct_conn / struct_site / struct_site_gen Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_mod_residue.label_asym_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1	Nov 8, 2023	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5gy2.cif.gz	491.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5gy2.ent.gz	403.3 KB	Display	PDB format
PDBx/mmJSON format	5gy2.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5gy2_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	5gy2_full_validation.pdf.gz	1.1 MB	Display
Data in XML	5gy2_validation.xml.gz	49.1 KB	Display
Data in CIF	5gy2_validation.cif.gz	70 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gy/5gy2 ftp://data.pdbj.org/pub/pdb/validation_reports/gy/5gy2	HTTPS FTP

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Related structure data

Related structure data	3v47S S: Starting model for refinement
Similar structure data	2zpa-1 6ysw-2 2xzs-d 5a7y-d 5m70-d 3o47-1 7814 1kfs-d 2i0e-d 5c7j-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#143 - Nov 2011 Toll-like Receptors similarity (20) #248 - Aug 2020 Phytosulfokine Receptor similarity (6) #68 - Aug 2005 Neurotrophins similarity (4) #105 - Sep 2008 Ribonuclease A similarity (2) #245 - May 2020 Spliceosomes similarity (2)

Deposited unit

A: Tlr5b protein,Variable lymphocyte receptor B

C: Flagellin

B: Tlr5b protein,Variable lymphocyte receptor B

D: Flagellin

hetero molecules

143 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Tlr5b protein,Variable lymphocyte receptor B

C: Flagellin

hetero molecules

defined by author
71.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Tlr5b protein,Variable lymphocyte receptor B

D: Flagellin

hetero molecules

defined by author
71.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	78.146, 54.281, 165.980
Angle α, β, γ (deg.)	90.00, 98.62, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	3	A	25 - 46
2	1	1	3	B	25 - 46
1	1	2	3	A	351 - 357
2	1	2	3	B	351 - 357
1	2	2	3	A	365 - 381
2	2	2	3	B	365 - 381
1	3	2	3	A	383 - 400
2	3	2	3	B	383 - 400
1	1	3	3	A	401 - 409
2	1	3	3	B	401 - 409
1	2	3	3	A	411 - 464
2	2	3	3	B	411 - 464
1	1	4	3	C	54 - 141
2	1	4	3	D	54 - 141
1	2	4	3	C	145 - 222
2	2	4	3	D	145 - 222
1	1	5	6	A	1101 - 1102
2	1	5	6	B	1101 - 1102
1	1	6	6	A	801
2	1	6	6	B	801
1	1	7	6	A	901
2	1	7	6	B	901
1	1	8	3	A	101 - 150
2	1	8	3	B	101 - 150
1	1	9	3	A	201 - 250
2	1	9	3	B	201 - 250
1	1	10	3	A	50 - 70
2	1	10	3	B	50 - 70
1	2	10	3	A	72 - 100
2	2	10	3	B	72 - 100
1	1	11	3	A	151 - 200
2	1	11	3	B	151 - 200
1	1	12	3	A	251 - 300
2	1	12	3	B	251 - 300
1	1	13	3	A	301 - 319
2	1	13	3	B	301 - 319
1	2	13	3	A	321 - 350
2	2	13	3	B	321 - 350
1	1	14	6	A	1401
2	1	14	6	B	1401
1	1	15	6	A	1001 - 1011
2	1	15	6	B	1001 - 1011

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Protein , 2 types, 4 molecules ABCD

#1: Protein	Tlr5b protein,Variable lymphocyte receptor B / TOLL-LIKE RECEPTOR 5B Mass: 51169.230 Da / Num. of mol.: 2 / Mutation: V24E/L124V/Q159K/R227K/S229T/D334N Source method: isolated from a genetically manipulated source Details: Fusion protein of tlr5B (B3DIN1, UNP residues 23-390) and Variable lymphocyte receptor B (Q4G1L2, UNP residues 126-200) Source: (gene. exp.) Danio rerio (zebrafish), (gene. exp.) Eptatretus burgeri (inshore hagfish) Gene: tlr5b, VLRB / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: B3DIN1, UniProt: Q4G1L2
#2: Protein	Flagellin Mass: 19254.148 Da / Num. of mol.: 2 / Fragment: UNP residues 54-230 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. spizizenii strain W23 (bacteria) Strain: W23 / Gene: hag, BSUW23_17335 / Production host: Escherichia coli (E. coli) / References: UniProt: E0U497

#1: Protein

Tlr5b protein,Variable lymphocyte receptor B / TOLL-LIKE RECEPTOR 5B

Mass: 51169.230 Da / Num. of mol.: 2 / Mutation: V24E/L124V/Q159K/R227K/S229T/D334N
Source method: isolated from a genetically manipulated source
Details: Fusion protein of tlr5B (B3DIN1, UNP residues 23-390) and Variable lymphocyte receptor B (Q4G1L2, UNP residues 126-200)
Source: (gene. exp.)

Danio rerio (zebrafish), (gene. exp.)

Eptatretus burgeri (inshore hagfish)
Gene: tlr5b, VLRB / Production host:

Trichoplusia ni (cabbage looper) / References: UniProt: B3DIN1, UniProt: Q4G1L2

#2: Protein

Flagellin

Mass: 19254.148 Da / Num. of mol.: 2 / Fragment: UNP residues 54-230
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Bacillus subtilis subsp. spizizenii strain W23 (bacteria)
Strain: W23 / Gene: hag, BSUW23_17335 / Production host:

Escherichia coli (E. coli) / References: UniProt: E0U497

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Sugars , 2 types, 8 molecules

#3: Polysaccharide

2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DGlcpNAcb1-4DGlcpNAcb1-	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1	WURCS	PDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}	LINUCS	PDB-CARE

#4: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

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Non-polymers , 2 types, 467 molecules

#5: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 465 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.47 Å³/Da / Density % sol: 50.23 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.4 / Details: PEG 300, sodium acetate, pH 4.4

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 8, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9796 Å / Relative weight: 1
Reflection	Resolution: 2.1→30 Å / Num. obs: 80115 / % possible obs: 98.1 % / Redundancy: 3.4 % / R_merge(I) obs: 0.091 / Net I/σ(I): 16.8

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0109	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3V47

3v47

Resolution: 2.1→30 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.926 / Cross valid method: THROUGHOUT / ESU R: 0.227 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23627	3987	5 %	RANDOM
R_work	0.19477	-	-	-
obs	0.19691	75311	97.95 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 33.3 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.3 Å²	0 Å²	1.11 Å²
2-	-	0.55 Å²	0 Å²
3-	-	-	-0.51 Å²

Refinement step

Cycle: 1 / Resolution: 2.1→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9429	0	166	465	10060

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	9880
X-RAY DIFFRACTION	r_bond_other_d	0	0.02	6525
X-RAY DIFFRACTION	r_angle_refined_deg	1.507	1.973	13401
X-RAY DIFFRACTION	r_angle_other_deg	4.28	3	16025
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.946	5	1255
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.542	25.759	448
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.559	15	1720
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.421	15	36
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	1569
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	10991
X-RAY DIFFRACTION	r_gen_planes_other	0.008	0.02	1875
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.71	1.5	6103
X-RAY DIFFRACTION	r_mcbond_other	0	1.5	2516
X-RAY DIFFRACTION	r_mcangle_it	1.371	2	9818
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.64	3	3777
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	4.461	4.5	3565
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	128	TIGHT POSITIONAL	0.04	0.05
1	A	145	LOOSE POSITIONAL	0.03	5
1	A	128	TIGHT THERMAL	0.15	0.5
1	A	145	LOOSE THERMAL	0.16	10
2	A	248	TIGHT POSITIONAL	0.06	0.05
2	A	297	LOOSE POSITIONAL	0.06	5
2	A	248	TIGHT THERMAL	0.21	0.5
2	A	297	LOOSE THERMAL	0.19	10
3	A	367	TIGHT POSITIONAL	0.05	0.05
3	A	460	LOOSE POSITIONAL	0.05	5
3	A	367	TIGHT THERMAL	0.22	0.5
3	A	460	LOOSE THERMAL	0.21	10
4	C	973	TIGHT POSITIONAL	0.04	0.05
4	C	977	LOOSE POSITIONAL	0.05	5
4	C	973	TIGHT THERMAL	0.16	0.5
4	C	977	LOOSE THERMAL	0.17	10
5	A	44	LOOSE POSITIONAL	0.49	5
5	A	44	LOOSE THERMAL	3.6	10
6	A	22	LOOSE POSITIONAL	0.24	5
6	A	22	LOOSE THERMAL	3.5	10
7	A	22	LOOSE POSITIONAL	0.23	5
7	A	22	LOOSE THERMAL	0.48	10
8	A	295	TIGHT POSITIONAL	0.03	0.05
8	A	340	LOOSE POSITIONAL	0.04	5
8	A	295	TIGHT THERMAL	0.16	0.5
8	A	340	LOOSE THERMAL	0.16	10
9	A	299	TIGHT POSITIONAL	0.04	0.05
9	A	409	LOOSE POSITIONAL	0.04	5
9	A	299	TIGHT THERMAL	0.2	0.5
9	A	409	LOOSE THERMAL	0.21	10
10	A	295	TIGHT POSITIONAL	0.04	0.05
10	A	346	LOOSE POSITIONAL	0.05	5
10	A	295	TIGHT THERMAL	0.17	0.5
10	A	346	LOOSE THERMAL	0.15	10
11	A	300	TIGHT POSITIONAL	0.04	0.05
11	A	425	LOOSE POSITIONAL	0.04	5
11	A	300	TIGHT THERMAL	0.17	0.5
11	A	425	LOOSE THERMAL	0.19	10
12	A	292	TIGHT POSITIONAL	0.05	0.05
12	A	325	LOOSE POSITIONAL	0.06	5
12	A	292	TIGHT THERMAL	0.2	0.5
12	A	325	LOOSE THERMAL	0.24	10
13	A	295	TIGHT POSITIONAL	0.06	0.05
13	A	375	LOOSE POSITIONAL	0.07	5
13	A	295	TIGHT THERMAL	0.19	0.5
13	A	375	LOOSE THERMAL	0.21	10
14	A	30	LOOSE POSITIONAL	0.27	5
14	A	30	LOOSE THERMAL	2.14	10
15	A	22	LOOSE POSITIONAL	0.06	5
15	A	22	LOOSE THERMAL	0.32	10

LS refinement shell

Resolution: 2.1→2.154 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.294	254	-
R_work	0.252	5416	-
obs	-	-	95.6 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.726	0.1538	-0.1938	0.4347	-0.0093	0.6925	0.1085	0.0123	0.0555	-0.0753	-0.0272	0.0062	-0.0523	-0.0441	-0.0814	0.3923	0.0332	0.0024	0.1133	0.0148	0.0178	-7.996	1.054	57.484
2	0.9072	-0.3095	-0.0103	1.1961	0.069	0.7078	0.0048	-0.0238	0.047	0.1772	0.0205	0.1791	0.0168	-0.074	-0.0253	0.287	-0.0148	0.0578	0.2331	-0.0036	0.052	24.369	-5.154	20.156
3	1.175	0.0311	-1.0723	1.2469	0.2098	3.0572	-0.121	-0.0039	-0.1798	-0.1917	0.0028	-0.1276	0.3482	0.051	0.1183	0.4354	0.0003	0.0369	0.0829	0.0058	0.0489	3.112	-10.523	71.276
4	2.1679	0.262	-1.5654	1.6697	-0.2996	1.9636	-0.0679	0.0081	-0.2251	0.1372	-0.0272	0.2517	0.1253	-0.0882	0.0951	0.2879	-0.0306	0.0241	0.2427	0.016	0.0948	20.371	-16.718	2.89

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	23 - 464
2	X-RAY DIFFRACTION	2	B	24 - 464
3	X-RAY DIFFRACTION	3	C	54 - 222
4	X-RAY DIFFRACTION	4	D	54 - 222

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Protein , 2 types, 4 molecules ABCD

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Sugars , 2 types, 8 molecules

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Non-polymers , 2 types, 467 molecules

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-Yorodumi

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Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 2 types, 4 molecules ABCD

-
Sugars , 2 types, 8 molecules

-
Non-polymers , 2 types, 467 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi