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

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Basic information

Entry
Database: PDB / ID: 5gy2
TitleCrystal structure of a complex between Bacillus subtilis flagellin and zebrafish Toll-like receptor 5
Components
  • Flagellin
  • Tlr5b protein,Variable lymphocyte receptor B
KeywordsIMMUNE 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 / transmembrane signaling receptor activity / signaling receptor activity / inflammatory response / innate immune response / structural molecule activity / extracellular region / plasma membrane
Similarity search - Function
f41 fragment of flagellin, N-terminal domain / f41 fragment of flagellin, N-terminal domain / Variable lymphocyte receptor, C-terminal / Domain of unknown function (DUF3439) / Toll-like receptor / : / Flagellin, C-terminal domain, subdomain 2 / Flagellin, C-terminal domain / Bacterial flagellin C-terminal helical region / Flagellin ...f41 fragment of flagellin, N-terminal domain / f41 fragment of flagellin, N-terminal domain / Variable lymphocyte receptor, C-terminal / Domain of unknown function (DUF3439) / Toll-like receptor / : / Flagellin, C-terminal domain, subdomain 2 / Flagellin, C-terminal domain / Bacterial flagellin C-terminal helical region / Flagellin / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / TIR domain / Leucine Rich Repeat / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / TIR domain profile. / Leucine-rich repeat, SDS22-like subfamily / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Tlr5b protein / Flagellin / Variable lymphocyte receptor B
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Eptatretus burgeri (inshore hagfish)
Bacillus subtilis subsp. spizizenii strain W23 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSong, W.S. / Yoon, S.I.
CitationJournal: 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
DepositionSep 21, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: 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 2.1Nov 8, 2023Group: 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
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tlr5b protein,Variable lymphocyte receptor B
C: Flagellin
B: Tlr5b protein,Variable lymphocyte receptor B
D: Flagellin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,41114
Polymers140,8474
Non-polymers2,56510
Water8,377465
1
A: Tlr5b protein,Variable lymphocyte receptor B
C: Flagellin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7067
Polymers70,4232
Non-polymers1,2825
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tlr5b protein,Variable lymphocyte receptor B
D: Flagellin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7067
Polymers70,4232
Non-polymers1,2825
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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 number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14C
24D
15A
25B
16A
26B
17A
27B
18A
28B
19A
29B
110A
210B
111A
211B
112A
212B
113A
213B
114A
214B
115A
215B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A25 - 46
2113B25 - 46
1123A351 - 357
2123B351 - 357
1223A365 - 381
2223B365 - 381
1323A383 - 400
2323B383 - 400
1133A401 - 409
2133B401 - 409
1233A411 - 464
2233B411 - 464
1143C54 - 141
2143D54 - 141
1243C145 - 222
2243D145 - 222
1156A1101 - 1102
2156B1101 - 1102
1166A801
2166B801
1176A901
2176B901
1183A101 - 150
2183B101 - 150
1193A201 - 250
2193B201 - 250
11103A50 - 70
21103B50 - 70
12103A72 - 100
22103B72 - 100
11113A151 - 200
21113B151 - 200
11123A251 - 300
21123B251 - 300
11133A301 - 319
21133B301 - 319
12133A321 - 350
22133B321 - 350
11146A1401
21146B1401
11156A1001 - 1011
21156B1001 - 1011

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

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Components

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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

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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
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-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
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 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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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 80115 / % possible obs: 98.1 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 16.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V47

3v47


Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc 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
RfactorNum. reflection% reflectionSelection details
Rfree0.23627 3987 5 %RANDOM
Rwork0.19477 ---
obs0.19691 75311 97.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å21.11 Å2
2--0.55 Å20 Å2
3----0.51 Å2
Refinement stepCycle: 1 / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9429 0 166 465 10060
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0229880
X-RAY DIFFRACTIONr_bond_other_d00.026525
X-RAY DIFFRACTIONr_angle_refined_deg1.5071.97313401
X-RAY DIFFRACTIONr_angle_other_deg4.28316025
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.94651255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.54225.759448
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.559151720
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4211536
X-RAY DIFFRACTIONr_chiral_restr0.0910.21569
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210991
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021875
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.711.56103
X-RAY DIFFRACTIONr_mcbond_other01.52516
X-RAY DIFFRACTIONr_mcangle_it1.37129818
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6433777
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.4614.53565
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A128TIGHT POSITIONAL0.040.05
1A145LOOSE POSITIONAL0.035
1A128TIGHT THERMAL0.150.5
1A145LOOSE THERMAL0.1610
2A248TIGHT POSITIONAL0.060.05
2A297LOOSE POSITIONAL0.065
2A248TIGHT THERMAL0.210.5
2A297LOOSE THERMAL0.1910
3A367TIGHT POSITIONAL0.050.05
3A460LOOSE POSITIONAL0.055
3A367TIGHT THERMAL0.220.5
3A460LOOSE THERMAL0.2110
4C973TIGHT POSITIONAL0.040.05
4C977LOOSE POSITIONAL0.055
4C973TIGHT THERMAL0.160.5
4C977LOOSE THERMAL0.1710
5A44LOOSE POSITIONAL0.495
5A44LOOSE THERMAL3.610
6A22LOOSE POSITIONAL0.245
6A22LOOSE THERMAL3.510
7A22LOOSE POSITIONAL0.235
7A22LOOSE THERMAL0.4810
8A295TIGHT POSITIONAL0.030.05
8A340LOOSE POSITIONAL0.045
8A295TIGHT THERMAL0.160.5
8A340LOOSE THERMAL0.1610
9A299TIGHT POSITIONAL0.040.05
9A409LOOSE POSITIONAL0.045
9A299TIGHT THERMAL0.20.5
9A409LOOSE THERMAL0.2110
10A295TIGHT POSITIONAL0.040.05
10A346LOOSE POSITIONAL0.055
10A295TIGHT THERMAL0.170.5
10A346LOOSE THERMAL0.1510
11A300TIGHT POSITIONAL0.040.05
11A425LOOSE POSITIONAL0.045
11A300TIGHT THERMAL0.170.5
11A425LOOSE THERMAL0.1910
12A292TIGHT POSITIONAL0.050.05
12A325LOOSE POSITIONAL0.065
12A292TIGHT THERMAL0.20.5
12A325LOOSE THERMAL0.2410
13A295TIGHT POSITIONAL0.060.05
13A375LOOSE POSITIONAL0.075
13A295TIGHT THERMAL0.190.5
13A375LOOSE THERMAL0.2110
14A30LOOSE POSITIONAL0.275
14A30LOOSE THERMAL2.1410
15A22LOOSE POSITIONAL0.065
15A22LOOSE THERMAL0.3210
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 254 -
Rwork0.252 5416 -
obs--95.6 %
Refinement TLS params.

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

IDL11 (°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)
10.7260.1538-0.19380.4347-0.00930.69250.10850.01230.0555-0.0753-0.02720.0062-0.0523-0.0441-0.08140.39230.03320.00240.11330.01480.0178-7.9961.05457.484
20.9072-0.3095-0.01031.19610.0690.70780.0048-0.02380.0470.17720.02050.17910.0168-0.074-0.02530.287-0.01480.05780.2331-0.00360.05224.369-5.15420.156
31.1750.0311-1.07231.24690.20983.0572-0.121-0.0039-0.1798-0.19170.0028-0.12760.34820.0510.11830.43540.00030.03690.08290.00580.04893.112-10.52371.276
42.16790.262-1.56541.6697-0.29961.9636-0.06790.0081-0.22510.1372-0.02720.25170.1253-0.08820.09510.2879-0.03060.02410.24270.0160.094820.371-16.7182.89
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 464
2X-RAY DIFFRACTION2B24 - 464
3X-RAY DIFFRACTION3C54 - 222
4X-RAY DIFFRACTION4D54 - 222

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