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- PDB-3v47: Crystal structure of the N-terminal fragment of zebrafish TLR5 in... -

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Basic information

Entry
Database: PDB / ID: 3v47
TitleCrystal structure of the N-terminal fragment of zebrafish TLR5 in complex with Salmonella flagellin
Components
  • Flagellin
  • Toll-like receptor 5b and variable lymphocyte receptor B.61 chimeric protein
KeywordsIMMUNE SYSTEM / Innate immunity / Leucine-rich repeat / innate immune receptor
Function / homology
Function and homology information


toll-like receptor 5 signaling pathway / bacterial-type flagellum filament / activation of immune response / 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 ...toll-like receptor 5 signaling pathway / bacterial-type flagellum filament / activation of immune response / 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 / extracellular region / 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) / Bacterial flagellin C-terminal helical region / Flagellin / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region / Toll-like receptor / Leucine rich repeat N-terminal domain ...f41 fragment of flagellin, N-terminal domain / f41 fragment of flagellin, N-terminal domain / Variable lymphocyte receptor, C-terminal / Domain of unknown function (DUF3439) / Bacterial flagellin C-terminal helical region / Flagellin / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region / Toll-like receptor / 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 / Leucine-rich repeat, SDS22-like subfamily / TIR domain profile. / 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)
Salmonella enterica subsp. enterica serovar Dublin (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsYoon, S.I. / Hong, H. / Wilson, I.A.
CitationJournal: Science / Year: 2012
Title: Structural basis of TLR5-flagellin recognition and signaling.
Authors: Yoon, S.I. / Kurnasov, O. / Natarajan, V. / Hong, M. / Gudkov, A.V. / Osterman, A.L. / Wilson, I.A.
History
DepositionDec 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2012Group: Structure summary
Revision 1.2Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 2018Group: Structure summary / Category: struct / Item: _struct.title
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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 / struct_asym / struct_conn / struct_ref_seq_dif / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Toll-like receptor 5b and variable lymphocyte receptor B.61 chimeric protein
B: Toll-like receptor 5b and variable lymphocyte receptor B.61 chimeric protein
C: Flagellin
D: Flagellin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,79711
Polymers191,4364
Non-polymers2,3617
Water5,242291
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.406, 181.495, 186.367
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
13C
23D
14A
24B
15A
25B
16A
26B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A1 - 150
2113B1 - 150
1123C1 - 174
2123D1 - 174
1223C414 - 459
2223D414 - 459
1134C192 - 242
2134D192 - 242
1234C344 - 392
2234D344 - 392
1143A151 - 300
2143B151 - 300
1153A301 - 360
2153B301 - 360
1255A361
2255B361
1353A362 - 390
2353B362 - 390
1163A391 - 442
2163B391 - 442
1265A443
2265B443
1363A444 - 464
2363B444 - 464

NCS ensembles :
ID
1
2
4
5
6
3

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Components

#1: Protein Toll-like receptor 5b and variable lymphocyte receptor B.61 chimeric protein


Mass: 51169.230 Da / Num. of mol.: 2
Fragment: zebrafish Toll-like receptor 5b (UNP residues 22-390), hagfish variable lymphocyte receptor B.61 (UNP residues 126-200)
Mutation: V24E, L124V, Q159K, R227K, S229T, D334N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish), (gene. exp.) Eptatretus burgeri (inshore hagfish)
Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: B3DIN1, UniProt: Q4G1L2
#2: Protein Flagellin / Phase 1-C flagellin


Mass: 44548.656 Da / Num. of mol.: 2 / Fragment: UNP residues 48-466
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Dublin (bacteria)
Gene: fliC, fliC1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q06971
#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.: 4
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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O

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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: 2.58 Å3/Da / Density % sol: 52.32 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 15% PEG8000, 0.2 M magnesium chloride, 0.1 M Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 23, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.47→20 Å / Num. all: 69591 / Num. obs: 69591 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.086
Reflection shellResolution: 2.47→2.56 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.491 / % possible all: 93.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.47→20 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.89 / Cross valid method: THROUGHOUT / ESU R: 0.424 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25924 3513 5.1 %RANDOM
Rwork0.22119 ---
all0.22313 ---
obs0.22313 66000 96.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.4 Å20 Å20 Å2
2---2.15 Å20 Å2
3---0.75 Å2
Refinement stepCycle: LAST / Resolution: 2.47→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11017 0 154 291 11462
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02211349
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.9715408
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.12351454
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.926.137497
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.045151881
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3421535
X-RAY DIFFRACTIONr_chiral_restr0.0960.21839
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028465
X-RAY DIFFRACTIONr_mcbond_it0.5561.57237
X-RAY DIFFRACTIONr_mcangle_it1.142211566
X-RAY DIFFRACTIONr_scbond_it2.35334112
X-RAY DIFFRACTIONr_scangle_it4.0044.53842
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A508TIGHT POSITIONAL0.050.05
1A463LOOSE POSITIONAL0.065
1A508TIGHT THERMAL0.110.5
1A463LOOSE THERMAL0.1510
2C628TIGHT POSITIONAL0.040.05
2C516LOOSE POSITIONAL0.095
2C628TIGHT THERMAL0.110.5
2C516LOOSE THERMAL0.1410
3C597MEDIUM POSITIONAL0.270.5
3C597MEDIUM THERMAL0.372
4A600TIGHT POSITIONAL0.040.05
4A587LOOSE POSITIONAL0.085
4A600TIGHT THERMAL0.130.5
4A587LOOSE THERMAL0.1510
5A356TIGHT POSITIONAL0.060.05
5A4MEDIUM POSITIONAL0.030.5
5A355LOOSE POSITIONAL0.075
5A356TIGHT THERMAL0.160.5
5A4MEDIUM THERMAL0.082
5A355LOOSE THERMAL0.1710
6A292TIGHT POSITIONAL0.050.05
6A4MEDIUM POSITIONAL0.040.5
6A271LOOSE POSITIONAL0.085
6A292TIGHT THERMAL0.120.5
6A4MEDIUM THERMAL0.122
6A271LOOSE THERMAL0.1410
LS refinement shellResolution: 2.471→2.534 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 276 -
Rwork0.304 4541 -
obs--92.6 %
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)
10.5630.15850.14251.20930.50591.04740.00570.07880.0631-0.0230.0352-0.10480.10950.1192-0.0410.02110.03680.01270.20190.01360.1353-13.395-9.23319.533
20.48830.00210.15231.20150.45821.0872-0.0118-0.0041-0.02850.186-0.0180.17520.0241-0.07720.02980.03450.02080.02560.13460.01340.2244-29.58926.74556.801
31.6295-0.1308-0.2112.2232-0.17234.33080.11640.19190.1306-0.148-0.06940.2663-0.0797-0.3767-0.04710.06790.0234-0.00410.1738-0.03430.2398-34.212-11.31624.901
41.3288-0.5810.02185.3335-0.10831.840.02470.11730.2026-0.05070.0502-0.4388-0.1580.212-0.0750.11250.0133-0.03220.2376-0.02840.203-9.05421.02459.169
56.6658-8.17625.034513.5172-7.23187.2636-0.0874-0.35010.29971.04610.5366-0.0488-0.4888-0.1848-0.44910.6361-0.06570.02650.46460.02170.4841-27.397-45.9374.327
63.58081.3098-3.70633.4389-6.383213.80950.0188-0.3881-0.337-0.5697-0.24560.06550.43770.07230.22680.72510.0615-0.11910.69210.15870.4535-11-24.3191.384
72.2247-1.70533.35121.2649-19.046719.7015-0.39260.09410.15951.75630.0777-1.0158-1.45620.45280.3150.7370.13330.05690.5688-0.04790.893-33.914-24.59161.036
80.887-0.6124-2.452414.2195-7.585313.0867-0.06830.2206-0.1041-0.7726-0.07980.27850.9151-0.70630.1480.74910.1115-0.14650.54010.09440.5303-8.156-14.21671.127
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 464
2X-RAY DIFFRACTION2B24 - 464
3X-RAY DIFFRACTION3C64 - 174
4X-RAY DIFFRACTION3C404 - 459
5X-RAY DIFFRACTION4D62 - 174
6X-RAY DIFFRACTION4D404 - 460
7X-RAY DIFFRACTION5C192 - 242
8X-RAY DIFFRACTION5C344 - 382
9X-RAY DIFFRACTION6D192 - 237
10X-RAY DIFFRACTION6D347 - 382
11X-RAY DIFFRACTION7C175 - 191
12X-RAY DIFFRACTION7C383 - 403
13X-RAY DIFFRACTION8D175 - 191
14X-RAY DIFFRACTION8D383 - 403

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