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- PDB-6bxc: Crystal structure of N-terminal fragment of Zebrafish Toll-Like R... -

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Basic information

Entry
Database: PDB / ID: 6bxc
TitleCrystal structure of N-terminal fragment of Zebrafish Toll-Like Receptor 5 (TLR5) with Lamprey Variable Lymphocyte Receptor 9 (VLR9) bound
Components
  • Toll-like receptor 5b, Variable lymphocyte receptor B chimera
  • Variable Lymphocyte Receptor 9 (VLR9)
KeywordsIMMUNE SYSTEM / VLR / LEUCINE-RICH REPEAT / antibody
Function / homology
Function and homology information


toll-like receptor 5 signaling pathway / activation of immune response / toll-like receptor signaling pathway / transmembrane signaling receptor activity / signaling receptor activity / inflammatory response / innate immune response / plasma membrane
Similarity search - Function
Variable lymphocyte receptor, C-terminal / Domain of unknown function (DUF3439) / Toll-like receptor / : / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / TIR domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain ...Variable lymphocyte receptor, C-terminal / Domain of unknown function (DUF3439) / Toll-like receptor / : / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / TIR domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Leucine-rich repeat, SDS22-like subfamily / 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
Similarity search - Domain/homology
Toll-like receptor 5b / Variable lymphocyte receptor B
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Eptatretus burgeri (inshore hagfish)
Petromyzon marinus (sea lamprey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGunn, R.J. / Wilson, I.A. / Cooper, M.D. / Herrin, B.R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)A1042266 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI072435 United States
CitationJournal: J. Mol. Biol. / Year: 2018
Title: VLR Recognition of TLR5 Expands the Molecular Characterization of Protein Antigen Binding by Non-Ig-based Antibodies.
Authors: Gunn, R.J. / Herrin, B.R. / Acharya, S. / Cooper, M.D. / Wilson, I.A.
History
DepositionDec 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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 / 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_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_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 2.1Mar 23, 2022Group: Author supporting evidence / Database references / Structure summary
Category: chem_comp / database_2 / pdbx_audit_support
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 2.2Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Oct 23, 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: Toll-like receptor 5b, Variable lymphocyte receptor B chimera
B: Toll-like receptor 5b, Variable lymphocyte receptor B chimera
D: Variable Lymphocyte Receptor 9 (VLR9)
C: Variable Lymphocyte Receptor 9 (VLR9)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,0649
Polymers140,9144
Non-polymers1,1505
Water2,180121
1
A: Toll-like receptor 5b, Variable lymphocyte receptor B chimera
D: Variable Lymphocyte Receptor 9 (VLR9)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9615
Polymers70,4572
Non-polymers5043
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint3 kcal/mol
Surface area25190 Å2
MethodPISA
2
B: Toll-like receptor 5b, Variable lymphocyte receptor B chimera
hetero molecules

C: Variable Lymphocyte Receptor 9 (VLR9)


Theoretical massNumber of molelcules
Total (without water)71,1024
Polymers70,4572
Non-polymers6462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_665x+1,y+1,z1
Buried area2420 Å2
ΔGint2 kcal/mol
Surface area25750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.380, 69.413, 84.561
Angle α, β, γ (deg.)112.14, 104.12, 100.81
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 4 molecules ABDC

#1: Protein Toll-like receptor 5b, Variable lymphocyte receptor B chimera


Mass: 51169.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish), (gene. exp.) Eptatretus burgeri (inshore hagfish)
Gene: tlr5b, VLRB / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: F8W3J5, UniProt: Q4G1L2
#2: Protein Variable Lymphocyte Receptor 9 (VLR9)


Mass: 19287.643 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Petromyzon marinus (sea lamprey) / Production host: Spodoptera frugiperda (fall armyworm)

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Sugars , 2 types, 4 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.: 1
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.: 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

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Non-polymers , 2 types, 122 molecules

#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.57 Å3/Da / Density % sol: 52.09 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 15% Peg3350, 170 mM MgNO3, 80 mM MES pH 6.0, 15% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.5→45.3 Å / Num. obs: 42427 / % possible obs: 88.9 % / Redundancy: 1.6 % / CC1/2: 0.92 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.05 / Net I/σ(I): 14.6
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1062 / CC1/2: 0.71 / Rpim(I) all: 0.33 / % possible all: 46

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V47

3v47


Resolution: 2.5→45.272 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 32
RfactorNum. reflection% reflection
Rfree0.2703 2086 4.99 %
Rwork0.2295 --
obs0.2315 41823 89.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→45.272 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9320 0 74 121 9515
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059607
X-RAY DIFFRACTIONf_angle_d1.10513073
X-RAY DIFFRACTIONf_dihedral_angle_d10.2975732
X-RAY DIFFRACTIONf_chiral_restr0.0641528
X-RAY DIFFRACTIONf_plane_restr0.0071667
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.55820.3189750.30641606X-RAY DIFFRACTION54
2.5582-2.62210.36851100.2891819X-RAY DIFFRACTION64
2.6221-2.6930.3221990.28432234X-RAY DIFFRACTION75
2.693-2.77220.33321240.27952499X-RAY DIFFRACTION84
2.7722-2.86170.31621330.27962644X-RAY DIFFRACTION90
2.8617-2.9640.31551470.27322818X-RAY DIFFRACTION95
2.964-3.08260.3341860.28932817X-RAY DIFFRACTION97
3.0826-3.22290.3151400.27042879X-RAY DIFFRACTION98
3.2229-3.39270.29321450.26962960X-RAY DIFFRACTION99
3.3927-3.60520.29981580.2432863X-RAY DIFFRACTION98
3.6052-3.88350.2741620.22272902X-RAY DIFFRACTION98
3.8835-4.2740.26951640.20292911X-RAY DIFFRACTION99
4.274-4.89180.22641250.19182953X-RAY DIFFRACTION99
4.8918-6.16070.21941500.19752934X-RAY DIFFRACTION99
6.1607-45.27940.22111680.2022898X-RAY DIFFRACTION98
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)
12.7146-2.0196-0.13784.78112.15926.11260.43490.45240.3938-0.6968-0.5093-0.7635-0.8972-0.26370.04970.71190.00860.14770.54110.10130.6076-17.6398-15.2417-27.9202
27.7312-0.7510.42591.7693-0.38375.9209-0.12340.5671-0.1419-0.44230.0101-0.2438-0.35960.32820.10790.4073-0.07110.07710.3466-0.06610.5533-13.5217-26.7373-18.1182
32.4849-1.706-0.32983.82020.7492.9677-0.0631-0.0609-0.41060.31420.018-0.24550.09260.0233-0.00760.31950.0114-0.05570.23990.03110.5732-16.7041-30.54875.6065
43.21980.73770.16384.05582.07354.63540.1033-0.33450.1230.8195-0.01370.2111-0.8701-0.2824-0.08150.85290.0988-0.03020.39010.01630.4265-24.3101-13.815323.225
51.17390.09120.39430.3452-0.06130.53010.0145-0.10391.119-0.2676-0.1297-0.1476-1.3177-0.5905-0.05832.56310.53060.18650.3-0.21210.9697-28.66169.814624.4727
67.786-0.8265-3.84724.2102-2.24746.7419-0.1605-0.58460.73550.7132-0.3619-0.0534-0.32751.01520.54010.6849-0.1094-0.13940.511-0.00660.436410.911618.521722.7954
72.1027-1.08-1.07768.6868-1.4594.74450.2751-0.42120.31610.54830.0502-0.4157-0.8680.2149-0.37050.6405-0.09160.05480.4247-0.04840.4841.98219.971319.4645
82.4289-0.08070.86861.8212-0.77745.2725-0.1134-0.02740.2710.1852-0.12130.2748-0.30930.08620.20910.3386-0.01220.00520.25820.01480.6814-3.84420.12882.931
99.0063.36472.43218.7575-0.49054.60.06210.7719-0.3164-0.93710.22870.89850.2677-0.0957-0.22460.3625-0.0386-0.03440.3318-0.00770.4019-8.070413.1045-15.07
104.52931.47410.06816.45852.61166.2349-0.0890.60950.0494-0.288-0.0523-0.18850.07420.1430.12820.30380.03420.05180.4390.10310.39952.953911.5132-21.3849
114.8193-0.7997-0.42197.8974-0.65734.03780.22280.4895-0.2449-0.5433-0.2088-0.04740.11880.89220.01480.38240.0610.02841.00120.15970.427113.951912.7804-28.4273
122.8512-0.3171-0.51178.6761-2.76342.97150.14170.27560.311-1.3209-0.0582-0.22740.55431.657-0.03850.66810.14080.05371.83240.20880.672723.639612.3509-32.3303
130.5887-0.3291-0.24993.4752-0.24120.78580.01820.49370.3501-0.56950.1034-0.9937-0.19321.135-0.16210.5104-0.11730.14242.08540.03090.811431.422414.3086-30.1569
142.49551.6014-1.491.835-0.73960.9373-0.12311.06580.3981-0.75780.2349-1.29710.38031.5351-0.01560.81640.32160.14572.66360.04331.240742.55158.8957-28.8095
153.24122.1631-1.22686.0663-2.2222.6804-0.0548-0.37150.0810.3441-0.0683-0.1856-0.45680.15550.16580.4633-0.14590.14320.3722-0.09630.8244-15.0462-11.5843-8.0721
164.763.399-2.11163.6253-3.04866.56260.26860.42770.2624-0.23380.26550.7837-0.1365-0.2971-0.46890.40160.0234-0.02460.273-0.02880.5925-6.7209-6.336-6.4933
171.90730.7980.36751.6538-0.87213.4766-0.1146-0.1787-0.20660.00850.0138-0.06110.40050.14740.08310.41080.08730.05840.29490.00030.61215.5762-7.29062.2163
187.3387-1.6158-1.64476.1679-0.60014.274-0.16280.10.4150.5781-0.0223-0.64560.25410.73190.11810.26890.0764-0.12620.5519-0.07310.670315.8796-1.64329.6815
195.6759-5.19293.18666.3355-2.88736.0456-0.40290.201-0.84760.83390.3371-0.2805-0.44871.08340.05840.91020.412-0.45341.194-0.41570.837519.8176-9.733518.1271
204.40563.65452.46544.06313.40763.24650.0190.14340.4367-0.00940.3552-0.1716-0.22560.7246-0.15450.341-0.1138-0.02360.3756-0.01670.7779-42.0911-46.43993.0914
213.13051.7333.37515.79093.72957.22740.5185-0.1397-0.62330.484-0.0602-0.7750.7720.2095-0.52630.2817-0.02660.00840.36790.00160.4754-38.5149-37.36111.3568
224.59894.06420.28867.58252.37236.6376-0.18841.06560.24150.2817-0.2533-0.23210.5066-0.37020.36020.30590.0015-0.03690.43640.02550.7629-41.7464-35.7949-9.7672
230.52830.0071.26712.26932.47629.1690.11380.0070.0111-0.1256-0.16480.4086-0.3395-0.4170.00180.2471-0.0181-0.04630.4436-0.08390.6656-43.5004-28.5907-3.6686
247.64770.00432.8314.01151.24443.4463-0.09590.0671-0.3176-0.13510.1040.5737-0.4960.52070.0170.31060.00590.03940.1647-0.00110.5737-39.1487-24.9667-4.776
253.7443-0.80190.99720.79881.36115.9888-0.32990.03811.1039-0.0763-0.45070.692-0.6467-0.57410.66060.37590.06920.02110.28110.01640.7335-42.1626-18.6002-6.2876
268.5835-3.01774.51186.8489-0.80582.514-0.49891.6977-0.4058-0.3295-0.08771.5734-0.27110.34990.3470.38770.0765-0.10310.7317-0.06330.613-41.1635-20.2111-19.4398
275.0784-4.0316-2.71155.83160.96571.9875-1.14040.18021.1833-0.0222-0.0825-0.8241-1.0432-0.13411.08430.71770.1185-0.00950.39710.15950.7674-41.4006-12.4332-11.1387
283.41540.42763.18458.7511-1.54653.52860.44431.59760.8694-1.37220.6558-0.3624-0.77980.376-1.03190.6220.0650.21050.82930.10180.5015-34.1673-16.9784-19.4705
291.8976-2.44121.0644.036-2.43691.8717-0.18470.18130.494-0.26360.13240.4068-0.39940.11450.42021.26860.5939-0.01650.99610.62180.7741-46.7802-10.9369-22.8626
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 63 )
2X-RAY DIFFRACTION2chain 'A' and (resid 64 through 152 )
3X-RAY DIFFRACTION3chain 'A' and (resid 153 through 267 )
4X-RAY DIFFRACTION4chain 'A' and (resid 268 through 385 )
5X-RAY DIFFRACTION5chain 'A' and (resid 386 through 464 )
6X-RAY DIFFRACTION6chain 'B' and (resid 24 through 63 )
7X-RAY DIFFRACTION7chain 'B' and (resid 64 through 92 )
8X-RAY DIFFRACTION8chain 'B' and (resid 93 through 203 )
9X-RAY DIFFRACTION9chain 'B' and (resid 204 through 232 )
10X-RAY DIFFRACTION10chain 'B' and (resid 233 through 303 )
11X-RAY DIFFRACTION11chain 'B' and (resid 304 through 356 )
12X-RAY DIFFRACTION12chain 'B' and (resid 357 through 385 )
13X-RAY DIFFRACTION13chain 'B' and (resid 386 through 418 )
14X-RAY DIFFRACTION14chain 'B' and (resid 419 through 464 )
15X-RAY DIFFRACTION15chain 'D' and (resid 16 through 26 )
16X-RAY DIFFRACTION16chain 'D' and (resid 27 through 55 )
17X-RAY DIFFRACTION17chain 'D' and (resid 56 through 138 )
18X-RAY DIFFRACTION18chain 'D' and (resid 139 through 166 )
19X-RAY DIFFRACTION19chain 'D' and (resid 167 through 181 )
20X-RAY DIFFRACTION20chain 'C' and (resid 16 through 26 )
21X-RAY DIFFRACTION21chain 'C' and (resid 27 through 55 )
22X-RAY DIFFRACTION22chain 'C' and (resid 56 through 65 )
23X-RAY DIFFRACTION23chain 'C' and (resid 66 through 94 )
24X-RAY DIFFRACTION24chain 'C' and (resid 95 through 108 )
25X-RAY DIFFRACTION25chain 'C' and (resid 109 through 127 )
26X-RAY DIFFRACTION26chain 'C' and (resid 128 through 138 )
27X-RAY DIFFRACTION27chain 'C' and (resid 139 through 153 )
28X-RAY DIFFRACTION28chain 'C' and (resid 154 through 166 )
29X-RAY DIFFRACTION29chain 'C' and (resid 167 through 180 )

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