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- PDB-6nig: Crystal structure of the human TLR2-Diprovocim complex -

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Basic information

Entry
Database: PDB / ID: 6nig
TitleCrystal structure of the human TLR2-Diprovocim complex
ComponentsToll-like receptor 2,Variable lymphocyte receptor B
KeywordsIMMUNE SYSTEM/AGONIST / Toll-like receptors / innate immune agonist / IMMUNE SYSTEM-AGONIST complex
Function / homology
Function and homology information


Toll Like Receptor TLR6:TLR2 Cascade / triacyl lipopeptide binding / Toll-like receptor 2-Toll-like receptor 6 protein complex / detection of diacyl bacterial lipopeptide / cellular response to diacyl bacterial lipopeptide / Toll-like receptor 1-Toll-like receptor 2 protein complex / detection of triacyl bacterial lipopeptide / cellular response to triacyl bacterial lipopeptide / cellular response to bacterial lipopeptide / negative regulation of synapse assembly ...Toll Like Receptor TLR6:TLR2 Cascade / triacyl lipopeptide binding / Toll-like receptor 2-Toll-like receptor 6 protein complex / detection of diacyl bacterial lipopeptide / cellular response to diacyl bacterial lipopeptide / Toll-like receptor 1-Toll-like receptor 2 protein complex / detection of triacyl bacterial lipopeptide / cellular response to triacyl bacterial lipopeptide / cellular response to bacterial lipopeptide / negative regulation of synapse assembly / positive regulation of cellular response to macrophage colony-stimulating factor stimulus / Toll Like Receptor TLR1:TLR2 Cascade / Beta defensins / lipopolysaccharide immune receptor activity / toll-like receptor 2 signaling pathway / positive regulation of matrix metallopeptidase secretion / positive regulation of interleukin-18 production / Toll-like receptor binding / toll-like receptor TLR6:TLR2 signaling pathway / Regulation of TLR by endogenous ligand / peptidoglycan binding / NAD+ nucleosidase activity, cyclic ADP-ribose generating / microglia development / MyD88 deficiency (TLR2/4) / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / negative regulation of phagocytosis / toll-like receptor signaling pathway / pattern recognition receptor activity / RSV-host interactions / cellular response to lipoteichoic acid / positive regulation of Wnt signaling pathway / positive regulation of chemokine production / positive regulation of interleukin-12 production / positive regulation of interferon-beta production / secretory granule membrane / positive regulation of interleukin-8 production / learning / lipopolysaccharide binding / : / cellular response to type II interferon / positive regulation of interleukin-6 production / phagocytic vesicle membrane / positive regulation of inflammatory response / positive regulation of tumor necrosis factor production / Modulation by Mtb of host immune system / transmembrane signaling receptor activity / signaling receptor activity / amyloid-beta binding / ER-Phagosome pathway / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / receptor complex / defense response to Gram-positive bacterium / immune response / membrane raft / inflammatory response / innate immune response / intracellular membrane-bounded organelle / apoptotic process / Neutrophil degranulation / positive regulation of gene expression / protein-containing complex binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / cell surface / Golgi apparatus / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Leucine rich repeat C-terminal domain / Variable lymphocyte receptor, C-terminal / Domain of unknown function (DUF3439) / Toll-like receptor / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain ...: / Leucine rich repeat C-terminal domain / Variable lymphocyte receptor, C-terminal / Domain of unknown function (DUF3439) / Toll-like receptor / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / 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 repeats, bacterial type / 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
Similarity search - Domain/homology
Chem-KQD / Toll-like receptor 2 / Variable lymphocyte receptor B
Similarity search - Component
Biological speciesHomo sapiens (human)
Eptatretus stoutii (Pacific hagfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsZhang, H. / Beutler, B.A. / Tomchick, D.R. / Su, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: J. Med. Chem. / Year: 2019
Title: Structural Basis of TLR2/TLR1 Activation by the Synthetic Agonist Diprovocim.
Authors: Su, L. / Wang, Y. / Wang, J. / Mifune, Y. / Morin, M.D. / Jones, B.T. / Moresco, E.M.Y. / Boger, D.L. / Beutler, B. / Zhang, H.
History
DepositionDec 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / 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_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 2.1Oct 11, 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 20, 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 2,Variable lymphocyte receptor B
B: Toll-like receptor 2,Variable lymphocyte receptor B
C: Toll-like receptor 2,Variable lymphocyte receptor B
D: Toll-like receptor 2,Variable lymphocyte receptor B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,43521
Polymers261,1114
Non-polymers7,32517
Water68538
1
A: Toll-like receptor 2,Variable lymphocyte receptor B
B: Toll-like receptor 2,Variable lymphocyte receptor B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,55012
Polymers130,5552
Non-polymers3,99410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint10 kcal/mol
Surface area49840 Å2
MethodPISA
2
C: Toll-like receptor 2,Variable lymphocyte receptor B
D: Toll-like receptor 2,Variable lymphocyte receptor B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,8869
Polymers130,5552
Non-polymers3,3317
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint5 kcal/mol
Surface area49370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.098, 201.252, 109.359
Angle α, β, γ (deg.)90.000, 94.260, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Toll-like receptor 2,Variable lymphocyte receptor B / Toll/interleukin-1 receptor-like protein 4


Mass: 65277.645 Da / Num. of mol.: 4
Fragment: TLR (UNP residues 1-507) + linker + VLR (UNP residues 181-248)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Eptatretus stoutii (Pacific hagfish)
Gene: TLR2, TIL4, VLRB / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O60603, UniProt: Q2YE02
#2: 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 natural 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
#3: Chemical
ChemComp-KQD / (3S,4S,3'S,4'S)-1,1'-(1,4-phenylenedicarbonyl)bis{N~3~,N~4~-bis[(1S,2R)-2-phenylcyclopropyl]pyrrolidine-3,4-dicarboxami de} / Diprovocim


Mass: 909.080 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C56H56N6O6
#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.: 9 / Source method: isolated from a natural 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.: 38 / Source method: isolated from a natural source / Formula: H2O
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: 2.72 Å3/Da / Density % sol: 54.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium citrate tribasic, pH 7.0, 0.1 M imidazole, pH 7.5, 18% PEG1900 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 16, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 118654 / % possible obs: 94.7 % / Redundancy: 4.3 % / Biso Wilson estimate: 66.79 Å2 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.036 / Rrim(I) all: 0.08 / Χ2: 1.464 / Net I/σ(I): 8.2 / Num. measured all: 506871
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.343.80.74549630.7550.3760.8390.45979.2
2.34-2.383.80.70354330.7580.3620.7960.46786.4
2.38-2.433.90.60256360.8160.3140.6830.46789.9
2.43-2.483.90.54858440.8280.2890.6230.4894.5
2.48-2.533.80.47358930.8720.2580.5420.48793.5
2.53-2.594.10.42757970.9010.2240.4850.51493.8
2.59-2.664.40.32960900.9380.1660.370.55597.4
2.66-2.734.40.26461400.9590.1330.2970.6197.7
2.73-2.814.40.21561000.9710.1090.2420.68197.7
2.81-2.94.40.17461160.9810.0880.1960.79897.4
2.9-34.30.15860830.9810.0810.1780.88997.2
3-3.124.10.13959010.9810.0750.1591.03794.4
3.12-3.264.50.11360780.9890.0560.1261.41697.5
3.26-3.444.60.09561600.9920.0460.1061.89498.1
3.44-3.654.60.08561170.9940.0420.0952.38997.3
3.65-3.934.50.07461010.9950.0360.0822.88297.8
3.93-4.334.30.06759390.9950.0340.0763.11994.8
4.33-4.954.60.06161320.9960.030.0683.15197.6
4.95-6.244.40.05760220.9960.0280.0642.90495.7
6.24-504.60.04361090.9980.0220.0492.50395.8

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Z7X

2z7x


Resolution: 2.35→37.761 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 27.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2361 3364 3 %
Rwork0.2098 108592 -
obs0.2105 111956 94.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 263.33 Å2 / Biso mean: 93.801 Å2 / Biso min: 42.14 Å2
Refinement stepCycle: final / Resolution: 2.35→37.761 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17383 0 950 38 18371
Biso mean--82.89 59.17 -
Num. residues----2186
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3499-2.38350.35311360.31593819395581
2.3835-2.41910.33851470.30314025417286
2.4191-2.45690.3311340.29384289442389
2.4569-2.49710.3291350.29454371450693
2.4971-2.54020.33091430.28884366450990
2.5402-2.58640.281470.27094426457394
2.5864-2.63610.30571400.27484666480697
2.6361-2.68990.31531230.26154642476598
2.6899-2.74840.31731340.26454693482797
2.7484-2.81230.27381550.26274612476798
2.8123-2.88260.30561300.25834668479897
2.8826-2.96050.31541530.26894639479298
2.9605-3.04760.27541310.2754607473896
3.0476-3.14590.32031200.27144432455292
3.1459-3.25830.30831390.26734684482399
3.2583-3.38870.26791460.25984699484598
3.3887-3.54280.28931520.23874652480498
3.5428-3.72940.24091740.20934619479398
3.7294-3.96280.20371460.19124645479197
3.9628-4.26840.17861240.18194510463494
4.2684-4.69720.21861410.16324700484198
4.6972-5.37530.20861350.1624682481798
5.3753-6.76590.21751260.19764583470995
6.7659-37.76550.18121530.18014563471694
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)
10.9351-0.87720.29584.0754-1.94613.66830.02370.1976-0.0188-0.46230.04290.1110.3508-0.5025-0.09020.5808-0.146-0.00320.59440.00420.5182-3.975220.018560.7457
28.22311.0372-4.40870.71390.45476.746-0.6816-0.0945-0.6712-0.13740.1492-0.231.35360.26050.46940.80920.04240.00340.543-0.0390.69238.32026.687384.1145
33.50712.8985-0.5364.61510.37434.2065-0.1081-0.28410.07250.12980.1898-0.10970.5860.3717-0.05620.49550.0964-0.01690.526-0.06880.524613.038416.428994.2743
41.46970.1276-0.22454.9246-2.40554.37820.01850.22640.2058-0.0686-0.0417-0.3992-0.25370.43270.04450.2937-0.0483-0.04390.6632-0.11360.764223.970246.275489.8048
51.5768-0.01190.26182.44051.44114.96320.0696-0.46180.30560.55250.4622-0.52450.37160.7549-0.51740.82940.3046-0.11241.005-0.1460.826415.534116.7219148.0206
63.8312-1.34490.35453.5465-1.45694.23140.12610.065-0.31720.07960.1322-0.01560.7888-0.0467-0.20.64720.0405-0.09580.4646-0.00540.5086-0.13819.3099117.4438
71.450.49460.40266.05112.27784.0191-0.068-0.3370.3049-0.0134-0.09690.3758-0.3772-0.30220.20340.36560.0731-0.0190.637-0.00260.5926-12.666644.2873117.1789
82.4383-0.5707-0.86482.68071.12043.6350.22350.3844-0.08-0.61120.0559-0.4036-0.2550.4743-0.28051.0315-0.24020.18560.7935-0.05510.701122.227678.535962.1537
93.98571.8845-0.21543.9683-1.80194.2941-0.00040.05520.5132-0.22260.17840.0938-0.73760.1365-0.16620.7458-0.0970.06520.4697-0.02590.54334.24888.581888.4363
100.8170.1952-0.15935.86032.22954.1902-0.10320.1513-0.0648-0.06750.06130.10730.3725-0.18050.0680.3533-0.12730.01730.58740.08120.5055-10.402654.393189.5439
111.30471.0066-0.84745.2657-1.85542.43960.0293-0.13890.07980.55270.02860.223-0.0896-0.1394-0.07820.73230.12250.05450.5984-0.00710.5543-11.979473.6134147.5858
127.7286-0.63092.22015.798-0.73787.3098-0.0356-0.24860.5180.50270.1059-0.1937-0.8228-0.0272-0.03460.57050.05740.06250.483-0.04250.52543.753989.4354128.0948
130.7625-0.89810.04333.867-0.22631.9874-0.1192-0.0491-0.15840.05190.262-0.32460.11180.3357-0.11150.354-0.0031-0.01610.7308-0.140.692118.545659.2734118.6096
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 275 )A27 - 275
2X-RAY DIFFRACTION2chain 'A' and (resid 276 through 315 )A276 - 315
3X-RAY DIFFRACTION3chain 'A' and (resid 316 through 401 )A316 - 401
4X-RAY DIFFRACTION4chain 'A' and (resid 402 through 575 )A402 - 575
5X-RAY DIFFRACTION5chain 'B' and (resid 27 through 240 )B27 - 240
6X-RAY DIFFRACTION6chain 'B' and (resid 241 through 390 )B241 - 390
7X-RAY DIFFRACTION7chain 'B' and (resid 391 through 575 )B391 - 575
8X-RAY DIFFRACTION8chain 'C' and (resid 27 through 240 )C27 - 240
9X-RAY DIFFRACTION9chain 'C' and (resid 241 through 366 )C241 - 366
10X-RAY DIFFRACTION10chain 'C' and (resid 367 through 575 )C367 - 575
11X-RAY DIFFRACTION11chain 'D' and (resid 27 through 240 )D27 - 240
12X-RAY DIFFRACTION12chain 'D' and (resid 241 through 315 )D241 - 315
13X-RAY DIFFRACTION13chain 'D' and (resid 316 through 575 )D316 - 575

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