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- PDB-6nih: Crystal structure of human TLR1 -

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Basic information

Entry
Database: PDB / ID: 6nih
TitleCrystal structure of human TLR1
ComponentsToll-like receptor 1,Variable lymphocyte receptor B
KeywordsIMMUNE SYSTEM / Toll-like receptors
Function / homology
Function and homology information


Toll-like receptor 1-Toll-like receptor 2 protein complex / detection of triacyl bacterial lipopeptide / cellular response to triacyl bacterial lipopeptide / positive regulation of toll-like receptor 2 signaling pathway / Toll Like Receptor TLR1:TLR2 Cascade / Beta defensins / Toll-like receptor 2 binding / macrophage activation / Regulation of TLR by endogenous ligand / lipopeptide binding ...Toll-like receptor 1-Toll-like receptor 2 protein complex / detection of triacyl bacterial lipopeptide / cellular response to triacyl bacterial lipopeptide / positive regulation of toll-like receptor 2 signaling pathway / Toll Like Receptor TLR1:TLR2 Cascade / Beta defensins / Toll-like receptor 2 binding / macrophage activation / Regulation of TLR by endogenous ligand / lipopeptide binding / NAD+ nucleotidase, cyclic ADP-ribose generating / MyD88 deficiency (TLR2/4) / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor signaling pathway / positive regulation of interleukin-8 production / phagocytic vesicle membrane / transmembrane signaling receptor activity / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / signaling receptor activity / ER-Phagosome pathway / membrane => GO:0016020 / receptor complex / inflammatory response / immune response / membrane raft / innate immune response / SARS-CoV-2 activates/modulates innate and adaptive immune responses / Golgi apparatus / signal transduction / identical protein binding / membrane / plasma membrane
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 N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / TIR domain / Leucine-rich repeats, bacterial type / 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 / Leucine-rich repeats, bacterial type / 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 / 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
triacetyl-beta-chitotriose / Toll-like receptor 1 / Variable lymphocyte receptor B
Similarity search - Component
Biological speciesHomo sapiens (human)
Eptatretus stoutii (Pacific hagfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSu, L. / Zhang, H.
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: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / 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_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_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 / _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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Toll-like receptor 1,Variable lymphocyte receptor B
B: Toll-like receptor 1,Variable lymphocyte receptor B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,2589
Polymers124,6942
Non-polymers2,5647
Water3,891216
1
A: Toll-like receptor 1,Variable lymphocyte receptor B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4174
Polymers62,3471
Non-polymers1,0703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Toll-like receptor 1,Variable lymphocyte receptor B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8415
Polymers62,3471
Non-polymers1,4944
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.028, 74.377, 106.076
Angle α, β, γ (deg.)90.000, 96.970, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 26 through 93 or resid 95...
21(chain B and (resid 26 through 93 or resid 95...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUGLNGLN(chain A and (resid 26 through 93 or resid 95...AA26 - 9326 - 93
12LEULEUTHRTHR(chain A and (resid 26 through 93 or resid 95...AA95 - 14995 - 149
13LEULEUSERSER(chain A and (resid 26 through 93 or resid 95...AA151 - 247151 - 247
14LEULEUSERSER(chain A and (resid 26 through 93 or resid 95...AA249 - 279249 - 279
15VALVALVALVAL(chain A and (resid 26 through 93 or resid 95...AA281 - 339281 - 339
16METMETCYSCYS(chain A and (resid 26 through 93 or resid 95...AA341 - 543341 - 543
21GLUGLUGLNGLN(chain B and (resid 26 through 93 or resid 95...BB26 - 9326 - 93
22LEULEUTHRTHR(chain B and (resid 26 through 93 or resid 95...BB95 - 14995 - 149
23LEULEUSERSER(chain B and (resid 26 through 93 or resid 95...BB151 - 247151 - 247
24LEULEUSERSER(chain B and (resid 26 through 93 or resid 95...BB249 - 279249 - 279
25GLUGLUTHRTHR(chain B and (resid 26 through 93 or resid 95...BB26 - 54526 - 545

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Components

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


Mass: 62346.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Eptatretus stoutii (Pacific hagfish)
Gene: TLR1, KIAA0012, VLRB / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q15399, UniProt: Q2YDZ3
#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.: 3 / 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: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / triacetyl-beta-chitotriose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 627.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: oligosaccharide / References: triacetyl-beta-chitotriose
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(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 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.: 216 / 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: 2.5 Å3/Da / Density % sol: 50.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium citrate tribasic pH7.0, 0.1 M imidazole pH7.5 and 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: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 59039 / % possible obs: 99.1 % / Redundancy: 8.5 % / CC1/2: 0.946 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.034 / Rrim(I) all: 0.101 / Χ2: 1.027 / Net I/σ(I): 5.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.25-2.297.41.44729210.7080.5481.5520.8398.8
2.29-2.337.71.28329420.790.4791.3730.81898.5
2.33-2.388.61.03229350.850.361.0950.82299.5
2.38-2.428.50.85529530.8950.30.9080.82599.5
2.42-2.488.60.76729500.9230.2680.8140.82899.6
2.48-2.538.50.65129000.9320.2290.6910.83599.4
2.53-2.68.50.54329730.9560.1920.5780.81699.2
2.6-2.678.40.45829320.9640.1630.4880.83199.1
2.67-2.758.20.35929370.9760.1290.3820.83999.2
2.75-2.837.60.31729090.980.1190.340.8597.9
2.83-2.948.90.2429270.990.0830.2550.88699.4
2.94-3.058.80.20629820.9910.0710.2180.92699.9
3.05-3.198.90.16629310.9930.0570.1751.02699.3
3.19-3.368.80.1329520.9950.0450.1381.14399.3
3.36-3.578.50.11429640.9950.040.1211.32299.1
3.57-3.858.30.129410.9960.0360.1061.598.7
3.85-4.2390.08829760.9970.030.0931.55999.8
4.23-4.858.90.08429800.9960.0290.0891.53899.1
4.85-6.18.40.07829890.9960.0280.0831.26398.6
6.1-508.70.06130450.9980.0220.0650.95698.9

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2z7x

2z7x


Resolution: 2.3→46.397 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 31.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2736 1958 4.81 %
Rwork0.2435 38761 -
obs0.2449 40719 74.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 183.68 Å2 / Biso mean: 50.5567 Å2 / Biso min: 6.86 Å2
Refinement stepCycle: final / Resolution: 2.3→46.397 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8336 0 318 216 8870
Biso mean--48.78 32.06 -
Num. residues----1039
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4954X-RAY DIFFRACTION9.217TORSIONAL
12B4954X-RAY DIFFRACTION9.217TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.35750.3715480.308593898626
2.3575-2.42120.3761570.3031148120531
2.4212-2.49250.3178740.29241460153440
2.4925-2.57290.2954930.29431834192750
2.5729-2.66490.30731110.29642207231860
2.6649-2.77150.35081330.29362622275571
2.7715-2.89770.3041530.29573029318282
2.8977-3.05040.31291700.29283371354192
3.0504-3.24150.30041850.27583661384698
3.2415-3.49170.30121840.2553637382199
3.4917-3.84290.24621840.22483666385099
3.8429-4.39860.26091900.201737323922100
4.3986-5.54030.22581840.19783663384798
5.5403-46.40670.24491920.22773793398599
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)
15.0271.28030.80681.56540.48492.61250.1811-0.7915-0.5220.4583-0.2343-0.45470.04540.06150.0190.1879-0.097-0.08870.27440.02340.354683.6658-47.995140.4426
21.26610.7217-0.91730.9516-0.42180.729-0.12980.77890.006-0.20860.22570.15720.0568-0.30430.43150.0955-0.19270.02940.6034-0.1380.260975.1983-41.48923.3074
31.9376-1.73890.48156.1758-1.08243.5010.21651.1277-0.2809-1.213-0.0663-0.00330.399-0.4386-0.110.4869-0.22460.07951.1543-0.09090.375485.6732-41.64951.8113
41.9532-2.6326-3.10357.10962.73345.52040.19230.4769-0.1395-0.706-0.37260.23410.0345-0.41980.16840.3413-0.17540.02390.9285-0.10770.270393.219-35.27161.1476
50.7295-0.8330.49195.0614-0.46960.35260.24110.3697-0.0853-0.7219-0.3796-0.0206-0.03010.03320.1420.4121-0.0250.04490.60830.01620.223798.5577-33.46310.5697
61.7473-0.0863-0.06212.1076-0.0361.0682-0.06270.2135-0.0197-0.2754-0.1462-0.5377-0.00040.47710.18590.41580.00140.10970.63770.13690.3575115.3412-30.57444.8096
72.5448-1.4999-0.35045.891-0.67492.8334-0.1077-0.48830.2430.67250.1937-1.1058-0.23660.6707-0.09530.4865-0.1117-0.11841.05440.1430.5702127.8145-23.339319.5564
84.4604-1.25751.63592.96110.544.9356-0.0608-1.05220.09650.97360.1393-1.17230.11310.7701-0.02840.926-0.0901-0.32851.10530.17220.6942129.7808-25.163633.4527
90.56020.8141-0.0522.6717-0.10563.68630.1338-1.3194-0.34591.78350.238-0.96220.22490.316-0.38251.01160.0998-0.28041.72680.23950.8269127.8119-24.363342.669
101.4697-1.72910.08562.13130.24981.35950.04960.44130.4004-0.3630.1048-0.7033-0.09980.4853-0.17430.2706-0.03980.15270.6662-0.07880.2747104.87620.986913.908
111.51310.4155-1.67341.1803-0.34274.0990.15670.53890.0277-0.26660.15520.3678-0.1499-0.6051-0.17110.18240.0143-0.01360.2903-0.03740.185880.0469-4.432525.4064
122.15540.56780.25492.5501-0.60442.51620.0841-0.01370.01030.20.09480.2643-0.0274-0.3385-0.04460.1546-0.0570.01780.1187-0.04030.163878.0523-9.009639.8714
132.96690.92620.0121.5387-0.70144.11360.061-0.21060.32070.03980.02150.4434-0.4084-0.4841-0.04890.0877-0.01870.01250.2012-0.10650.210578.161-8.233149.9376
142.39690.2411-0.270.7301-0.03610.2719-0.0453-0.4135-0.50450.09250.0804-0.28780.09250.114-0.06390.1552-0.004-0.05520.066-0.02260.3878101.9012-18.278563.233
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 61 )A25 - 61
2X-RAY DIFFRACTION2chain 'A' and (resid 62 through 195 )A62 - 195
3X-RAY DIFFRACTION3chain 'A' and (resid 196 through 241 )A196 - 241
4X-RAY DIFFRACTION4chain 'A' and (resid 242 through 270 )A242 - 270
5X-RAY DIFFRACTION5chain 'A' and (resid 271 through 305 )A271 - 305
6X-RAY DIFFRACTION6chain 'A' and (resid 306 through 416 )A306 - 416
7X-RAY DIFFRACTION7chain 'A' and (resid 417 through 471 )A417 - 471
8X-RAY DIFFRACTION8chain 'A' and (resid 472 through 511 )A472 - 511
9X-RAY DIFFRACTION9chain 'A' and (resid 512 through 543 )A512 - 543
10X-RAY DIFFRACTION10chain 'B' and (resid 26 through 159 )B26 - 159
11X-RAY DIFFRACTION11chain 'B' and (resid 160 through 270 )B160 - 270
12X-RAY DIFFRACTION12chain 'B' and (resid 271 through 309 )B271 - 309
13X-RAY DIFFRACTION13chain 'B' and (resid 310 through 344 )B310 - 344
14X-RAY DIFFRACTION14chain 'B' and (resid 345 through 545 )B345 - 545

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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