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- PDB-5zsg: Crystal structure of monkey TLR7 in complex with gardiquimod -

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Basic information

Entry
Database: PDB / ID: 5zsg
TitleCrystal structure of monkey TLR7 in complex with gardiquimod
ComponentsToll-like receptor 7
KeywordsIMMUNE SYSTEM / Innate immunity Toll-like receptors
Function / homology
Function and homology information


regulation of macromolecule metabolic process / inflammatory response / innate immune response / signal transduction / membrane
Similarity search - Function
BspA type Leucine rich repeat region (6 copies) / TIR domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / TIR domain profile. / Alpha-Beta Horseshoe / Toll/interleukin-1 receptor homology (TIR) domain ...BspA type Leucine rich repeat region (6 copies) / TIR domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / TIR domain profile. / Alpha-Beta Horseshoe / 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 / Alpha Beta
Similarity search - Domain/homology
Chem-9K3 / Toll-like receptor 7
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhang, Z. / Ohto, U. / Shimizu, T.
CitationJournal: Cell Rep / Year: 2018
Title: Structural Analyses of Toll-like Receptor 7 Reveal Detailed RNA Sequence Specificity and Recognition Mechanism of Agonistic Ligands.
Authors: Zhang, Z. / Ohto, U. / Shibata, T. / Taoka, M. / Yamauchi, Y. / Sato, R. / Shukla, N.M. / David, S.A. / Isobe, T. / Miyake, K. / Shimizu, T.
History
DepositionApr 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
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_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_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _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 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / citation / citation_author / database_2
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Toll-like receptor 7
A: Toll-like receptor 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,01727
Polymers189,4912
Non-polymers5,52625
Water11,872659
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12160 Å2
ΔGint-56 kcal/mol
Surface area64340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.337, 140.182, 151.661
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein Toll-like receptor 7


Mass: 94745.594 Da / Num. of mol.: 2 / Fragment: UNP residues 27-839 / Mutation: N167Q,N389Q,N488Q,N799Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: EGK_20273 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: G7NS93

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Sugars , 2 types, 15 molecules

#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 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
#3: 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.: 11
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 , 3 types, 669 molecules

#4: Chemical ChemComp-9K3 / 1-{4-amino-2-[(ethylamino)methyl]-1H-imidazo[4,5-c]quinolin-1-yl}-2-methylpropan-2-ol


Mass: 313.397 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H23N5O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 659 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsThe residues 440-445 (SEVGFC) are replaced by a thrombin-cleavage sequence (LVPRGS) for artificial ...The residues 440-445 (SEVGFC) are replaced by a thrombin-cleavage sequence (LVPRGS) for artificial cleavage of Z-loop. This engineered site in Z-loop was further cleaved during purification and the cleaved protein remained associated via interactions between LRRs and a disulfide bond. Therefore, although cleaved, the cleaved version of protein is considered as one single component (chain).

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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: 2.78 Å3/Da / Density % sol: 55.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, ammonium sulfate, sodium citrate pH 5.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 94528 / % possible obs: 100 % / Redundancy: 13.5 % / Net I/σ(I): 18.8
Reflection shellResolution: 2.3→2.34 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→47.202 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.46
RfactorNum. reflection% reflection
Rfree0.2243 4671 4.94 %
Rwork0.1864 --
obs0.1882 94528 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→47.202 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12500 0 352 659 13511
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113165
X-RAY DIFFRACTIONf_angle_d1.22417896
X-RAY DIFFRACTIONf_dihedral_angle_d6.78311042
X-RAY DIFFRACTIONf_chiral_restr0.0672085
X-RAY DIFFRACTIONf_plane_restr0.0072244
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.32610.27821550.23712940X-RAY DIFFRACTION100
2.3261-2.35350.30151430.25222975X-RAY DIFFRACTION100
2.3535-2.38220.32371650.25042951X-RAY DIFFRACTION100
2.3822-2.41240.30661640.24912959X-RAY DIFFRACTION100
2.4124-2.44410.31561730.2392913X-RAY DIFFRACTION100
2.4441-2.47760.29061810.24722935X-RAY DIFFRACTION100
2.4776-2.5130.27981560.23842992X-RAY DIFFRACTION100
2.513-2.55050.28751740.24092964X-RAY DIFFRACTION100
2.5505-2.59030.28551580.23352940X-RAY DIFFRACTION100
2.5903-2.63280.28931550.23172966X-RAY DIFFRACTION100
2.6328-2.67820.29591670.22952964X-RAY DIFFRACTION100
2.6782-2.72690.24731580.21322968X-RAY DIFFRACTION100
2.7269-2.77930.2611570.212967X-RAY DIFFRACTION100
2.7793-2.83610.2411670.20292969X-RAY DIFFRACTION100
2.8361-2.89770.25081600.2012942X-RAY DIFFRACTION100
2.8977-2.96510.27411750.21112969X-RAY DIFFRACTION100
2.9651-3.03920.27481300.21473030X-RAY DIFFRACTION100
3.0392-3.12140.25821510.21712989X-RAY DIFFRACTION100
3.1214-3.21320.2811430.21622974X-RAY DIFFRACTION100
3.2132-3.31690.28381430.2113009X-RAY DIFFRACTION100
3.3169-3.43540.22911350.19313020X-RAY DIFFRACTION100
3.4354-3.57290.18841500.18423005X-RAY DIFFRACTION100
3.5729-3.73550.20851550.1682993X-RAY DIFFRACTION100
3.7355-3.93230.20631160.15563056X-RAY DIFFRACTION100
3.9323-4.17860.18021180.14423055X-RAY DIFFRACTION100
4.1786-4.5010.17681830.14053002X-RAY DIFFRACTION100
4.501-4.95350.15921430.13973044X-RAY DIFFRACTION100
4.9535-5.66920.1621630.15463065X-RAY DIFFRACTION100
5.6692-7.13870.19951620.18093098X-RAY DIFFRACTION100
7.1387-47.21160.19471710.18853203X-RAY DIFFRACTION100

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