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- PDB-5zsf: Crystal structure of monkey TLR7 in complex with imiquimod -

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Basic information

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


toll-like receptor 7 signaling pathway / response to cGMP / siRNA binding / early phagosome / positive regulation of macrophage cytokine production / pattern recognition receptor activity / toll-like receptor signaling pathway / positive regulation of interferon-alpha production / canonical NF-kappaB signal transduction / positive regulation of chemokine production ...toll-like receptor 7 signaling pathway / response to cGMP / siRNA binding / early phagosome / positive regulation of macrophage cytokine production / pattern recognition receptor activity / toll-like receptor signaling pathway / positive regulation of interferon-alpha production / canonical NF-kappaB signal transduction / positive regulation of chemokine production / JNK cascade / positive regulation of interferon-beta production / positive regulation of interleukin-8 production / regulation of protein phosphorylation / cellular response to virus / positive regulation of interleukin-6 production / cellular response to mechanical stimulus / positive regulation of non-canonical NF-kappaB signal transduction / double-stranded RNA binding / positive regulation of type II interferon production / defense response to virus / lysosome / single-stranded RNA binding / receptor complex / endosome / inflammatory response / innate immune response / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / plasma membrane
Similarity search - Function
BspA type Leucine rich repeat region (6 copies) / TIR domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Leucine-rich repeat, SDS22-like subfamily / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain ...BspA type Leucine rich repeat region (6 copies) / TIR domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Leucine-rich repeat, SDS22-like subfamily / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Alpha-Beta Horseshoe / 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
1-(2-methylpropyl)imidazo[4,5-c]quinolin-4-amine / Toll-like receptor 7
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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: 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_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 / _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

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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)194,17021
Polymers189,4912
Non-polymers4,67819
Water15,583865
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10990 Å2
ΔGint11 kcal/mol
Surface area63930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.265, 140.115, 151.336
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: TLR7 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: B3Y653

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Sugars , 2 types, 14 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 10
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, 870 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: SO4
#5: Chemical ChemComp-6T0 / 1-(2-methylpropyl)imidazo[4,5-c]quinolin-4-amine / Imiquimod


Mass: 240.304 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C14H16N4 / Comment: medication*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 865 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 55.71 %
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 / Serial crystal experiment: N
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: 2.1→50 Å / Num. obs: 123381 / % possible obs: 100 % / Redundancy: 13.5 % / Net I/σ(I): 19.9
Reflection shellResolution: 2.1→2.14 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: 2.1→47.161 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2369 6049 4.9 %
Rwork0.1923 --
obs0.1944 123381 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→47.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12500 0 303 865 13668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00913120
X-RAY DIFFRACTIONf_angle_d1.11917828
X-RAY DIFFRACTIONf_dihedral_angle_d6.9611030
X-RAY DIFFRACTIONf_chiral_restr0.0652080
X-RAY DIFFRACTIONf_plane_restr0.0072242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.12390.31732120.27653848X-RAY DIFFRACTION100
2.1239-2.14890.33152100.2783853X-RAY DIFFRACTION100
2.1489-2.17510.31191990.27263851X-RAY DIFFRACTION100
2.1751-2.20260.30232170.26553894X-RAY DIFFRACTION100
2.2026-2.23160.30832140.25123825X-RAY DIFFRACTION100
2.2316-2.26210.30672020.25983896X-RAY DIFFRACTION100
2.2621-2.29450.30572110.24583859X-RAY DIFFRACTION100
2.2945-2.32870.28951890.23683854X-RAY DIFFRACTION100
2.3287-2.36510.30322040.23643912X-RAY DIFFRACTION100
2.3651-2.40390.2871780.23413861X-RAY DIFFRACTION100
2.4039-2.44530.27721940.22993894X-RAY DIFFRACTION100
2.4453-2.48980.28391920.2253920X-RAY DIFFRACTION100
2.4898-2.53770.27121890.22413867X-RAY DIFFRACTION100
2.5377-2.58950.28891880.22733906X-RAY DIFFRACTION100
2.5895-2.64580.28772080.22483893X-RAY DIFFRACTION100
2.6458-2.70730.28941930.22283879X-RAY DIFFRACTION100
2.7073-2.7750.26711820.21363912X-RAY DIFFRACTION100
2.775-2.850.25462210.20533873X-RAY DIFFRACTION100
2.85-2.93390.26371910.20833909X-RAY DIFFRACTION100
2.9339-3.02860.27342010.22193912X-RAY DIFFRACTION100
3.0286-3.13680.2861950.21973912X-RAY DIFFRACTION100
3.1368-3.26230.26432450.21323882X-RAY DIFFRACTION100
3.2623-3.41080.26642460.19553877X-RAY DIFFRACTION100
3.4108-3.59050.23031820.18163946X-RAY DIFFRACTION100
3.5905-3.81540.1921840.16693975X-RAY DIFFRACTION100
3.8154-4.10980.18691990.14993931X-RAY DIFFRACTION100
4.1098-4.52310.17951890.14743996X-RAY DIFFRACTION100
4.5231-5.17690.16062000.14323978X-RAY DIFFRACTION100
5.1769-6.51960.22112210.17094012X-RAY DIFFRACTION100
6.5196-47.17280.2111930.18844205X-RAY DIFFRACTION100

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