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- PDB-5zsl: Crystal structure of monkey TLR7 in complex with GGUUGG -

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Basic information

Entry
Database: PDB / ID: 5zsl
TitleCrystal structure of monkey TLR7 in complex with GGUUGG
Components
  • RNA (5'-R(P*UP*UP*GP*A)-3')
  • Toll-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
Chem-9K9 / RNA / Toll-like receptor 7
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 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: 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 ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / citation / citation_author / database_2 / struct_ncs_dom_lim
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 / _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
B: Toll-like receptor 7
A: Toll-like receptor 7
D: RNA (5'-R(P*UP*UP*GP*A)-3')
E: RNA (5'-R(P*UP*UP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,84928
Polymers193,3564
Non-polymers5,49424
Water27015
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.630, 139.424, 150.893
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: 27 - 835 / Label seq-ID: 5 - 813

Dom-IDAuth asym-IDLabel asym-ID
1BA
2AB

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Components

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Protein / RNA chain , 2 types, 4 molecules BADE

#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
#2: RNA chain RNA (5'-R(P*UP*UP*GP*A)-3')


Mass: 1932.198 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Sugars , 2 types, 15 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.: 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
#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 / N-Acetylglucosamine


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, 24 molecules

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


Mass: 96.063 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: SO4
#6: Chemical ChemComp-9K9 / 2-amino-9-[(2S,3aR,4R,6R,6aR)-2-hydroxy-6-(hydroxymethyl)-2-oxotetrahydro-2H-2lambda~5~-furo[3,4-d][1,3,2]dioxaphosphol-4-yl]-3,9-dihydro-6H-purin-6-one


Mass: 345.205 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C10H12N5O7P
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.71 Å3/Da / Density % sol: 54.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PEG 8000, ammonium sulfate, sodium citrate pH 5.0, Tris-HCl pH 7.5 and NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 16, 2017
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: 93814 / % possible obs: 99.9 % / Redundancy: 6.7 % / Net I/σ(I): 15.1
Reflection shellResolution: 2.3→2.34 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementResolution: 2.3→47.36 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.922 / SU B: 8.159 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.302 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25843 4644 4.9 %RANDOM
Rwork0.2175 ---
obs0.21946 89187 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.597 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å20 Å2
2--1.12 Å2-0 Å2
3----0.76 Å2
Refinement stepCycle: 1 / Resolution: 2.3→47.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12550 134 347 15 13046
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01413343
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711980
X-RAY DIFFRACTIONr_angle_refined_deg1.3691.68118163
X-RAY DIFFRACTIONr_angle_other_deg0.8371.66128164
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.22151544
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.67523.258663
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.388152341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7991565
X-RAY DIFFRACTIONr_chiral_restr0.0620.21783
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214376
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022390
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.8274.9396194
X-RAY DIFFRACTIONr_mcbond_other3.8274.9396193
X-RAY DIFFRACTIONr_mcangle_it5.4817.4047736
X-RAY DIFFRACTIONr_mcangle_other5.4827.4057733
X-RAY DIFFRACTIONr_scbond_it4.5155.5117149
X-RAY DIFFRACTIONr_scbond_other4.5155.5117146
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7788.09510425
X-RAY DIFFRACTIONr_long_range_B_refined8.50456.90513887
X-RAY DIFFRACTIONr_long_range_B_other8.50456.90513888
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 25139 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1B
2A
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 343 -
Rwork0.332 6556 -
obs--99.83 %

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