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- PDB-5gmg: Crystal structure of monkey TLR7 in complex with loxoribine and polyU -

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Basic information

Entry
Database: PDB / ID: 5gmg
TitleCrystal structure of monkey TLR7 in complex with loxoribine and polyU
Components
  • RNA (5'-R(P*UP*UP*UP*U)-3')
  • Toll-like receptor 7
KeywordsIMMUNE SYSTEM/RNA / IMMUNE SYSTEM / TLR7 / innate immunity / ssRNA recogniton / IMMUNE SYSTEM-RNA complex
Function / homology
Function and homology information


toll-like receptor 7 signaling pathway / toll-like receptor 8 signaling pathway / response to cGMP / siRNA binding / early phagosome / positive regulation of macrophage cytokine production / toll-like receptor signaling pathway / pattern recognition receptor activity / positive regulation of interferon-alpha production / canonical NF-kappaB signal transduction ...toll-like receptor 7 signaling pathway / toll-like receptor 8 signaling pathway / response to cGMP / siRNA binding / early phagosome / positive regulation of macrophage cytokine production / toll-like receptor signaling pathway / pattern recognition receptor activity / 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 / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of interleukin-6 production / cellular response to virus / cellular response to mechanical stimulus / positive regulation of type II interferon production / double-stranded RNA binding / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / single-stranded RNA binding / lysosome / receptor complex / endosome / inflammatory response / innate immune response / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / metal ion binding / 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 / TIR domain profile. / Leucine-rich repeat, SDS22-like subfamily / Alpha-Beta Horseshoe ...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 / TIR domain profile. / Leucine-rich repeat, SDS22-like subfamily / Alpha-Beta Horseshoe / 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 / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Chem-SDL / RNA / Toll-like receptor 7
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsZhang, Z. / Ohto, U. / Shimizu, T.
CitationJournal: Immunity / Year: 2016
Title: Structural Analysis Reveals that Toll-like Receptor 7 Is a Dual Receptor for Guanosine and Single-Stranded RNA
Authors: Zhang, Z. / Ohto, U. / Shibata, T. / Krayukhina, E. / Taoka, M. / Yamauchi, Y. / Tanji, H. / Isobe, T. / Uchiyama, S. / Miyake, K. / Shimizu, T.
History
DepositionJul 14, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / citation ...chem_comp / citation / diffrn_source / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _chem_comp.type / _citation.journal_id_CSD ..._chem_comp.type / _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
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 / _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 2.1Nov 8, 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
Revision 2.2Oct 23, 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 7
B: Toll-like receptor 7
C: RNA (5'-R(P*UP*UP*UP*U)-3')
D: RNA (5'-R(P*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,33815
Polymers190,3894
Non-polymers2,95011
Water59433
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.277, 99.410, 112.096
Angle α, β, γ (deg.)90.00, 98.58, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: _ / Auth seq-ID: 28 - 833 / Label seq-ID: 6 - 811

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein / RNA chain , 2 types, 4 molecules ABCD

#1: Protein Toll-like receptor 7 / Uncharacterized protein


Mass: 94014.656 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 / Plasmid: pMT/BiP/V5-His / Production host: Drosophila (fruit flies) / References: UniProt: B3Y653
#2: RNA chain RNA (5'-R(P*UP*UP*UP*U)-3')


Mass: 1179.706 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Sugars , 2 types, 8 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.: 2 / Source method: obtained synthetically
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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6 / Source method: obtained synthetically / 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, 36 molecules

#5: Chemical ChemComp-SDL / 2-azanyl-9-[(2~{R},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-7-prop-2-enyl-1~{H}-purine-6,8-dione / Loxoribine


Mass: 339.304 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H17N5O6
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.84 Å3/Da / Density % sol: 56.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PEG 3350, magnesium chloride, sodium citrate pH 5.0

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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: Oct 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.59→50.01 Å / Num. obs: 58705 / % possible obs: 93.9 % / Redundancy: 2.8 % / Rsym value: 0.08 / Net I/σ(I): 15.1
Reflection shellResolution: 2.6→2.64 Å / Rsym value: 0.41

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GMF

5gmf


Resolution: 2.6→50.01 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.905 / SU B: 13.255 / SU ML: 0.27 / Cross valid method: THROUGHOUT / ESU R: 0.743 / ESU R Free: 0.325 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25833 3088 5 %RANDOM
Rwork0.21502 ---
obs0.21719 58494 93.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.759 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å22.59 Å2
2--3.04 Å20 Å2
3----3.26 Å2
Refinement stepCycle: 1 / Resolution: 2.6→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12326 128 193 33 12680
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01912946
X-RAY DIFFRACTIONr_bond_other_d0.0040.0212384
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.98217593
X-RAY DIFFRACTIONr_angle_other_deg1.13328514
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.93951516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.64824.719587
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.374152289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.861563
X-RAY DIFFRACTIONr_chiral_restr0.0910.22036
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02114255
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022982
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_it5.056.5066090
X-RAY DIFFRACTIONr_mcbond_other5.056.5056088
X-RAY DIFFRACTIONr_mcangle_it7.4389.767596
X-RAY DIFFRACTIONr_mcangle_other7.4379.7617597
X-RAY DIFFRACTIONr_scbond_it5.3877.0476856
X-RAY DIFFRACTIONr_scbond_other5.3837.0476852
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.24910.3749995
X-RAY DIFFRACTIONr_long_range_B_refined10.75551.63113720
X-RAY DIFFRACTIONr_long_range_B_other10.75351.62713719
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 101972 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.04 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 204 -
Rwork0.347 3796 -
obs--83 %

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