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- PDB-8tty: Crystal structure of monkey TLR7 ectodomain with compound 5 -

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Basic information

Entry
Database: PDB / ID: 8tty
TitleCrystal structure of monkey TLR7 ectodomain with compound 5
ComponentsToll-like receptor 7
KeywordsIMMUNE SYSTEM / Toll-like receptor 7
Function / homology
Function and homology information


toll-like receptor 7 signaling pathway / pattern recognition receptor activity / toll-like receptor signaling pathway / canonical NF-kappaB signal transduction / positive regulation of interleukin-6 production / defense response to virus / inflammatory response / innate immune response / plasma membrane
Similarity search - Function
TIR domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / Leucine-rich repeat, SDS22-like subfamily / 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 ...TIR domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / Leucine-rich repeat, SDS22-like subfamily / 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
: / Toll-like receptor 7
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.101 Å
AuthorsCritton, D.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Med.Chem.Lett. / Year: 2024
Title: Discovery of Novel TLR7 Agonists as Systemic Agent for Combination With aPD1 for Use in Immuno-oncology.
Authors: Poudel, Y.B. / He, L. / Cox, M. / Zhang, Q. / Johnson, W.L. / Cong, Q. / Cheng, H. / Chowdari, N.S. / Tarby, C. / Donnell, A.F. / Broekema, M. / O'Malley, D.P. / Zhang, Y. / A M Subbaiah, M. ...Authors: Poudel, Y.B. / He, L. / Cox, M. / Zhang, Q. / Johnson, W.L. / Cong, Q. / Cheng, H. / Chowdari, N.S. / Tarby, C. / Donnell, A.F. / Broekema, M. / O'Malley, D.P. / Zhang, Y. / A M Subbaiah, M. / Kumar, B.V. / Subramani, L. / Wang, B. / Li, Y.X. / Sivaprakasam, P. / Critton, D. / Mulligan, D. / Sandhu, B. / Xie, C. / Ramakrishnan, R. / Nagar, J. / Dudhgaonkar, S. / Oderinde, M.S. / Murtaza, A. / Schieven, G.L. / Mathur, A. / Gavai, A.V. / Vite, G. / Gangwar, S.
History
DepositionAug 15, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,09325
Polymers188,0292
Non-polymers6,06423
Water13,583754
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12060 Å2
ΔGint12 kcal/mol
Surface area63200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.860, 139.890, 149.710
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 AB

#1: Protein Toll-like receptor 7 /


Mass: 94014.656 Da / Num. of mol.: 2
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: G8E2R2

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Sugars , 3 types, 18 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#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.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-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.: 14 / 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, 759 molecules

#5: Chemical ChemComp-QEC / N~7~-butyl-2-({4-[(cyclobutylamino)methyl]-2-methoxyphenyl}methyl)-2H-pyrazolo[4,3-d]pyrimidine-5,7-diamine


Mass: 409.528 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H31N7O / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 754 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.75 Å3/Da / Density % sol: 55.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.2 M ammonium citrate, 0.1 M nickel (II) chloride, 20% (w/v) PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Aug 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→102.21 Å / Num. obs: 97119 / % possible obs: 95.8 % / Redundancy: 6.9 % / CC1/2: 0.998 / Net I/σ(I): 10
Reflection shellResolution: 2.1→2.28 Å / Num. unique obs: 4856 / CC1/2: 0.571

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Processing

Software
NameVersionClassification
BUSTER2.11.7 (20-MAY-2020)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.101→102.21 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.925 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.263 / SU Rfree Blow DPI: 0.2
Details: HYDROGENS WERE FULLY REFINED WITH ZERO OCCUPANCY AT NUCLEAR POSITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2385 4728 4.87 %RANDOM
Rwork0.2048 ---
obs0.2064 97119 80.1 %-
Displacement parametersBiso mean: 66.67 Å2
Baniso -1Baniso -2Baniso -3
1--1.1137 Å20 Å20 Å2
2--1.027 Å20 Å2
3---0.0866 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.101→102.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12270 0 394 754 13418
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00825421HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0145970HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d7701SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes4041HARMONIC5
X-RAY DIFFRACTIONt_it12977HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.36
X-RAY DIFFRACTIONt_other_torsion15.13
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1768SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact18838SEMIHARMONIC4
LS refinement shellResolution: 2.101→2.23 Å
RfactorNum. reflection% reflection
Rfree0.2101 -4.84 %
Rwork0.2037 1849 -
obs--10.19 %
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)
10.6695-0.1146-0.49750.38230.06740.7412-0.00010.00220.0068-0.06130.0303-0.04530.06780.0682-0.0302-0.1188-0.0025-0.0473-0.09-0.0027-0.099717.9039-1.6308-16.2511
20.82880.125-0.45850.96880.04050.66790.01090.29840.0457-0.09140.01050.23560.0246-0.2698-0.0215-0.19140.0177-0.10040.0386-0.0011-0.0735-23.452-1.7088-17.3777
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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