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- PDB-4qdh: Crystal Structure of the C-terminal Domain of Mouse TLR9 -

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Basic information

Entry
Database: PDB / ID: 4qdh
TitleCrystal Structure of the C-terminal Domain of Mouse TLR9
ComponentsVariable lymphocyte receptor B, Toll-like receptor 9 chimera
KeywordsIMMUNE SYSTEM / glycosylation
Function / homology
Function and homology information


Toll Like Receptor 9 (TLR9) Cascade / cellular response to chloroquine / positive regulation of intestinal epithelial cell development / regulation of B cell activation / Trafficking and processing of endosomal TLR / PI3K Cascade / detection of molecule of bacterial origin / regulation of B cell differentiation / endolysosome / cellular response to metal ion ...Toll Like Receptor 9 (TLR9) Cascade / cellular response to chloroquine / positive regulation of intestinal epithelial cell development / regulation of B cell activation / Trafficking and processing of endosomal TLR / PI3K Cascade / detection of molecule of bacterial origin / regulation of B cell differentiation / endolysosome / cellular response to metal ion / positive regulation of toll-like receptor 9 signaling pathway / regulation of dendritic cell cytokine production / maintenance of gastrointestinal epithelium / positive regulation of B cell activation / positive regulation of interleukin-18 production / unmethylated CpG binding / toll-like receptor 9 signaling pathway / siRNA binding / early phagosome / interleukin-1 receptor binding / positive regulation of granulocyte macrophage colony-stimulating factor production / MyD88-dependent toll-like receptor signaling pathway / positive regulation of immunoglobulin production / pattern recognition receptor activity / positive regulation of interferon-alpha production / positive regulation of interleukin-10 production / canonical NF-kappaB signal transduction / positive regulation of chemokine production / phagocytic vesicle / positive regulation of autophagy / positive regulation of B cell proliferation / positive regulation of interleukin-12 production / activation of innate immune response / positive regulation of interferon-beta production / positive regulation of cytokine production / positive regulation of interleukin-8 production / positive regulation of JNK cascade / microglial cell activation / response to molecule of bacterial origin / positive regulation of non-canonical NF-kappaB signal transduction / negative regulation of ERK1 and ERK2 cascade / response to virus / positive regulation of interleukin-6 production / positive regulation of type II interferon production / male gonad development / positive regulation of tumor necrosis factor production / cellular response to lipopolysaccharide / regulation of inflammatory response / early endosome membrane / defense response to Gram-negative bacterium / basolateral plasma membrane / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / lysosome / positive regulation of MAPK cascade / endosome / immune response / apical plasma membrane / innate immune response / endoplasmic reticulum membrane / endoplasmic reticulum / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / plasma membrane
Similarity search - Function
Leucine-rich repeat unit / Leucine-rich repeat / Variable lymphocyte receptor, C-terminal / Domain of unknown function (DUF3439) / : / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / TIR domain / Toll - interleukin 1 - resistance ...Leucine-rich repeat unit / Leucine-rich repeat / Variable lymphocyte receptor, C-terminal / Domain of unknown function (DUF3439) / : / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / TIR domain / Toll - interleukin 1 - resistance / TIR domain profile. / Leucine-rich repeat, SDS22-like subfamily / 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
Variable lymphocyte receptor B / Toll-like receptor 9
Similarity search - Component
Biological speciesEptatretus burgeri (inshore hagfish)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.399 Å
AuthorsCollins, B.C. / Wilson, I.A.
CitationJournal: Proteins / Year: 2014
Title: Crystal structure of the C-terminal domain of mouse TLR9.
Authors: Collins, B. / Wilson, I.A.
History
DepositionMay 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Database references
Revision 1.2Oct 8, 2014Group: Database references
Revision 1.3Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Sep 20, 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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Oct 30, 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
A: Variable lymphocyte receptor B, Toll-like receptor 9 chimera
B: Variable lymphocyte receptor B, Toll-like receptor 9 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,53020
Polymers97,5492
Non-polymers2,98118
Water2,162120
1
A: Variable lymphocyte receptor B, Toll-like receptor 9 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,26510
Polymers48,7751
Non-polymers1,4909
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Variable lymphocyte receptor B, Toll-like receptor 9 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,26510
Polymers48,7751
Non-polymers1,4909
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.025, 106.025, 221.549
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Variable lymphocyte receptor B, Toll-like receptor 9 chimera / Innate Immune Receptor


Mass: 48774.543 Da / Num. of mol.: 2 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eptatretus burgeri (inshore hagfish), (gene. exp.) Mus musculus (house mouse)
Gene: Tlr9, VLRB / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q4G1L2, UniProt: Q9EQU3
#2: 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.: 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
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsPROTEIN IS A CHIMERA COMPRISING RESIDUES 21-81 FROM UNP Q4G1L2, RESIDUES 480-753 FROM UNP Q9EQU3, ...PROTEIN IS A CHIMERA COMPRISING RESIDUES 21-81 FROM UNP Q4G1L2, RESIDUES 480-753 FROM UNP Q9EQU3, AND RESIDUES 126-200 FROM UNP Q4G1L2 FOLLOWED BY A C-TERMINAL EXPRESSION TAG.

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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: 3.69 Å3/Da / Density % sol: 66.62 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.77
Details: 100 mM sodium citrate, 1.5 M ammonium sulfate, pH 4.77, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97939 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 20, 2013
RadiationMonochromator: double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionResolution: 2.399→91.82 Å / Num. all: 57289 / Num. obs: 57046 / Redundancy: 3.7 % / Rsym value: 0.13 / Net I/σ(I): 6.8
Reflection shellResolution: 2.399→2.47 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 4388 / Rsym value: 0.73 / % possible all: 99.4

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3W3G

3w3g


Resolution: 2.399→47.819 Å / SU ML: 0.32 / σ(F): 1.36 / Phase error: 26.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2473 2888 5.06 %
Rwork0.2144 --
obs0.2161 57040 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.399→47.819 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6232 0 180 120 6532
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096552
X-RAY DIFFRACTIONf_angle_d1.5018887
X-RAY DIFFRACTIONf_dihedral_angle_d15.9072414
X-RAY DIFFRACTIONf_chiral_restr0.1011039
X-RAY DIFFRACTIONf_plane_restr0.0061110
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.399-2.43850.32251190.29272481X-RAY DIFFRACTION97
2.4385-2.48050.32351400.27422585X-RAY DIFFRACTION100
2.4805-2.52560.29971470.26992534X-RAY DIFFRACTION100
2.5256-2.57420.32831420.25672519X-RAY DIFFRACTION100
2.5742-2.62670.29971240.26252559X-RAY DIFFRACTION100
2.6267-2.68390.3431520.27682538X-RAY DIFFRACTION100
2.6839-2.74630.25351430.26282565X-RAY DIFFRACTION100
2.7463-2.8150.36391200.2642583X-RAY DIFFRACTION100
2.815-2.89110.29591570.26712521X-RAY DIFFRACTION100
2.8911-2.97610.31271320.26992548X-RAY DIFFRACTION100
2.9761-3.07220.28731270.26722595X-RAY DIFFRACTION100
3.0722-3.18190.29581420.2512554X-RAY DIFFRACTION100
3.1819-3.30930.28211390.24972602X-RAY DIFFRACTION100
3.3093-3.45990.25581380.22332573X-RAY DIFFRACTION100
3.4599-3.64220.25041310.19812602X-RAY DIFFRACTION100
3.6422-3.87030.18471370.16472554X-RAY DIFFRACTION100
3.8703-4.1690.19021380.15732628X-RAY DIFFRACTION100
4.169-4.58820.18891350.16232605X-RAY DIFFRACTION100
4.5882-5.25150.21351530.16292621X-RAY DIFFRACTION100
5.2515-6.61350.22041430.20662650X-RAY DIFFRACTION99
6.6135-47.82830.22651290.21342735X-RAY DIFFRACTION97
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)
10.42320.2388-0.14051.1748-0.80422.0621-0.0262-0.04660.06740.0525-0.03930.0402-0.17730.07960.05150.18040.0475-0.00390.1946-0.01620.179945.5548-17.148711.066
21.1604-0.14390.46641.05570.05442.2024-0.1179-0.0847-0.0867-0.02910.0148-0.2302-0.01160.32710.0840.17830.05770.02090.27210.01030.241463.0701-39.16141.2399
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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