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- PDB-5gs0: Crystal structure of the complex of TLR3 and bi-specific diabody -

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Basic information

Entry
Database: PDB / ID: 5gs0
TitleCrystal structure of the complex of TLR3 and bi-specific diabody
Components
  • (heavy chain (anti- ...) x 2
  • (light chain (anti- ...) x 2
  • Toll-like receptor 3
KeywordsIMMUNE SYSTEM / diabody / antibody fragment / complex
Function / homology
Function and homology information


TLR3 deficiency - HSE / UNC93B1 deficiency - HSE / TICAM1 deficiency - HSE / type III interferon production / positive regulation of type III interferon production / response to dsRNA / TRAF3 deficiency - HSE / regulation of dendritic cell cytokine production / Toll Like Receptor 3 (TLR3) Cascade / TLR3-mediated TICAM1-dependent programmed cell death ...TLR3 deficiency - HSE / UNC93B1 deficiency - HSE / TICAM1 deficiency - HSE / type III interferon production / positive regulation of type III interferon production / response to dsRNA / TRAF3 deficiency - HSE / regulation of dendritic cell cytokine production / Toll Like Receptor 3 (TLR3) Cascade / TLR3-mediated TICAM1-dependent programmed cell death / I-kappaB phosphorylation / inflammatory response to wounding / toll-like receptor 3 signaling pathway / detection of virus / necroptotic signaling pathway / activation of NF-kappaB-inducing kinase activity / RIP-mediated NFkB activation via ZBP1 / positive regulation of cytokine production involved in inflammatory response / endolysosome membrane / hyperosmotic response / Trafficking and processing of endosomal TLR / positive regulation of macrophage cytokine production / pattern recognition receptor activity / toll-like receptor signaling pathway / cellular response to exogenous dsRNA / response to exogenous dsRNA / negative regulation of osteoclast differentiation / positive regulation of interferon-alpha production / cellular response to interferon-beta / extrinsic apoptotic signaling pathway / positive regulation of chemokine production / JNK cascade / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / extracellular matrix / positive regulation of interferon-beta production / positive regulation of interleukin-12 production / TICAM1, RIP1-mediated IKK complex recruitment / positive regulation of interleukin-8 production / positive regulation of JNK cascade / microglial cell activation / cellular response to virus / positive regulation of inflammatory response / positive regulation of interleukin-6 production / cellular response to type II interferon / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to mechanical stimulus / male gonad development / positive regulation of angiogenesis / transmembrane signaling receptor activity / positive regulation of type II interferon production / cellular response to xenobiotic stimulus / double-stranded RNA binding / positive regulation of tumor necrosis factor production / signaling receptor activity / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / early endosome / endosome membrane / defense response to bacterium / positive regulation of apoptotic process / lysosomal membrane / Golgi membrane / innate immune response / endoplasmic reticulum membrane / positive regulation of gene expression / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / membrane / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Toll-like receptor 3 trans-membrane domain / Toll-like receptor 3 trans-membrane domain / Toll-like receptor / Leucine Rich repeat / TIR domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / Leucine-rich repeat, SDS22-like subfamily / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) ...Toll-like receptor 3 trans-membrane domain / Toll-like receptor 3 trans-membrane domain / Toll-like receptor / Leucine Rich repeat / TIR domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / Leucine-rich repeat, SDS22-like subfamily / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
beta-D-mannopyranose / alpha-D-mannopyranose / Toll-like receptor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.275 Å
AuthorsKim, J.H. / Song, D.H. / Youn, S.J. / Kim, J.W. / Cho, G. / Lee, H. / Lee, J.O.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
Ministry of Science, ICT and Future PlanningNRF-2014R1A2A1A10050436 Korea, Republic Of
Ministry of Health & WelfareHI15C1886 Korea, Republic Of
CitationJournal: Sci Rep / Year: 2016
Title: Crystal structure of mono- and bi-specific diabodies and reduction of their structural flexibility by introduction of disulfide bridges at the Fv interface.
Authors: Kim, J.H. / Song, D.H. / Youn, S.J. / Kim, J.W. / Cho, G. / Kim, S.C. / Lee, H. / Jin, M.S. / Lee, J.O.
History
DepositionAug 13, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / 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 / _pdbx_struct_oper_list.symmetry_operation
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Mar 20, 2024Group: Source and taxonomy / Category: entity_src_gen

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Toll-like receptor 3
C: light chain (anti-TLR3)
D: heavy chain (anti-TLR3)
B: Toll-like receptor 3
E: light chain (anti-TLR3)
F: heavy chain (anti-TLR3)
X: heavy chain (anti-Lid)
Y: light chain (anti-Lid)
H: heavy chain (anti-Lid)
L: light chain (anti-Lid)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)262,27150
Polymers253,66910
Non-polymers8,60240
Water0
1
A: Toll-like receptor 3
C: light chain (anti-TLR3)
D: heavy chain (anti-TLR3)
X: heavy chain (anti-Lid)
Y: light chain (anti-Lid)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,13625
Polymers126,8355
Non-polymers4,30120
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Toll-like receptor 3
E: light chain (anti-TLR3)
F: heavy chain (anti-TLR3)
H: heavy chain (anti-Lid)
L: light chain (anti-Lid)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,13625
Polymers126,8355
Non-polymers4,30120
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.519, 141.329, 150.831
Angle α, β, γ (deg.)90.00, 106.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Toll-like receptor 3 /


Mass: 76399.133 Da / Num. of mol.: 2 / Fragment: ectodomain (UNP RESIDUES 27-697)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TLR3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O15455

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Antibody , 4 types, 8 molecules CEDFXHYL

#2: Antibody light chain (anti-TLR3)


Mass: 11492.433 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Trichoplusia ni (cabbage looper)
#3: Antibody heavy chain (anti-TLR3)


Mass: 13862.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Trichoplusia ni (cabbage looper)
#4: Antibody heavy chain (anti-Lid)


Mass: 13364.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Trichoplusia ni (cabbage looper)
#5: Antibody light chain (anti-Lid)


Mass: 11715.908 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Trichoplusia ni (cabbage looper)

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Sugars , 3 types, 40 molecules

#6: 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.: 34
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
#7: Sugar
ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#8: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 3.85 Å3/Da / Density % sol: 68.05 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Sodium citrate tribasic pH 5.5, 19.5% PEG 2,000, 0.75 M Sodium chloride

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 3.275→50 Å / Num. obs: 58328 / % possible obs: 96.6 % / Redundancy: 3.2 % / Net I/σ(I): 18.5
Reflection shellResolution: 3.3→3.42 Å

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ULU, 5GRU

3ulu

5gru


Resolution: 3.275→35.074 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 26.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2478 2795 4.79 %
Rwork0.1919 --
obs0.1945 58301 95.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.275→35.074 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17637 0 582 0 18219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01118639
X-RAY DIFFRACTIONf_angle_d1.3725372
X-RAY DIFFRACTIONf_dihedral_angle_d16.08111048
X-RAY DIFFRACTIONf_chiral_restr0.0742975
X-RAY DIFFRACTIONf_plane_restr0.013182
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.275-3.33140.37551270.32442144X-RAY DIFFRACTION75
3.3314-3.3920.37151290.29922752X-RAY DIFFRACTION95
3.392-3.45710.29681310.28162720X-RAY DIFFRACTION95
3.4571-3.52760.31761210.26152780X-RAY DIFFRACTION95
3.5276-3.60430.32291240.25582734X-RAY DIFFRACTION95
3.6043-3.6880.29971200.2312787X-RAY DIFFRACTION95
3.688-3.78020.29761470.2182765X-RAY DIFFRACTION96
3.7802-3.88220.26351550.21092714X-RAY DIFFRACTION96
3.8822-3.99630.26541320.19662769X-RAY DIFFRACTION95
3.9963-4.12510.25031430.18822788X-RAY DIFFRACTION96
4.1251-4.27230.22731430.17752793X-RAY DIFFRACTION97
4.2723-4.4430.22961520.17382821X-RAY DIFFRACTION98
4.443-4.64480.2321380.16242828X-RAY DIFFRACTION98
4.6448-4.88910.2281490.15022850X-RAY DIFFRACTION98
4.8891-5.19450.20141640.15262851X-RAY DIFFRACTION99
5.1945-5.59410.21231460.15022846X-RAY DIFFRACTION99
5.5941-6.15430.21511420.16542938X-RAY DIFFRACTION99
6.1543-7.03860.24021380.18132905X-RAY DIFFRACTION100
7.0386-8.84440.2411540.19942888X-RAY DIFFRACTION100
8.8444-35.07630.23941400.18792833X-RAY DIFFRACTION95

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