[English] 日本語
Yorodumi
- PDB-1o77: CRYSTAL STRUCTURE OF THE C713S MUTANT OF THE TIR DOMAIN OF HUMAN TLR2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1o77
TitleCRYSTAL STRUCTURE OF THE C713S MUTANT OF THE TIR DOMAIN OF HUMAN TLR2
ComponentsTOLL-LIKE RECEPTOR 2
KeywordsIMMUNE SYSTEM/MEMBRANE PROTEIN / KNOWN BIOLOGICAL ACTIVITY RECEPTOR / IMMUNE RESPONSE / INFLAMMATORY RESPONSE / TRANSMEMBRANE / LEUCINE-RICH REPEAT / GLYCOPROTEIN / 3D-STRUCTURE. / IMMUNE SYSTEM-MEMBRANE PROTEIN complex
Function / homology
Function and homology information


toll-like receptor TLR6:TLR2 signaling pathway / Toll Like Receptor TLR6:TLR2 Cascade / triacyl lipopeptide binding / Toll-like receptor 2-Toll-like receptor 6 protein complex / detection of diacyl bacterial lipopeptide / cellular response to diacyl bacterial lipopeptide / Toll-like receptor 1-Toll-like receptor 2 protein complex / detection of triacyl bacterial lipopeptide / cellular response to triacyl bacterial lipopeptide / cellular response to bacterial lipopeptide ...toll-like receptor TLR6:TLR2 signaling pathway / Toll Like Receptor TLR6:TLR2 Cascade / triacyl lipopeptide binding / Toll-like receptor 2-Toll-like receptor 6 protein complex / detection of diacyl bacterial lipopeptide / cellular response to diacyl bacterial lipopeptide / Toll-like receptor 1-Toll-like receptor 2 protein complex / detection of triacyl bacterial lipopeptide / cellular response to triacyl bacterial lipopeptide / cellular response to bacterial lipopeptide / positive regulation of cellular response to macrophage colony-stimulating factor stimulus / negative regulation of synapse assembly / lipopolysaccharide immune receptor activity / Toll Like Receptor TLR1:TLR2 Cascade / Beta defensins / positive regulation of matrix metallopeptidase secretion / toll-like receptor 2 signaling pathway / I-kappaB phosphorylation / positive regulation of interleukin-18 production / Toll-like receptor binding / central nervous system myelin formation / leukotriene metabolic process / Regulation of TLR by endogenous ligand / response to fatty acid / peptidoglycan binding / NAD+ nucleotidase, cyclic ADP-ribose generating / microglia development / MyD88 deficiency (TLR2/4) / negative regulation of phagocytosis / pattern recognition receptor activity / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor signaling pathway / nitric oxide metabolic process / positive regulation of oligodendrocyte differentiation / RSV-host interactions / positive regulation of nitric-oxide synthase biosynthetic process / cellular response to lipoteichoic acid / positive regulation of interleukin-10 production / positive regulation of Wnt signaling pathway / positive regulation of chemokine production / positive regulation of interleukin-12 production / positive regulation of interferon-beta production / secretory granule membrane / learning / cell projection / positive regulation of interleukin-8 production / response to progesterone / lipopolysaccharide binding / microglial cell activation / response to insulin / response to toxic substance / cellular response to type II interferon / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / phagocytic vesicle membrane / transmembrane signaling receptor activity / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / Modulation by Mtb of host immune system / signaling receptor activity / positive regulation of NF-kappaB transcription factor activity / amyloid-beta binding / ER-Phagosome pathway / cell body / defense response to virus / receptor complex / response to hypoxia / defense response to Gram-positive bacterium / inflammatory response / immune response / membrane raft / negative regulation of cell population proliferation / innate immune response / apoptotic process / Neutrophil degranulation / protein-containing complex binding / positive regulation of gene expression / SARS-CoV-2 activates/modulates innate and adaptive immune responses / Golgi apparatus / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Leucine rich repeat C-terminal domain / Toll/interleukin-1 receptor homology (TIR) domain / Toll-like receptor / TIR domain / Leucine Rich Repeat / Leucine-rich repeats, bacterial type / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / TIR domain profile. ...Leucine rich repeat C-terminal domain / Toll/interleukin-1 receptor homology (TIR) domain / Toll-like receptor / TIR domain / Leucine Rich Repeat / Leucine-rich repeats, bacterial type / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Toll-like receptor 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsTao, X. / Xu, Y. / Ye, Z. / Beg, A.A. / Tong, L.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2002
Title: An Extensively Associated Dimer in the Structure of the C713S Mutant of the Tir Domain of Human Tlr2
Authors: Tao, X. / Xu, Y. / Zheng, Y. / Beg, A.A. / Tong, L.
History
DepositionOct 24, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 21, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TOLL-LIKE RECEPTOR 2
B: TOLL-LIKE RECEPTOR 2
C: TOLL-LIKE RECEPTOR 2
D: TOLL-LIKE RECEPTOR 2
E: TOLL-LIKE RECEPTOR 2


Theoretical massNumber of molelcules
Total (without water)87,6215
Polymers87,6215
Non-polymers00
Water00
1
A: TOLL-LIKE RECEPTOR 2
B: TOLL-LIKE RECEPTOR 2
C: TOLL-LIKE RECEPTOR 2
D: TOLL-LIKE RECEPTOR 2


Theoretical massNumber of molelcules
Total (without water)70,0974
Polymers70,0974
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-25.28 kcal/mol
Surface area29180 Å2
MethodPISA
2
E: TOLL-LIKE RECEPTOR 2


Theoretical massNumber of molelcules
Total (without water)17,5241
Polymers17,5241
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)112.300, 112.300, 362.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsCHAINS A,B,C AND D FORM A TETRAMER- LIKE ASSOCIATIONIN THE ASYMMETRIC UNIT

-
Components

#1: Protein
TOLL-LIKE RECEPTOR 2 / TOLL/INTERLEUKIN 1 RECEPTOR-LIKE PROTEIN 4 / TLR2 / TIL4


Mass: 17524.141 Da / Num. of mol.: 5 / Fragment: TIR DOMAIN, RESIDUES 639-784 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O60603
Compound detailsENGINEERED MUTATION CYS 713 SER IN CHAINS A, B, C D AND E MEDIATES THE INNATE IMMUNE RESPONSE TO ...ENGINEERED MUTATION CYS 713 SER IN CHAINS A, B, C D AND E MEDIATES THE INNATE IMMUNE RESPONSE TO BACTERIAL LIPOPROTEINS AND OTHER MICROBIAL CELL WALL COMPONENTS LEADING TO THE ACTIVATION OF NF-KAPPA-B, SECRETION OF CYTOKINES AND AN INFLAMMATORY RESPONSE. HIGH LEVEL OF EXPRESSION IN PERIPHERAL BLOOD LEUKOCYTES (MONOCYTES), BONE MARROW AND SPLEEN. SIMILAR TO THE TOLL FAMILY OF RECEPTORS.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.48 Å3/Da / Density % sol: 64.33 %
Crystal growpH: 7 / Details: 1.4M (NH4)2HPO4, 0.1M MES PH 6.5
Crystal grow
*PLUS
Temperature: 21 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMMES1reservoirpH6.5, or HEPES(pH7.5)
21.2-1.4 M1reservoir(NH4)2HPO4
35 mMdithiothreitol1reservoir
410-20 mg/mlprotein1drop
520 mMMOPS1droppH7.0
6150 mM1dropNaCl
72 mMdithiothreitol1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.9876
DetectorDate: Jun 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9876 Å / Relative weight: 1
ReflectionResolution: 3.2→20 Å / Num. obs: 23135 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 15
Reflection shellResolution: 3.31→3.4 Å / Redundancy: 3 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 10 / % possible all: 99.1
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 99505

-
Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FYW

1fyw


Resolution: 3.2→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.315 1453 7.4 %RANDOM
Rwork0.249 ---
obs0.249 19713 84.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.3326 Å2 / ksol: 0.284113 e/Å3
Displacement parametersBiso mean: 71.8 Å2
Baniso -1Baniso -2Baniso -3
1--4.12 Å2-7.86 Å20 Å2
2--13.77 Å20 Å2
3----9.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 3.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5824 0 0 0 5824
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTRAINED
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.344 166 7.5 %
Rwork0.28 2045 -
obs--58.6 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.316
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77
LS refinement shell
*PLUS
Rfactor Rfree: 0.368 / Rfactor Rwork: 0.308

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more