[English] 日本語
Yorodumi
- PDB-1fyv: CRYSTAL STRUCTURE OF THE TIR DOMAIN OF HUMAN TLR1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fyv
TitleCRYSTAL STRUCTURE OF THE TIR DOMAIN OF HUMAN TLR1
ComponentsTOLL-LIKE RECEPTOR 1
KeywordsSIGNALING PROTEIN / beta-alpha-beta fold parallel beta sheet
Function / homology
Function and homology information


Toll-like receptor 1-Toll-like receptor 2 protein complex / detection of triacyl bacterial lipopeptide / cellular response to triacyl bacterial lipopeptide / Toll-like receptor 2 binding / positive regulation of toll-like receptor 2 signaling pathway / Toll Like Receptor TLR1:TLR2 Cascade / Beta defensins / Regulation of TLR by endogenous ligand / macrophage activation / lipopeptide binding ...Toll-like receptor 1-Toll-like receptor 2 protein complex / detection of triacyl bacterial lipopeptide / cellular response to triacyl bacterial lipopeptide / Toll-like receptor 2 binding / positive regulation of toll-like receptor 2 signaling pathway / Toll Like Receptor TLR1:TLR2 Cascade / Beta defensins / Regulation of TLR by endogenous ligand / macrophage activation / lipopeptide binding / NAD+ nucleotidase, cyclic ADP-ribose generating / MyD88 deficiency (TLR2/4) / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor signaling pathway / positive regulation of interleukin-8 production / positive regulation of interleukin-6 production / phagocytic vesicle membrane / positive regulation of tumor necrosis factor production / transmembrane signaling receptor activity / signaling receptor activity / ER-Phagosome pathway / receptor complex / inflammatory response / immune response / membrane raft / innate immune response / SARS-CoV-2 activates/modulates innate and adaptive immune responses / Golgi apparatus / signal transduction / identical protein binding / membrane / plasma membrane
Similarity search - Function
Leucine rich repeat C-terminal domain / Toll/interleukin-1 receptor homology (TIR) domain / Toll-like receptor / TIR domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine-rich repeats, bacterial type / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain ...Leucine rich repeat C-terminal domain / Toll/interleukin-1 receptor homology (TIR) domain / Toll-like receptor / TIR domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine-rich repeats, bacterial type / 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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsXu, Y. / Tao, X. / Shen, B. / Horng, T. / Medzhitov, R. / Manley, J.L. / Tong, L.
CitationJournal: Nature / Year: 2000
Title: Structural basis for signal transduction by the Toll/interleukin-1 receptor domains.
Authors: Xu, Y. / Tao, X. / Shen, B. / Horng, T. / Medzhitov, R. / Manley, J.L. / Tong, L.
History
DepositionOct 3, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Advisory / Experimental preparation
Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TOLL-LIKE RECEPTOR 1


Theoretical massNumber of molelcules
Total (without water)19,0821
Polymers19,0821
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.3, 101.3, 137.9
Angle α, β, γ (deg.)90, 90, 120
Int Tables number181
Space group name H-MP6422

-
Components

#1: Protein TOLL-LIKE RECEPTOR 1


Mass: 19081.670 Da / Num. of mol.: 1 / Fragment: TIR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q15399

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.35 Å3/Da / Density % sol: 77.02 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM Tris, 1.2M NaH2PO4/K2HPO4 5 mM DTT, 20% glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 21K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMTris1reservoir
21.2 Msodium potassium phosphate1reservoir
35 mMdithiothreitol1reservoir
420 %glycerol1reservoir

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONNSLS X4A10.98
SYNCHROTRONCHESS A120.909
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDNov 12, 1999
ADSC QUANTUM 42CCDJan 20, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
20.9091
ReflectionResolution: 2.9→40 Å / Num. all: 9700 / Num. obs: 9374 / % possible obs: 97 % / Observed criterion σ(F): 0.5 / Observed criterion σ(I): 1 / Redundancy: 5 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 40
Reflection shellResolution: 2.9→3 Å / Redundancy: 3 % / Rmerge(I) obs: 0.17 / % possible all: 91

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MADSYSphasing
CNSrefinement
RefinementResolution: 2.9→20 Å / σ(F): 1 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.296 600 7.5%
Rwork0.254 --
all0.26 9700 -
obs0.254 8496 -
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1342 0 0 0 1342
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 20 Å / σ(F): 1 / % reflection Rfree: 7.5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.4

+
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://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