[English] 日本語
Yorodumi
- PDB-1d4v: Crystal structure of trail-DR5 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1d4v
TitleCrystal structure of trail-DR5 complex
Components
  • DEATH RECEPTOR 5
  • TNF-RELATED APOPTOSIS INDUCING LIGAND
KeywordsAPOPTOSIS / LIGAND-RECEPTOR COMPLEX / TRIMERIC JELLY-ROLL / TNF-R SUPERFAMILY
Function / homology
Function and homology information


TRAIL receptor activity / TRAIL binding / TRAIL signaling / TRAIL-activated apoptotic signaling pathway / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / Caspase activation via Death Receptors in the presence of ligand / activation of NF-kappaB-inducing kinase activity / defense response to tumor cell ...TRAIL receptor activity / TRAIL binding / TRAIL signaling / TRAIL-activated apoptotic signaling pathway / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / Caspase activation via Death Receptors in the presence of ligand / activation of NF-kappaB-inducing kinase activity / defense response to tumor cell / tumor necrosis factor receptor binding / positive regulation of extrinsic apoptotic signaling pathway / TP53 Regulates Transcription of Death Receptors and Ligands / RIPK1-mediated regulated necrosis / positive regulation of release of cytochrome c from mitochondria / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / extrinsic apoptotic signaling pathway via death domain receptors / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / response to endoplasmic reticulum stress / cytokine activity / Cell surface interactions at the vascular wall / response to insulin / cellular response to mechanical stimulus / male gonad development / cell-cell signaling / signaling receptor activity / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / cell surface receptor signaling pathway / immune response / positive regulation of apoptotic process / signaling receptor binding / apoptotic process / cell surface / signal transduction / zinc ion binding / extracellular exosome / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Tumour necrosis factor receptor 10 / Tumor necrosis factor receptor 10, N-terminal / Tumour necrosis factor receptor 10A/B, death domain / Tumour necrosis factor ligand 10/11 / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / TNF(Tumour Necrosis Factor) family ...Tumour necrosis factor receptor 10 / Tumor necrosis factor receptor 10, N-terminal / Tumour necrosis factor receptor 10A/B, death domain / Tumour necrosis factor ligand 10/11 / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor (TNF) homology domain (THD) profile. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Ribbon / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Tumor necrosis factor receptor superfamily member 10B / Tumor necrosis factor ligand superfamily member 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsMongkolsapaya, J. / Grimes, J.M. / Stuart, D.I. / Jones, E.Y. / Screaton, G.R.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: Structure of the TRAIL-DR5 complex reveals mechanisms conferring specificity in apoptotic initiation
Authors: Mongkolsapaya, J. / Grimes, J.M. / Chen, N. / Xu, X.N. / Stuart, D.I. / Jones, E.Y. / Screaton, G.R.
History
DepositionOct 6, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 1999Provider: 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 / Item: _exptl_crystal_grow.temp

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: TNF-RELATED APOPTOSIS INDUCING LIGAND
A: DEATH RECEPTOR 5


Theoretical massNumber of molelcules
Total (without water)32,0652
Polymers32,0652
Non-polymers00
Water2,774154
1
B: TNF-RELATED APOPTOSIS INDUCING LIGAND
A: DEATH RECEPTOR 5

B: TNF-RELATED APOPTOSIS INDUCING LIGAND
A: DEATH RECEPTOR 5

B: TNF-RELATED APOPTOSIS INDUCING LIGAND
A: DEATH RECEPTOR 5


Theoretical massNumber of molelcules
Total (without water)96,1946
Polymers96,1946
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Unit cell
Length a, b, c (Å)95.520, 95.520, 69.810
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

-
Components

#1: Protein TNF-RELATED APOPTOSIS INDUCING LIGAND / TRAIL


Mass: 18921.166 Da / Num. of mol.: 1 / Fragment: SINGLE SUBUNIT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET-9C / Production host: Escherichia coli (E. coli) / References: UniProt: P50591
#2: Protein DEATH RECEPTOR 5 / DR5


Mass: 13143.660 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR REGION
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRANSIENT EXPRESSION AS IG FUSION PROTEIN / Cell (production host): 293T CELLS / Production host: Homo sapiens (human) / References: GenBank: 2338420, UniProt: O14763*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 25% ETHYLENE GLYCOL, 0.1% N-OCTYL-BETA-GLUCOSIDE, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 20K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17 mg/mlprotein1drop
220 mMTris1drop
350 mM1dropNaCl
425 %ethylene glycol1reservoir
50.1 %n-octyl-beta-glucoside1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.2→15 Å / Num. obs: 18104 / % possible obs: 96 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.082 / Net I/σ(I): 30
Reflection
*PLUS
Num. measured all: 164565
Reflection shell
*PLUS
% possible obs: 80 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 1.3

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementResolution: 2.2→15 Å / σ(F): 0
RfactorNum. reflection
Rfree0.27 875
Rwork0.221 -
obs0.221 -
all-18029
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2242 0 0 154 2396
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 15 Å / σ(F): 0 / Rfactor Rfree: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.8

+
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