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- PDB-1d4v: Crystal structure of trail-DR5 complex -

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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 / activation of NF-kappaB-inducing kinase activity / Caspase activation via Death Receptors in the presence of ligand / 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 / activation of NF-kappaB-inducing kinase activity / Caspase activation via Death Receptors in the presence of ligand / 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 / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / extrinsic apoptotic signaling pathway via death domain receptors / response to endoplasmic reticulum stress / cytokine activity / Cell surface interactions at the vascular wall / cellular response to mechanical stimulus / cell-cell signaling / signaling receptor activity / regulation of apoptotic process / cell surface receptor signaling pathway / positive regulation of canonical NF-kappaB signal transduction / immune response / positive regulation of apoptotic process / signaling receptor binding / apoptotic process / cell surface / signal transduction / extracellular space / extracellular exosome / extracellular region / zinc ion binding / 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. ...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. / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNF(Tumour Necrosis Factor) family / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / Jelly Rolls - #40 / TNFR/NGFR cysteine-rich region / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / 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
Revision 1.4Oct 30, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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
Has protein modificationY

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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: 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

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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

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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

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