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- PDB-1du3: Crystal structure of TRAIL-SDR5 -

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Basic information

Entry
Database: PDB / ID: 1du3
TitleCrystal structure of TRAIL-SDR5
Components
  • DEATH RECEPTOR 5
  • TNF-RELATED APOPTOSIS INDUCING LIGAND
KeywordsAPOPTOSIS / TRAIL / DR5 / complex
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 / 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 / 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. / TNF(Tumour Necrosis Factor) family / TNFR/NGFR family cysteine-rich region domain profile. / Tumour necrosis factor domain / 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
AuthorsCha, S.-S. / Sung, B.-J. / Oh, B.-H.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: Crystal structure of TRAIL-DR5 complex identifies a critical role of the unique frame insertion in conferring recognition specificity
Authors: Cha, S.-S. / Sung, B.-J. / Kim, Y.A. / Song, Y.L. / Kim, H.J. / Kim, S. / Lee, M.S. / Oh, B.-H.
History
DepositionJan 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 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: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DEATH RECEPTOR 5
B: DEATH RECEPTOR 5
C: DEATH RECEPTOR 5
D: TNF-RELATED APOPTOSIS INDUCING LIGAND
E: TNF-RELATED APOPTOSIS INDUCING LIGAND
F: TNF-RELATED APOPTOSIS INDUCING LIGAND
G: DEATH RECEPTOR 5
H: DEATH RECEPTOR 5
I: DEATH RECEPTOR 5
J: TNF-RELATED APOPTOSIS INDUCING LIGAND
K: TNF-RELATED APOPTOSIS INDUCING LIGAND
L: TNF-RELATED APOPTOSIS INDUCING LIGAND
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,72614
Polymers204,59512
Non-polymers1312
Water2,918162
1
A: DEATH RECEPTOR 5
B: DEATH RECEPTOR 5
C: DEATH RECEPTOR 5
D: TNF-RELATED APOPTOSIS INDUCING LIGAND
E: TNF-RELATED APOPTOSIS INDUCING LIGAND
F: TNF-RELATED APOPTOSIS INDUCING LIGAND
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,3637
Polymers102,2986
Non-polymers651
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17070 Å2
ΔGint-44 kcal/mol
Surface area30830 Å2
MethodPISA
2
G: DEATH RECEPTOR 5
H: DEATH RECEPTOR 5
I: DEATH RECEPTOR 5
J: TNF-RELATED APOPTOSIS INDUCING LIGAND
K: TNF-RELATED APOPTOSIS INDUCING LIGAND
L: TNF-RELATED APOPTOSIS INDUCING LIGAND
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,3637
Polymers102,2986
Non-polymers651
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16920 Å2
ΔGint-48 kcal/mol
Surface area30490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.63, 124.81, 128.37
Angle α, β, γ (deg.)90.0, 104.489, 90.0
Int Tables number4
Space group name H-MP1211
DetailsChain D, E, F form a functional trimer Chain J, K, L form a functional trimer

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Components

#1: Protein
DEATH RECEPTOR 5


Mass: 14578.320 Da / Num. of mol.: 6 / Fragment: EXTRACELLULAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: O14763
#2: Protein
TNF-RELATED APOPTOSIS INDUCING LIGAND


Mass: 19520.852 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Bacteria (eubacteria) / References: UniProt: P50591
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.6 Å3/Da / Density % sol: 52.71 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 4.6
Details: PEG 1000, Sodium Acetate, Sodium Chloride, pH 4.6, EVAPORATION, temperature 22K
Crystal grow
*PLUS
pH: 4.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
116 %PEG300011
20.6 Msodium acetate11
30.6 M11NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Jan 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 346386 / Num. obs: 93618 / % possible obs: 89.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 12
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2 % / Rmerge(I) obs: 0.306 / % possible all: 70
Reflection
*PLUS
% possible obs: 93.1 %
Reflection shell
*PLUS
% possible obs: 70 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementResolution: 2.2→8 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.291 4680 random
Rwork0.291 --
all0.212 93618 -
obs0.212 346386 -
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11944 0 2 162 12108
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.772
X-RAY DIFFRACTIONx_bond_d0.011
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.212
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21.81 Å2

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