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- PDB-1d2q: CRYSTAL STRUCTURE OF HUMAN TRAIL -

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Basic information

Entry
Database: PDB / ID: 1d2q
TitleCRYSTAL STRUCTURE OF HUMAN TRAIL
ComponentsTNF-RELATED APOPTOSIS INDUCING LIGAND
KeywordsCYTOKINE / TRAIL
Function / homology
Function and homology information


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 / tumor necrosis factor receptor binding / positive regulation of extrinsic apoptotic signaling pathway / RIPK1-mediated regulated necrosis ...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 / tumor necrosis factor receptor binding / positive regulation of extrinsic apoptotic signaling pathway / RIPK1-mediated regulated necrosis / positive regulation of release of cytochrome c from mitochondria / cytokine activity / cell-cell signaling / 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 / signal transduction / extracellular space / extracellular exosome / extracellular region / zinc ion binding / identical protein binding / plasma membrane
Similarity search - Function
Tumour necrosis factor ligand 10/11 / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / TNF(Tumour Necrosis Factor) family / Jelly Rolls - #40 / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Tumour necrosis factor-like domain superfamily / Jelly Rolls ...Tumour necrosis factor ligand 10/11 / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / TNF(Tumour Necrosis Factor) family / Jelly Rolls - #40 / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Tumour necrosis factor-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tumor necrosis factor ligand superfamily member 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsCha, S.-S.
CitationJournal: Immunity / Year: 1999
Title: 2.8 A resolution crystal structure of human TRAIL, a cytokine with selective antitumor activity.
Authors: Cha, S.S. / Kim, M.S. / Choi, Y.H. / Sung, B.J. / Shin, N.K. / Shin, H.C. / Sung, Y.C. / Oh, B.H.
History
DepositionSep 27, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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 / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TNF-RELATED APOPTOSIS INDUCING LIGAND
B: TNF-RELATED APOPTOSIS INDUCING LIGAND


Theoretical massNumber of molelcules
Total (without water)39,0422
Polymers39,0422
Non-polymers00
Water00
1
A: TNF-RELATED APOPTOSIS INDUCING LIGAND


Theoretical massNumber of molelcules
Total (without water)19,5211
Polymers19,5211
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TNF-RELATED APOPTOSIS INDUCING LIGAND

B: TNF-RELATED APOPTOSIS INDUCING LIGAND

B: TNF-RELATED APOPTOSIS INDUCING LIGAND


Theoretical massNumber of molelcules
Total (without water)58,5633
Polymers58,5633
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area6480 Å2
ΔGint-33 kcal/mol
Surface area16410 Å2
MethodPISA
3
A: TNF-RELATED APOPTOSIS INDUCING LIGAND

A: TNF-RELATED APOPTOSIS INDUCING LIGAND

A: TNF-RELATED APOPTOSIS INDUCING LIGAND


Theoretical massNumber of molelcules
Total (without water)58,5633
Polymers58,5633
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)65.61, 65.61, 131.70
Angle α, β, γ (deg.)90, 90, 120
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, -0.00164, 0.0009), (-0.00162, 0.99988, 0.01547), (-0.00092, 0.01547, -0.99988)
Vector: 32.84122, 18.895, -32.54992)

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Components

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


Mass: 19520.852 Da / Num. of mol.: 2 / Fragment: EXTRA CELLULAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET 3A / Production host: Bacteria (eubacteria) / References: UniProt: P50591
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

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Sample preparation

CrystalDensity Matthews: 4.19 Å3/Da / Density % sol: 70.65 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 9
Details: PEG 550 MME, bicine pH 9.0, cadmium chloride, EVAPORATION, temperature 22K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125 %mPEG55011
20.05 Mbicine11
310 mM11CdCl2

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineTypeIDWavelength
ROTATING ANODEMACSCIENCE11.5418
SYNCHROTRONPhoton Factory BL-18B21.5418
Detector
TypeIDDetector
MACSCIENCE1IMAGE PLATE
FUJI2IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.8 Å / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.063
Reflection shellHighest resolution: 2.8 Å
Reflection
*PLUS
% possible obs: 89.6 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementHighest resolution: 2.8 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber /
RfactorSelection details
Rfree0.282 RANDOM
Rwork0.209 -
Refinement stepCycle: LAST / Highest resolution: 2.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2166 0 0 0 2166
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_d1.662
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 18.4 Å2

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