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- PDB-1dg6: CRYSTAL STRUCTURE OF APO2L/TRAIL -

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Basic information

Entry
Database: PDB / ID: 1dg6
TitleCRYSTAL STRUCTURE OF APO2L/TRAIL
ComponentsAPO2L/TNF-RELATED APOPOTIS INDUCING LIGAND (TRAIL)
KeywordsAPOPTOSIS / CYTOKINE / TNF / TRIMER / ZINC-BINDING SITE
Function / homology
Function and homology information


TRAIL binding / TRAIL signaling / 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 cysteine-type endopeptidase activity involved in apoptotic process ...TRAIL binding / TRAIL signaling / 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 cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of release of cytochrome c from mitochondria / cytokine activity / response to insulin / male gonad development / cell-cell signaling / positive regulation of canonical NF-kappaB signal transduction / immune response / positive regulation of apoptotic process / signaling receptor binding / apoptotic process / signal transduction / zinc ion binding / extracellular exosome / extracellular region / 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 / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Jelly Rolls - #40 / 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 / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Jelly Rolls - #40 / 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 / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsHymowitz, S.G. / O'ConnelL, M.P. / Ultsch, M.H. / de Vos, A.M. / Kelley, R.F.
CitationJournal: Biochemistry / Year: 2000
Title: A unique zinc-binding site revealed by a high-resolution X-ray structure of homotrimeric Apo2L/TRAIL.
Authors: Hymowitz, S.G. / O'Connell, M.P. / Ultsch, M.H. / Hurst, A. / Totpal, K. / Ashkenazi, A. / de Vos, A.M. / Kelley, R.F.
History
DepositionNov 23, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _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: APO2L/TNF-RELATED APOPOTIS INDUCING LIGAND (TRAIL)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2083
Polymers22,1071
Non-polymers1012
Water4,071226
1
A: APO2L/TNF-RELATED APOPOTIS INDUCING LIGAND (TRAIL)
hetero molecules

A: APO2L/TNF-RELATED APOPOTIS INDUCING LIGAND (TRAIL)
hetero molecules

A: APO2L/TNF-RELATED APOPOTIS INDUCING LIGAND (TRAIL)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6239
Polymers66,3203
Non-polymers3036
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area7730 Å2
ΔGint-126 kcal/mol
Surface area19360 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)66.435, 66.435, 197.727
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-300-

ZN

21A-406-

CL

31A-410-

HOH

41A-433-

HOH

51A-465-

HOH

61A-559-

HOH

71A-565-

HOH

81A-593-

HOH

91A-603-

HOH

101A-611-

HOH

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Components

#1: Protein APO2L/TNF-RELATED APOPOTIS INDUCING LIGAND (TRAIL)


Mass: 22106.832 Da / Num. of mol.: 1 / Fragment: TRIMERIC JELLY-ROLL DOMAIN OF APO2L / Mutation: D218A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: HUMAN PLACENTA / Description: HUMAN PLACENTA / Production host: Escherichia coli (E. coli) / References: UniProt: P50591
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O

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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: 1.9 Å3/Da / Density % sol: 32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: WELL SOLUTION 32% MPD; DROP 1.2MG/ML APO2L, 20MM TRIS HCL PH 7.5, 1% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14 %MPD1drop
21.7 mg/mlprotein1drop
320 mMTris-HCl1drop
432 %MPD1reservoir

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.03321
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Apr 23, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 1.3→20 Å / Num. all: 41901 / Num. obs: 41840 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.1 % / Biso Wilson estimate: 12.5 Å2 / Rsym value: 6.4 / Net I/σ(I): 12.4
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 4.5 % / Rsym value: 34 / % possible all: 100
Reflection
*PLUS
Rmerge(I) obs: 0.064
Reflection shell
*PLUS
Rmerge(I) obs: 0.34

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Processing

Software
NameClassification
AMoREphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: truncated model of tnfa pdb code 1tnf

1tnf


Resolution: 1.3→20 Å / Num. parameters: 13240 / Num. restraintsaints: 16022 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: USED CONJUGANT GRADIENT LEAST SQUARES AND ANISOTROPIC B-FACTOR REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.197 3346 -RANDOM
Rwork0.141 ---
obs0.141 40934 100 %-
all-41840 --
Solvent computationSolvent model: Moews & Krestsinger, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 5 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1452
Refinement stepCycle: LAST / Resolution: 1.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1232 0 2 226 1460
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d2.53
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.53

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