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- PDB-4n90: Crystal structure of ternary complex of TRAIL, DR5, and Fab fragm... -

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Basic information

Entry
Database: PDB / ID: 4n90
TitleCrystal structure of ternary complex of TRAIL, DR5, and Fab fragment from a DR5 agonist antibody
Components
  • Fab heavy chain
  • Fab light chain
  • Tumor necrosis factor ligand superfamily member 10
  • Tumor necrosis factor receptor superfamily member 10B
KeywordsApoptosis/Immune System / DR5 / TRAIL / Agonist / antibody / cooperation / clustering / Apoptosis-Immune System 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 / 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 / Immunoglobulins / Immunoglobulin-like / 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 / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsHuang, X.
CitationJournal: Cancer Cell / Year: 2014
Title: Apo2L/TRAIL and the Death Receptor 5 Agonist Antibody AMG 655 Cooperate to Promote Receptor Clustering and Antitumor Activity.
Authors: Graves, J.D. / Kordich, J.J. / Huang, T.H. / Piasecki, J. / Bush, T.L. / Sullivan, T. / Foltz, I.N. / Chang, W. / Douangpanya, H. / Dang, T. / O'Neill, J.W. / Mallari, R. / Zhao, X. / ...Authors: Graves, J.D. / Kordich, J.J. / Huang, T.H. / Piasecki, J. / Bush, T.L. / Sullivan, T. / Foltz, I.N. / Chang, W. / Douangpanya, H. / Dang, T. / O'Neill, J.W. / Mallari, R. / Zhao, X. / Branstetter, D.G. / Rossi, J.M. / Long, A.M. / Huang, X. / Holland, P.M.
History
DepositionOct 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
R: Tumor necrosis factor receptor superfamily member 10B
S: Tumor necrosis factor receptor superfamily member 10B
T: Tumor necrosis factor receptor superfamily member 10B
A: Tumor necrosis factor ligand superfamily member 10
B: Tumor necrosis factor ligand superfamily member 10
C: Tumor necrosis factor ligand superfamily member 10
E: Fab light chain
D: Fab heavy chain
G: Fab light chain
F: Fab heavy chain
I: Fab light chain
H: Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,77813
Polymers242,71312
Non-polymers651
Water00
1
T: Tumor necrosis factor receptor superfamily member 10B
C: Tumor necrosis factor ligand superfamily member 10
I: Fab light chain
H: Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)80,9044
Polymers80,9044
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
S: Tumor necrosis factor receptor superfamily member 10B
B: Tumor necrosis factor ligand superfamily member 10
G: Fab light chain
F: Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)80,9044
Polymers80,9044
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
R: Tumor necrosis factor receptor superfamily member 10B
A: Tumor necrosis factor ligand superfamily member 10
E: Fab light chain
D: Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9705
Polymers80,9044
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)152.006, 152.006, 613.155
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Tumor necrosis factor receptor superfamily member 10B / Death receptor 5 / TNF-related apoptosis-inducing ligand receptor 2 / TRAIL receptor 2 / TRAIL-R2


Mass: 14193.850 Da / Num. of mol.: 3 / Fragment: UNP residues 57-182
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: TNFRSF10B, DR5, KILLER, TRAILR2, TRICK2, ZTNFR9, UNQ160/PRO186
Production host: Escherichia coli (E. coli) / References: UniProt: O14763
#2: Protein Tumor necrosis factor ligand superfamily member 10 / Apo-2 ligand / Apo-2L / TNF-related apoptosis-inducing ligand / Protein TRAIL


Mass: 19520.852 Da / Num. of mol.: 3 / Fragment: UNP residues 114-281
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFSF10, APO2L, TRAIL / Production host: Escherichia coli (E. coli) / References: UniProt: P50591
#3: Antibody Fab light chain


Mass: 23414.953 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
#4: Antibody Fab heavy chain


Mass: 23774.559 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
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: 4.21 Å3/Da / Density % sol: 70.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM Tris pH 8.0, 1.0 M LiCl, 0.2 M MnCl2, 10% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 63798 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.166

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.286 3235 RANDOM
Rwork0.229 --
obs-60562 -
Refinement stepCycle: LAST / Resolution: 3.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15926 0 1 0 15927

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