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- PDB-4od2: Crystal structure of the Fab fragment of an anti-DR5 antibody bou... -

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Basic information

Entry
Database: PDB / ID: 4od2
TitleCrystal structure of the Fab fragment of an anti-DR5 antibody bound to DR5
Components
  • Fab fragment of drozitumab, heavy chain
  • Fab fragment of drozitumab, light chain
  • Tumor necrosis factor receptor superfamily member 10B
KeywordsAPOPTOSIS/IMMUNE SYSTEM / IgG / Fab fragment / CRD / TNFSF / 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 / Caspase activation via Death Receptors in the presence of ligand / activation of NF-kappaB-inducing kinase activity / 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 / Caspase activation via Death Receptors in the presence of ligand / activation of NF-kappaB-inducing kinase activity / defense response to tumor cell / TP53 Regulates Transcription of Death Receptors and Ligands / RIPK1-mediated regulated necrosis / extrinsic apoptotic signaling pathway via death domain receptors / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / response to endoplasmic reticulum stress / Cell surface interactions at the vascular wall / cellular response to mechanical stimulus / signaling receptor activity / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / cell surface receptor signaling pathway / positive regulation of apoptotic process / apoptotic process / cell surface / 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 / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region ...Tumour necrosis factor receptor 10 / Tumor necrosis factor receptor 10, N-terminal / Tumour necrosis factor receptor 10A/B, death domain / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Ribbon / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 10B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsHymowitz, S.G. / Compaan, D.
CitationJournal: Cell Death Differ. / Year: 2008
Title: Structural and functional analysis of the interaction between the agonistic monoclonal antibody Apomab and the proapoptotic receptor DR5.
Authors: Adams, C. / Totpal, K. / Lawrence, D. / Marsters, S. / Pitti, R. / Yee, S. / Ross, S. / Deforge, L. / Koeppen, H. / Sagolla, M. / Compaan, D. / Lowman, H. / Hymowitz, S. / Ashkenazi, A.
History
DepositionJan 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
A: Fab fragment of drozitumab, light chain
B: Fab fragment of drozitumab, heavy chain
S: Tumor necrosis factor receptor superfamily member 10B


Theoretical massNumber of molelcules
Total (without water)59,3593
Polymers59,3593
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-26 kcal/mol
Surface area24660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.317, 128.317, 68.386
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

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Components

#1: Antibody Fab fragment of drozitumab, light chain


Mass: 22418.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody Fab fragment of drozitumab, heavy chain


Mass: 24451.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein Tumor necrosis factor receptor superfamily member 10B / Death receptor 5 / TNF-related apoptosis-inducing ligand receptor 2 / TRAIL receptor 2 / TRAIL-R2


Mass: 12488.968 Da / Num. of mol.: 1 / Fragment: UNP residues 73-183
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: Death receptor 5, DR5, KILLER, TNFRSF10B, TRAILR2, TRICK2, UNQ160/PRO186, ZTNFR9
Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi5 cells / References: UniProt: O14763

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.08 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Protein (7mg/mL in 20 mM Tris-HCl, 150 mM NaCl) was mixed with equal volume of well solution (30% PEG 4K, 0.1 M Tris-HCl pH 8.5, 0.2M MgCl2), VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 14, 2004
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 10908 / Num. obs: 10792 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Rsym value: 0.087 / Net I/σ(I): 18.2
Reflection shellResolution: 3.2→3.39 Å / Redundancy: 8.3 % / Mean I/σ(I) obs: 5.7 / Num. unique all: 1741 / Rsym value: 0.305 / % possible all: 96.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 8FAB

8fab


Resolution: 3.2→30 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.829 / SU B: 73.538 / SU ML: 0.566 / Cross valid method: THROUGHOUT / ESU R Free: 0.654 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.30463 1060 10.1 %RANDOM
Rwork0.24115 ---
all0.24763 10792 --
obs0.24763 10792 97.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 111.762 Å2
Baniso -1Baniso -2Baniso -3
1--8.75 Å2-4.37 Å20 Å2
2---8.75 Å20 Å2
3---13.12 Å2
Refinement stepCycle: LAST / Resolution: 3.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3896 0 0 0 3896
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.023994
X-RAY DIFFRACTIONr_angle_refined_deg1.2261.9495441
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0875514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.4124.167156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.05215611
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8161519
X-RAY DIFFRACTIONr_chiral_restr0.0760.2601
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213029
LS refinement shellResolution: 3.201→3.266 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.381 52 -
Rwork0.333 501 -
obs--91.4 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.7918-0.70720.1971.4266-0.73526.9440.33210.82760.4255-0.9922-0.1684-0.61730.298-0.0043-0.16371.06620.09730.28650.77880.07650.3703-0.898593.49634.6691
29.586-8.3671-2.15788.20913.46443.92650.96620.81812.8628-1.6317-0.8042-2.1391-0.9343-0.4374-0.1621.317-0.1091-0.03961.32470.28481.2582-13.9792115.0678-14.9912
35.7654-2.17230.33997.1276-1.37183.90710.0694-0.23310.05450.0133-0.19251.2393-0.1363-0.09910.12310.3171-0.0387-0.05650.3806-0.12090.4547-17.243698.607318.1501
41.6630.4423.10967.21393.12159.6908-0.58680.57640.287-1.73750.2621.1032-0.7272-0.93750.32481.1113-0.1754-0.58062.40010.08841.2736-31.3972111.2662-16.2646
511.4991.4372-3.06152.98420.23091.44680.2592-0.6347-0.02760.4608-0.3933-0.547-0.0229-0.19140.13410.6762-0.0634-0.13310.51670.07490.563415.377393.662325.0819
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 109
2X-RAY DIFFRACTION2A110 - 209
3X-RAY DIFFRACTION3B1 - 122
4X-RAY DIFFRACTION4B123 - 222
5X-RAY DIFFRACTION5S22 - 122

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