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- PDB-2h9g: Crystal structure of phage derived Fab BdF1 with human Death Rece... -

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Basic information

Entry
Database: PDB / ID: 2h9g
TitleCrystal structure of phage derived Fab BdF1 with human Death Receptor 5 (DR5)
Components
  • Fab BdF1, heavy chain
  • Fab BdF1, light chain
  • Tumor necrosis factor receptor superfamily member 10B precursor
KeywordsIMMUNE SYSTEM/APOPTOSIS / PHAGE DISPLAY / PROTEIN ENGINEERING / COMBINATORIAL MUTAGENESIS / ANTIBODY LIBRARY / DEATH RECEPTOR-5 / agonists / IMMUNE SYSTEM-APOPTOSIS 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 / TP53 Regulates Transcription of Death Receptors and Ligands / RIPK1-mediated regulated necrosis / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / extrinsic apoptotic signaling pathway via death domain receptors / response to endoplasmic reticulum stress / Cell surface interactions at the vascular wall / cellular response to mechanical stimulus / signaling receptor activity / regulation of apoptotic process / cell surface receptor signaling pathway / positive regulation of canonical NF-kappaB signal transduction / 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. ...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: 2.32 Å
AuthorsHymowitz, S.G. / Compaan, D.M.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Activation of the Proapoptotic Death Receptor DR5 by Oligomeric Peptide and Antibody Agonists.
Authors: Li, B. / Russell, S.J. / Compaan, D.M. / Totpal, K. / Marsters, S.A. / Ashkenazi, A. / Cochran, A.G. / Hymowitz, S.G. / Sidhu, S.S.
History
DepositionJun 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 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 / struct_ncs_dom_lim / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_sheet.number_strands
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fab BdF1, light chain
B: Fab BdF1, heavy chain
R: Tumor necrosis factor receptor superfamily member 10B precursor
L: Fab BdF1, light chain
H: Fab BdF1, heavy chain
S: Tumor necrosis factor receptor superfamily member 10B precursor


Theoretical massNumber of molelcules
Total (without water)124,0116
Polymers124,0116
Non-polymers00
Water2,576143
1
A: Fab BdF1, light chain
B: Fab BdF1, heavy chain
R: Tumor necrosis factor receptor superfamily member 10B precursor


Theoretical massNumber of molelcules
Total (without water)62,0053
Polymers62,0053
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-36 kcal/mol
Surface area25150 Å2
MethodPISA
2
L: Fab BdF1, light chain
H: Fab BdF1, heavy chain
S: Tumor necrosis factor receptor superfamily member 10B precursor


Theoretical massNumber of molelcules
Total (without water)62,0053
Polymers62,0053
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-34 kcal/mol
Surface area22110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.814, 61.389, 108.269
Angle α, β, γ (deg.)90.00, 101.17, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21L
12B
22H

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPARGARGAA1 - 2111 - 211
21ASPASPARGARGLD1 - 2111 - 211
12GLUGLUPROPROBB1 - 2131 - 220
22GLUGLUPROPROHE1 - 2131 - 220

NCS ensembles :
ID
1
2
DetailsThe biological assembly consists of one light chain, one heavy chain bound to one receptor chain. The crystallographic assymetric unit contains two biologically relevent assemblies (chains A,B,R and chain H,L,S)

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Components

#1: Antibody Fab BdF1, light chain


Mass: 23287.793 Da / Num. of mol.: 2 / Fragment: Fab fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: protein selected by phage display / Production host: Escherichia coli (E. coli)
#2: Antibody Fab BdF1, heavy chain


Mass: 24139.262 Da / Num. of mol.: 2 / Fragment: Fab fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: protein selected by phage display / Production host: Escherichia coli (E. coli)
#3: Protein Tumor necrosis factor receptor superfamily member 10B precursor / Death receptor 5 / TNF-related apoptosis-inducing ligand receptor 2 / TRAIL receptor 2 / TRAIL-R2 / ...Death receptor 5 / TNF-related apoptosis-inducing ligand receptor 2 / TRAIL receptor 2 / TRAIL-R2 / CD262 antigen


Mass: 14578.320 Da / Num. of mol.: 2 / Fragment: extra cellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF10B, DR5, KILLER, TRAILR2, TRICK2, ZTNFR9 / Plasmid: pacgp67-b / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): HI5 / References: UniProt: O14763
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.62 Å3/Da / Density % sol: 53.1 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Crystals from drops containing an equal volume of protein and well solution consisting of 20% PEG 3350, 0.2M Na2HPO4, 0.1 M Bis-Tris, pH 6.1-6.8. The crystals were cryo-protected with well ...Details: Crystals from drops containing an equal volume of protein and well solution consisting of 20% PEG 3350, 0.2M Na2HPO4, 0.1 M Bis-Tris, pH 6.1-6.8. The crystals were cryo-protected with well solution supplemented with 20% PEG 200., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 14, 2003
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 54784 / Num. obs: 54784 / % possible obs: 97.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rsym value: 0.089 / Net I/σ(I): 6.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2 / Num. unique all: 5470 / Rsym value: 0.419 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
Blu-Icedata collection
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Chain S from 1d0g Chain AB from 1FVE

1d0g

1fve


Resolution: 2.32→30 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.884 / SU B: 16.749 / SU ML: 0.199 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic with TLS refinement / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.367 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS for refinement only
RfactorNum. reflection% reflectionSelection details
Rfree0.28164 5486 10.1 %RANDOM
Rwork0.22846 ---
all0.2338 54443 --
obs0.2338 48957 97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å20.66 Å2
2---1.09 Å20 Å2
3---0.87 Å2
Refinement stepCycle: LAST / Resolution: 2.32→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7756 0 0 143 7899
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0227840
X-RAY DIFFRACTIONr_bond_other_d0.0020.026822
X-RAY DIFFRACTIONr_angle_refined_deg1.31.95310678
X-RAY DIFFRACTIONr_angle_other_deg0.766315969
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5751007
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.30324.08299
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.824151226
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8411535
X-RAY DIFFRACTIONr_chiral_restr0.0750.21212
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028730
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021525
X-RAY DIFFRACTIONr_nbd_refined0.1920.21193
X-RAY DIFFRACTIONr_nbd_other0.1810.26513
X-RAY DIFFRACTIONr_nbtor_refined0.1720.23591
X-RAY DIFFRACTIONr_nbtor_other0.0830.24661
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2220
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1180.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.190.240
X-RAY DIFFRACTIONr_mcbond_it2.472.56413
X-RAY DIFFRACTIONr_mcbond_other0.5152.52066
X-RAY DIFFRACTIONr_mcangle_it3.32658177
X-RAY DIFFRACTIONr_scbond_it2.4132.53284
X-RAY DIFFRACTIONr_scangle_it3.4552501
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A3046medium positional0.280.5
2B3066medium positional0.180.5
1A3046medium thermal0.432
2B3066medium thermal0.442
LS refinement shellResolution: 2.32→2.367 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.341 346 -
Rwork0.268 2811 -
obs--95.87 %
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)
10.77080.7908-0.65291.8098-2.08383.4433-0.0408-0.00640.1586-0.15060.19870.41530.139-0.392-0.1579-0.051-0.0577-0.0737-0.06690.0395-0.0916-18.4009-0.169822.8133
23.53911.52870.8472.9070.00263.04520.0063-0.26910.05540.2737-0.0204-0.0378-0.150.13170.0141-0.17010.00170.0243-0.14660.0379-0.1734-8.9291-7.537756.9674
30.99480.30080.89111.4157-0.14373.9268-0.03360.02150.0695-0.4458-0.0185-0.13230.1381-0.08440.0521-0.09780.00350.0484-0.20050.0136-0.17941.147511.51921.5751
42.79741.8041-1.09975.4922-0.27682.1278-0.153-0.1989-0.52030.1991-0.0163-0.41960.29540.14080.1693-0.22030.01470.0081-0.16670.0243-0.09124.5405-9.210847.8886
54.82241.7348-0.777911.67271.14954.001-0.07190.1359-0.255-0.50260.0975-0.1264-0.0483-0.2276-0.02560.3120.0065-0.037-0.0168-0.0076-0.2178-9.5015-3.00551.0375
612.8026.4466-2.983817.0632-0.08944.9361-0.2832-0.09150.8289-0.89210.25510.6705-0.5284-0.50020.02810.4107-0.02350.02590.15150.15090.5037-25.5699-32.854813.14
71.10212.03651.38594.09272.71762.9561-0.24560.1863-0.4675-0.83540.596-1.0684-0.3680.5143-0.35040.119-0.18490.28250.0491-0.17660.217547.58613.690923.1797
83.91071.3101-0.90462.77420.16572.96660.0594-0.254-0.1240.3086-0.0275-0.03830.1399-0.1448-0.0319-0.1562-0.0134-0.0508-0.1329-0.0359-0.128537.842621.226357.0709
91.4060.699-0.68833.22331.26764.1162-0.08990.1394-0.126-0.85640.146-0.0976-0.37260.1778-0.0561-0.0207-0.0259-0.0224-0.1256-0.0302-0.106427.94452.183621.641
103.02891.69870.77675.2320.41182.3174-0.0547-0.22150.48830.1412-0.10130.2613-0.292-0.10250.156-0.24070.0049-0.0299-0.1491-0.0184-0.076224.388522.906147.8867
119.0546.4332.92097.15513.85335.0698-0.8541.02450.45-2.11620.80580.7056-1.11750.83160.04821.419-0.46450.25710.2928-0.0503-0.023238.783713.79490.787
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1121 - 112
2X-RAY DIFFRACTION2AA113 - 211113 - 211
3X-RAY DIFFRACTION3BB1 - 1141 - 121
4X-RAY DIFFRACTION4BB115 - 213122 - 220
5X-RAY DIFFRACTION5RC21 - 8621 - 86
6X-RAY DIFFRACTION6RC87 - 12887 - 128
7X-RAY DIFFRACTION7LD1 - 1121 - 112
8X-RAY DIFFRACTION8LD113 - 211113 - 211
9X-RAY DIFFRACTION9HE1 - 1141 - 121
10X-RAY DIFFRACTION10HE115 - 213122 - 220
11X-RAY DIFFRACTION11SF21 - 8421 - 84

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