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- PDB-1za3: The crystal structure of the YSd1 Fab bound to DR5 -

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Basic information

Entry
Database: PDB / ID: 1za3
TitleThe crystal structure of the YSd1 Fab bound to DR5
Components
  • Fab-YSd1 heavy chain
  • Fab-YSd1 light chain
  • Tumor necrosis factor receptor superfamily member 10B
KeywordsIMMUNE SYSTEM/SIGNALING PROTEIN / phage display / protein engineering / combinatorial mutagenesis / antibody library / death receptor-5 / IMMUNE SYSTEM-SIGNALING PROTEIN 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 / positive regulation of canonical NF-kappaB signal transduction / regulation of apoptotic process / 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. ...: / 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: 3.35 Å
AuthorsFellouse, F.A. / Li, B. / Compaan, D.M. / Peden, A.A. / Hymowitz, S.G. / Sidhu, S.S.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Molecular recognition by a binary code.
Authors: Fellouse, F.A. / Li, B. / Compaan, D.M. / Peden, A.A. / Hymowitz, S.G. / Sidhu, S.S.
History
DepositionApr 5, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 5, 2014Group: Source and taxonomy
Revision 1.4Aug 23, 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 / struct_ncs_dom_lim / struct_ref_seq_dif
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_ref_seq_dif.details
Remark 999SEQUENCE The heavy and light chain Fab fragments were isolated from a phage library, and have no ...SEQUENCE The heavy and light chain Fab fragments were isolated from a phage library, and have no corresponding entries in the standard databases.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fab-YSd1 light chain
B: Fab-YSd1 heavy chain
R: Tumor necrosis factor receptor superfamily member 10B
L: Fab-YSd1 light chain
H: Fab-YSd1 heavy chain
S: Tumor necrosis factor receptor superfamily member 10B


Theoretical massNumber of molelcules
Total (without water)126,7436
Polymers126,7436
Non-polymers00
Water00
1
A: Fab-YSd1 light chain
B: Fab-YSd1 heavy chain
S: Tumor necrosis factor receptor superfamily member 10B


Theoretical massNumber of molelcules
Total (without water)63,3713
Polymers63,3713
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
R: Tumor necrosis factor receptor superfamily member 10B
L: Fab-YSd1 light chain
H: Fab-YSd1 heavy chain


Theoretical massNumber of molelcules
Total (without water)63,3713
Polymers63,3713
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)147.059, 147.059, 144.947
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21L
31A
41L
12B
22H
32B
42H
13R
23S

NCS domain segments:

Refine code: 5

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPVALVALAA1 - 1091 - 109
211ASPASPVALVALLD1 - 1091 - 109
321ALAALACYSCYSAA110 - 213110 - 213
421ALAALACYSCYSLD110 - 213110 - 213
112GLUGLUSERSERBB1 - 1131 - 129
212GLUGLUSERSERHE1 - 1131 - 129
322ALAALALYSLYSBB114 - 214130 - 230
422ALAALALYSLYSHE114 - 214130 - 230
113SERSERCYSCYSRC22 - 8626 - 90
213SERSERCYSCYSSF22 - 8626 - 90

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody Fab-YSd1 light chain


Mass: 23148.602 Da / Num. of mol.: 2 / Fragment: Fab light chain
Source method: isolated from a genetically manipulated source
Details: Light chain was selected from a phage library based on human kappa light chain
Source: (gene. exp.) Homo sapiens (human)
#2: Antibody Fab-YSd1 heavy chain


Mass: 25230.965 Da / Num. of mol.: 2 / Fragment: Fab heavy chain
Source method: isolated from a genetically manipulated source
Details: Heavy chain was selected from a phage library based on human heavy chain
Source: (gene. exp.) Homo sapiens (human)
#3: Protein Tumor necrosis factor receptor superfamily member 10B / Death receptor 5 / TNF-related apoptosis-inducing ligand receptor 2 / TRAIL receptor-2 / TRAIL-R2 / DR5


Mass: 14991.793 Da / Num. of mol.: 2 / Fragment: Extra-cellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DR5 / Plasmid: pAcGP67-B / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi5 / References: UniProt: O14763

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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: 3.4 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 20% PEG 8000, 0.2M MgAcetate, 0.1M NaCacodylate pH 6.2-6.6, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.92086 / Wavelength: 0.92086 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jun 14, 2004
RadiationMonochromator: double crystal sagittally focused monochromoeter
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92086 Å / Relative weight: 1
ReflectionResolution: 3.35→50 Å / Num. all: 26539 / Num. obs: 26539 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 42 Å2 / Rsym value: 0.124 / Net I/σ(I): 8.3
Reflection shellResolution: 3.35→3.47 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 4.2 / Num. unique all: 2582 / Rsym value: 0.338 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FVE variants

1fve


Resolution: 3.35→30 Å / Cor.coef. Fo:Fc: 0.859 / Cor.coef. Fo:Fc free: 0.777 / SU B: 27.186 / SU ML: 0.456 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R Free: 0.573 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28028 2603 10 %RANDOM
Rwork0.22408 ---
all0.22975 26539 --
obs0.22975 26003 98.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.287 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å2-0.6 Å20 Å2
2---1.2 Å20 Å2
3---1.79 Å2
Refinement stepCycle: LAST / Resolution: 3.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8149 0 0 0 8149
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0218237
X-RAY DIFFRACTIONr_bond_other_d0.0020.026998
X-RAY DIFFRACTIONr_angle_refined_deg1.3391.9511217
X-RAY DIFFRACTIONr_angle_other_deg0.899316420
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4851045
X-RAY DIFFRACTIONr_chiral_restr0.0820.21243
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029193
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021654
X-RAY DIFFRACTIONr_nbd_refined0.210.21576
X-RAY DIFFRACTIONr_nbd_other0.2260.28196
X-RAY DIFFRACTIONr_nbtor_other0.0880.25359
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2118
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.250.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2750.27
X-RAY DIFFRACTIONr_mcbond_it2.1522.55249
X-RAY DIFFRACTIONr_mcangle_it3.66658485
X-RAY DIFFRACTIONr_scbond_it2.4912.52988
X-RAY DIFFRACTIONr_scangle_it3.93252732
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1254medium positional1.260.5
21B1311medium positional1.770.5
33R381medium positional0.20.5
11A1798loose positional1.435
21B1859loose positional1.935
33R534loose positional0.685
11A1254medium thermal0.622
21B1311medium thermal0.632
33R381medium thermal0.642
11A1798loose thermal1.4210
21B1859loose thermal1.510
33R534loose thermal2.4210
LS refinement shellResolution: 3.35→3.418 Å / Total num. of bins used: 25 /
RfactorNum. reflection
Rfree0.283 145
Rwork0.232 1350
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)
16.7184-1.76231.07565.59582.55894.8503-0.0739-0.3625-0.1619-0.0679-0.05570.35930.3556-0.26740.12950.6789-0.04250.01070.8021-0.26140.622238.142656.914539.7317
212.0818-0.54161.17223.98712.04294.53440.09380.1464-0.1677-0.4343-0.2663-0.045-0.2173-0.33760.17250.84770.03750.01850.5102-0.11890.623240.853243.500221.9088
310.65463.30895.58635.29233.86519.2896-0.3198-0.50170.9107-0.6519-0.17060.8432-0.1072-0.76530.49040.84160.2468-0.33120.8518-0.33330.90715.358165.554726.0365
45.55890.11011.224611.89250.69417.8794-0.79741.23991.04-0.95170.646-0.0201-1.21220.43520.15140.86420.0015-0.39981.1119-0.1910.857416.391163.638813.9699
57.7881-0.7099-1.3695.27160.27779.66670.216-0.29210.5020.6007-0.01060.10570.2932-0.135-0.20540.6219-0.0042-0.04970.7338-0.26410.617-26.901551.4519-2.2203
64.9923-0.21362.43365.02620.35639.6666-0.1327-0.34890.30540.23520.2934-0.40690.38790.4834-0.16070.53470.0104-0.00050.7451-0.17070.784-6.767446.8311-11.0679
724.8239-2.24398.22612.8957-1.62269.83980.6544-3.5063-1.15120.7132-0.2663-0.48730.3295-0.4808-0.38811.1954-0.284-0.1651.64040.33710.8599-13.18943.857230.3005
827.10758.1352-4.21719.3622-4.06646.78780.0554-0.9486-5.76370.6350.1344-0.56111.73040.0695-0.18971.33660.006-0.44811.1030.1152.3951-8.338631.035421.5542
912.33674.87853.62454.4531.58932.99050.1215-1.04110.8238-0.1397-0.41230.2601-0.2426-0.26150.29080.1313-0.05050.09670.129-0.05480.1932-11.661567.2178-22.6713
107.01636.93641.049811.76440.15372.92670.2997-0.3219-0.01461.0815-0.3678-0.0053-0.23980.00930.06810.24160.03640.12910.0945-0.10680.287953.883831.079637.4982
11105.5975-45.619719.391513.818-22.644549.7826-3.1624-3.69490.90333.81571.0595-1.4331-4.11751.21872.10291.3159-0.17680.02511.3783-0.53480.879811.451377.2524-6.7575
1255.588120.970322.142822.934917.82341.98040.81660.8027-0.2582-0.71440.45741.3963-0.3488-1.6305-1.2740.7265-0.20370.2440.99040.09360.813227.054110.155129.8876
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1091 - 109
2X-RAY DIFFRACTION2BB1 - 1151 - 131
3X-RAY DIFFRACTION3AA110 - 213110 - 213
4X-RAY DIFFRACTION4BB116 - 214132 - 230
5X-RAY DIFFRACTION5LD1 - 1091 - 109
6X-RAY DIFFRACTION6HE1 - 1151 - 131
7X-RAY DIFFRACTION7LD110 - 213110 - 213
8X-RAY DIFFRACTION8HE116 - 214132 - 230
9X-RAY DIFFRACTION9RC22 - 8626 - 90
10X-RAY DIFFRACTION10SF22 - 8626 - 90
11X-RAY DIFFRACTION11RC87 - 12391 - 127
12X-RAY DIFFRACTION12SF87 - 12691 - 130

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