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- PDB-3tje: Crystal structure of Fas receptor extracellular domain in complex... -

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Basic information

Entry
Database: PDB / ID: 3tje
TitleCrystal structure of Fas receptor extracellular domain in complex with Fab E09
Components
  • Fab E09, heavy chain
  • Fab E09, light chain
  • Tumor necrosis factor receptor superfamily member 6
KeywordsIMMUNE SYSTEM / Agonistic antibody / Fab fragment / antibody-receptor complex / tumor necrosis factor receptor / cysteine-rich domain / Fas
Function / homology
Function and homology information


Fas signaling pathway / cellular response to hyperoxia / tumor necrosis factor receptor activity / FasL/ CD95L signaling / CD95 death-inducing signaling complex / activation-induced cell death of T cells / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / Caspase activation via Death Receptors in the presence of ligand ...Fas signaling pathway / cellular response to hyperoxia / tumor necrosis factor receptor activity / FasL/ CD95L signaling / CD95 death-inducing signaling complex / activation-induced cell death of T cells / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / Caspase activation via Death Receptors in the presence of ligand / necroptotic signaling pathway / death-inducing signaling complex / TP53 Regulates Transcription of Death Receptors and Ligands / motor neuron apoptotic process / RIPK1-mediated regulated necrosis / regulation of stress-activated MAPK cascade / positive regulation of reactive oxygen species biosynthetic process / extrinsic apoptotic signaling pathway via death domain receptors / extrinsic apoptotic signaling pathway / cellular response to amino acid starvation / positive regulation of apoptotic signaling pathway / cellular response to mechanical stimulus / kinase binding / signaling receptor activity / protein-containing complex assembly / regulation of apoptotic process / calmodulin binding / nuclear body / immune response / positive regulation of apoptotic process / membrane raft / external side of plasma membrane / apoptotic process / negative regulation of apoptotic process / cell surface / signal transduction / extracellular exosome / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Fas receptor / Fas receptor, death domain / Fas receptor, N-terminal / 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 ...Fas receptor / Fas receptor, death domain / Fas receptor, N-terminal / 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 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.93 Å
AuthorsZuger, S. / Stirnimann, C. / Briand, C. / Grutter, M.G.
CitationJournal: Cell Death Differ. / Year: 2012
Title: A series of Fas receptor agonist antibodies that demonstrate an inverse correlation between affinity and potency.
Authors: Chodorge, M. / Zuger, S. / Stirnimann, C. / Briand, C. / Jermutus, L. / Grutter, M.G. / Minter, R.R.
History
DepositionAug 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Fab E09, light chain
H: Fab E09, heavy chain
F: Tumor necrosis factor receptor superfamily member 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,22111
Polymers66,6513
Non-polymers5718
Water7,116395
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-45 kcal/mol
Surface area25180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.490, 166.400, 110.720
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules F

#3: Protein Tumor necrosis factor receptor superfamily member 6 / Apo-1 antigen / Apoptosis-mediating surface antigen FAS / FASLG receptor


Mass: 17500.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APT1, FAS, FAS1, TNFRSF6 / Production host: Escherichia coli (E. coli) / References: UniProt: P25445

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Antibody , 2 types, 2 molecules LH

#1: Antibody Fab E09, light chain


Mass: 23358.947 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pEU4.4 / Cell (production host): HEK EBNA-293 / Production host: Homo sapiens (human)
#2: Antibody Fab E09, heavy chain


Mass: 25790.799 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pEU15.1 / Cell (production host): HEK EBNA-293 / Production host: Homo sapiens (human)

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Non-polymers , 4 types, 403 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.09 Å3/Da / Density % sol: 60.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG4000, 5 mM CdCl2, 100 mM Tris/HOAc, pH 8.5, vapor diffusion, sitting drop, temperature 277K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2007 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.93→50.848 Å / Num. obs: 61296 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 41.611 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 22.51
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
1.93-1.986.90.4394.733123731237454899.6
1.98-2.030.3146.1301914444100
2.03-2.090.2417.7428268433299.9
2.09-2.160.2139.79283954186100
2.16-2.230.17211.2527207409399.9
2.23-2.310.16411.6919364303876.7
2.31-2.390.12415.23257933774100
2.39-2.490.10418.21245163701100
2.49-2.60.08720.93229803521100
2.6-2.730.07123.921587335799.9
2.73-2.880.05828.4521790323199.9
2.88-3.050.0532.27201563050100
3.05-3.260.04334.7417762286799.7
3.26-3.520.03839.3816612266199.6
3.52-3.860.03442.3815119246699.6
3.86-4.320.0346.78140122247100
4.32-4.980.02948.2511716199999.7
4.98-6.10.02851.7610144168799.5
6.1-8.630.02851.537822132899
8.630.03251.81424876697.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å19.91 Å
Translation3 Å19.91 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER1.3.3phasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2H9G, 1GIG

2h9g

1gig


Resolution: 1.93→46.09 Å / Occupancy max: 1 / Occupancy min: 0.16 / SU ML: 0.7 / σ(F): 1.36 / Phase error: 25.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2317 3063 5 %5% random
Rwork0.2044 ---
obs0.2058 61200 98.19 %-
all-61200 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.962 Å2 / ksol: 0.388 e/Å3
Displacement parametersBiso max: 183.24 Å2 / Biso mean: 50.9624 Å2 / Biso min: 20.07 Å2
Baniso -1Baniso -2Baniso -3
1-1.5174 Å2-0 Å20 Å2
2---10.3075 Å20 Å2
3---11.7375 Å2
Refinement stepCycle: LAST / Resolution: 1.93→46.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4093 0 23 395 4511
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094283
X-RAY DIFFRACTIONf_angle_d1.0895815
X-RAY DIFFRACTIONf_chiral_restr0.072652
X-RAY DIFFRACTIONf_plane_restr0.005754
X-RAY DIFFRACTIONf_dihedral_angle_d13.7561546
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.93-1.9990.37633070.3495814612199
1.999-2.0790.33683090.277458536162100
2.079-2.17370.25493080.234458266134100
2.1737-2.28830.30582620.23134981524385
2.2883-2.43160.24993090.212458726181100
2.4316-2.61930.22853100.198158896199100
2.6193-2.88290.23863110.193559076218100
2.8829-3.30.23933110.195259136224100
3.3-4.15720.21743140.196959626276100
4.1572-46.10270.23220.19166120644299
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)
13.204-1.97980.32196.2561-1.00465.27340.29570.14010.37420.0783-0.4765-1.0921-0.1760.83920.12750.2648-0.0176-0.02910.36220.03460.5355-8.309116.06837.1598
22.2234-1.71691.22734.6471-4.45686.36340.48890.1809-0.2773-0.1918-0.7451-0.99730.83030.81060.21140.59140.1305-0.22010.4001-0.04930.6863-4.1012-5.038814.4474
34.11964.35082.16384.81191.97897.9570.8897-0.25281.88920.3966-0.98750.08040.4945-0.8570.09341.0007-0.03050.10420.47650.07541.2116-8.511-15.07923.0966
43.6524-2.5096-4.09583.64112.91414.6004-0.95190.2208-1.0055-1.0632-0.7051.38741.1715-1.45671.27891.3748-0.4433-0.2350.72080.02210.9171-8.2179-20.003724.1215
53.76781.1372.7592.01781.76718.3082-0.1082-0.16290.71470.5988-0.17470.515-0.183-0.0710.31620.4317-0.0350.16330.2-0.05760.6355-30.882436.42169.2745
63.16280.570.17245.7684-1.37662.64230.1638-0.0820.2890.1596-0.14350.2192-0.06130.0922-0.00660.2773-0.03060.02310.1369-0.0270.2943-25.865328.41126.6279
73.6142-1.13460.41752.115-0.05542.41790.07170.0082-0.26670.1153-0.08790.50710.0946-0.21340.01740.26720.07950.10570.22180.05650.5353-59.855828.4485-7.6023
87.51712.65440.03093.4068-0.07782.2934-0.11780.493-0.4294-0.02680.27111.72040.0569-0.3708-0.13180.3120.11370.00490.34650.07960.9273-69.340931.2442-9.4237
95.41781.2426-0.12942.37830.38180.27270.23810.03530.30310.0397-0.14440.1502-0.1217-0.1133-0.09990.3032-0.0013-0.00610.14490.01950.2009-34.7349.89145.7203
104.17611.9422-0.82912.2128-0.5761.22410.1776-0.23410.14820.284-0.07450.0652-0.00330.016-0.09850.3423-0.0076-0.01040.1614-0.01850.2301-32.487210.429610.1587
111.5859-0.48811.07974.033-2.86827.05930.06710.16770.1684-0.17840.09240.533-0.1173-0.4596-0.14930.21340.05940.04090.21670.02530.3885-56.487216.3486-9.4978
125.1804-4.4481-4.34249.28247.00885.6440.03760.32450.0308-0.0864-0.14-0.09230.49950.05310.07080.32690.0288-0.0620.23110.03180.3674-46.334617.4224-16.0967
132.1706-0.6446-0.64026.5401-0.99656.5499-0.00010.1887-0.0319-0.3859-0.05880.31160.0103-0.19630.04650.17420.0357-0.01710.23830.02270.3166-54.152115.2363-14.4152
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN F AND RESID 39:84)F39 - 84
2X-RAY DIFFRACTION2(CHAIN F AND RESID 85:113)F85 - 113
3X-RAY DIFFRACTION3(CHAIN F AND RESID 114:125)F114 - 125
4X-RAY DIFFRACTION4(CHAIN F AND RESID 126:146)F126 - 146
5X-RAY DIFFRACTION5(CHAIN H AND RESID 1:33)H1 - 33
6X-RAY DIFFRACTION6(CHAIN H AND RESID 34:127)H34 - 127
7X-RAY DIFFRACTION7(CHAIN H AND RESID 128:206)H128 - 206
8X-RAY DIFFRACTION8(CHAIN H AND RESID 207:233)H207 - 233
9X-RAY DIFFRACTION9(CHAIN L AND RESID 1:46)L1 - 46
10X-RAY DIFFRACTION10(CHAIN L AND RESID 47:107)L47 - 107
11X-RAY DIFFRACTION11(CHAIN L AND RESID 108:152)L108 - 152
12X-RAY DIFFRACTION12(CHAIN L AND RESID 153:167)L153 - 167
13X-RAY DIFFRACTION13(CHAIN L AND RESID 168:213)L168 - 213

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