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

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Basic information

Entry
Database: PDB / ID: 3thm
TitleCrystal structure of Fas receptor extracellular domain in complex with Fab EP6b_B01
Components
  • (Fab EP6b_B01, ...) x 2
  • 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 / FasL/ CD95L signaling / tumor necrosis factor receptor activity / CD95 death-inducing signaling complex / positive regulation of cysteine-type endopeptidase activity involved in 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 ...Fas signaling pathway / cellular response to hyperoxia / FasL/ CD95L signaling / tumor necrosis factor receptor activity / CD95 death-inducing signaling complex / positive regulation of cysteine-type endopeptidase activity involved in 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 / necroptotic signaling pathway / death-inducing signaling complex / motor neuron apoptotic process / TP53 Regulates Transcription of Death Receptors and Ligands / RIPK1-mediated regulated necrosis / regulation of stress-activated MAPK cascade / activation-induced cell death of T cells / extrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / cellular response to amino acid starvation / positive regulation of apoptotic signaling pathway / kinase binding / cellular response to mechanical stimulus / signaling receptor activity / protein-containing complex assembly / regulation of apoptotic process / nuclear body / calmodulin binding / positive regulation of protein phosphorylation / 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: 2.1 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 19, 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
L: Fab EP6b_B01, light chain
H: Fab EP6b_B01, heavy chain
F: Tumor necrosis factor receptor superfamily member 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7059
Polymers66,8243
Non-polymers8816
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7290 Å2
ΔGint-11 kcal/mol
Surface area24140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.510, 94.510, 139.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Antibody , 2 types, 2 molecules LH

#1: Antibody Fab EP6b_B01, light chain


Mass: 23247.736 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): CHO cells / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Fab EP6b_B01, heavy chain


Mass: 26075.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): CHO cells / Production host: Cricetulus griseus (Chinese hamster)

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Protein / Sugars , 2 types, 2 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 / Fragment: extracellular domain
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
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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Non-polymers , 2 types, 342 molecules

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


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O

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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: 2.69 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG4000, 10% isopropanol, 100 mM HEPES/NaOH, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 22, 2009 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→47.255 Å / Num. all: 42596 / Num. obs: 42586 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Redundancy: 10 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 16.04
Reflection shell
Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.1-2.1510.30.6374.131100
2.15-2.2110.10.5464.781100
2.21-2.289.80.495.191100
2.28-2.359.80.4056.131100
2.35-2.4210.40.3756.781100
2.42-2.5110.40.3078.11100
2.51-2.610.20.2599.271100
2.6-2.71100.20511.171100
2.71-2.839.30.16113.151100
2.83-2.9710.40.13216.821100
2.97-3.1310.30.10919.851100
3.13-3.3210.20.08923.111100
3.32-3.559.90.07526.621100
3.55-3.839.60.06629.85199.9
3.83-4.210.30.05935.061100
4.2-4.710.10.05138.331100
4.7-5.429.10.05535.831100
5.42-6.64100.06132.931100
6.64-9.399.40.05635.411100
9.398.60.04838.71198.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.1 Å47.26 Å
Translation2.1 Å47.26 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3TJE

3tje


Resolution: 2.1→47.255 Å / Occupancy max: 1 / Occupancy min: 0.23 / SU ML: 0.65 / σ(F): 1.37 / Phase error: 20 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2206 2128 5 %
Rwork0.1832 --
obs0.1851 42568 99.98 %
all-42568 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.6 Å2 / ksol: 0.38 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.345 Å20 Å20 Å2
2---0.345 Å20 Å2
3---5.0633 Å2
Refinement stepCycle: LAST / Resolution: 2.1→47.255 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3915 0 58 337 4310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064088
X-RAY DIFFRACTIONf_angle_d1.0075548
X-RAY DIFFRACTIONf_dihedral_angle_d14.7991482
X-RAY DIFFRACTIONf_chiral_restr0.063632
X-RAY DIFFRACTIONf_plane_restr0.004709
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.17510.26372080.2073954X-RAY DIFFRACTION100
2.1751-2.26220.27872090.1963972X-RAY DIFFRACTION100
2.2622-2.36510.2382130.18244043X-RAY DIFFRACTION100
2.3651-2.48980.21912100.17873995X-RAY DIFFRACTION100
2.4898-2.64580.24832100.18973993X-RAY DIFFRACTION100
2.6458-2.850.25482120.18264026X-RAY DIFFRACTION100
2.85-3.13680.21172130.17144032X-RAY DIFFRACTION100
3.1368-3.59060.2242140.18434068X-RAY DIFFRACTION100
3.5906-4.52320.20062150.16574096X-RAY DIFFRACTION100
4.5232-47.26690.19972240.19764261X-RAY DIFFRACTION100
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)
18.7106-1.3446-2.18096.0496-3.61643.2208-0.36770.764-0.778-1.0985-0.1054-0.09931.092-0.18420.44860.5066-0.12850.04160.2092-0.00660.2921-9.8358-30.598111.8322
27.19170.0639-0.27873.3945-0.43883.745-0.1732-0.0541-0.97080.02810.1035-0.410.8960.3370.06550.41630.0965-0.00670.213-0.00910.33460.4183-29.828116.0013
31.6971-0.84220.21854.03021.60890.8445-0.28970.27190.1987-0.94730.0414-1.549-0.04011.54960.21940.4180.10620.22610.90630.04250.876520.7809-23.41487.4522
45.70931.34330.5835.8501-1.20473.2371-0.0061-0.14350.3409-0.5669-0.6561-1.7645-0.16071.42110.63430.40350.09710.12130.7673-0.03990.768817.5767-20.778210.1059
52.48110.68610.41612.9484-0.58111.2718-0.09750.21990.0332-0.20030.2290.29450.2248-0.3419-0.08140.266-0.1341-0.01580.21610.03890.1996-25.3454-21.503816.5512
61.8956-0.3253-0.80621.31160.18811.7544-0.0070.25-0.0629-0.06350.09930.23170.1668-0.2853-0.10510.236-0.1062-0.01710.15980.03650.2293-21.612-17.009315.1141
73.2550.1853-0.05070.7247-0.57921.50960.07760.48930.65170.00550.07570.0093-0.4609-0.1462-0.07130.08130.04530.04380.40840.16230.4566-40.152415.057231.7228
87.0196-4.9476-3.31639.6231-0.5162.8938-0.3676-1.50250.61581.9146-0.02260.7524-0.2437-0.83050.38510.3406-0.02840.04430.4199-0.10920.2105-10.631-7.537328.0339
90.7080.0941-0.38373.08450.0190.8924-0.0510.04950.0593-0.14280.12830.07940.0562-0.1058-0.07050.1215-0.0608-0.01890.1651-0.00380.1464-9.0085-3.879214.2852
103.04180.7538-2.13291.7896-1.37484.46110.1385-0.21840.07790.1866-0.0363-0.0297-0.15130.1256-0.10990.1082-0.0239-0.02640.17540.00680.2177-24.78510.922836.1874
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN F AND RESID 36:45)
2X-RAY DIFFRACTION2(CHAIN F AND RESID 46:87)
3X-RAY DIFFRACTION3(CHAIN F AND RESID 88:104)
4X-RAY DIFFRACTION4(CHAIN F AND RESID 105:127)
5X-RAY DIFFRACTION5(CHAIN H AND RESID 1:81)
6X-RAY DIFFRACTION6(CHAIN H AND RESID 82:131)
7X-RAY DIFFRACTION7(CHAIN H AND RESID 132:233)
8X-RAY DIFFRACTION8(CHAIN L AND RESID 1:4)
9X-RAY DIFFRACTION9(CHAIN L AND RESID 5:112)
10X-RAY DIFFRACTION10(CHAIN L AND RESID 113:214)

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