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- PDB-5l36: Crystal Structure of a human FasL mutant in complex with human DcR3 -

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Basic information

Entry
Database: PDB / ID: 5l36
TitleCrystal Structure of a human FasL mutant in complex with human DcR3
Components
  • Tumor necrosis factor ligand superfamily member 6
  • Tumor necrosis factor receptor superfamily member 6B
KeywordsAPOPTOSIS / FasL / CD95L / DcR3 / TNF ligand and receptor / decoy receptor
Function / homology
Function and homology information


positive regulation of phosphatidylserine exposure on apoptotic cell surface / inflammatory cell apoptotic process / release of sequestered calcium ion into cytosol by endoplasmic reticulum / cytoplasmic vesicle lumen / FasL/ CD95L signaling / retinal cell programmed cell death / TNFs bind their physiological receptors / intracellular chloride ion homeostasis / Regulation by c-FLIP / CASP8 activity is inhibited ...positive regulation of phosphatidylserine exposure on apoptotic cell surface / inflammatory cell apoptotic process / release of sequestered calcium ion into cytosol by endoplasmic reticulum / cytoplasmic vesicle lumen / FasL/ CD95L signaling / retinal cell programmed cell death / TNFs bind their physiological receptors / intracellular chloride ion homeostasis / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / Caspase activation via Death Receptors in the presence of ligand / endosomal lumen acidification / T cell apoptotic process / response to growth factor / necroptotic signaling pathway / tumor necrosis factor receptor binding / death receptor binding / positive regulation of extrinsic apoptotic signaling pathway / RIPK1-mediated regulated necrosis / positive regulation of epidermal growth factor receptor signaling pathway / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / FOXO-mediated transcription of cell death genes / necroptotic process / positive regulation of endothelial cell apoptotic process / extrinsic apoptotic signaling pathway via death domain receptors / extrinsic apoptotic signaling pathway / lysosomal lumen / negative regulation of angiogenesis / cytokine activity / apoptotic signaling pathway / caveola / cellular response to type II interferon / cell-cell signaling / positive regulation of neuron apoptotic process / signaling receptor activity / Interleukin-4 and Interleukin-13 signaling / response to lipopolysaccharide / positive regulation of canonical NF-kappaB signal transduction / positive regulation of apoptotic process / signaling receptor binding / external side of plasma membrane / positive regulation of cell population proliferation / apoptotic process / negative regulation of apoptotic process / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular exosome / extracellular region / nucleus / plasma membrane
Similarity search - Function
Tumor necrosis factor ligand superfamily member 6 / Tumor necrosis factor receptor 6B, N-terminal / : / Tumour necrosis factor / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / TNFR/NGFR family cysteine-rich region domain profile. ...Tumor necrosis factor ligand superfamily member 6 / Tumor necrosis factor receptor 6B, N-terminal / : / Tumour necrosis factor / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNF(Tumour Necrosis Factor) family / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / Jelly Rolls - #40 / TNFR/NGFR cysteine-rich region / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Tumour necrosis factor-like domain superfamily / Ribbon / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 6B / Tumor necrosis factor ligand superfamily member 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsLiu, W. / Bonanno, J.B. / Almo, S.C.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094662 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094665 United States
Albert Einstein Cancer CenterP30CA013330 United States
CitationJournal: Structure / Year: 2016
Title: Crystal Structure of the Complex of Human FasL and Its Decoy Receptor DcR3.
Authors: Liu, W. / Ramagopal, U. / Cheng, H. / Bonanno, J.B. / Toro, R. / Bhosle, R. / Zhan, C. / Almo, S.C.
History
DepositionAug 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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
Revision 1.5Oct 23, 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
B: Tumor necrosis factor receptor superfamily member 6B
A: Tumor necrosis factor ligand superfamily member 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5163
Polymers36,4932
Non-polymers231
Water543
1
B: Tumor necrosis factor receptor superfamily member 6B
A: Tumor necrosis factor ligand superfamily member 6
hetero molecules

B: Tumor necrosis factor receptor superfamily member 6B
A: Tumor necrosis factor ligand superfamily member 6
hetero molecules

B: Tumor necrosis factor receptor superfamily member 6B
A: Tumor necrosis factor ligand superfamily member 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,5499
Polymers109,4806
Non-polymers693
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area11500 Å2
ΔGint-87 kcal/mol
Surface area41860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.267, 127.267, 206.262
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Tumor necrosis factor receptor superfamily member 6B / Decoy receptor 3 / DcR3 / Decoy receptor for Fas ligand / M68


Mass: 19044.217 Da / Num. of mol.: 1 / Fragment: UNP residues 30-195
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF6B, DCR3, TR6, UNQ186/PRO212 / Production host: Drosophila (fruit flies) / References: UniProt: O95407
#2: Protein Tumor necrosis factor ligand superfamily member 6 / Apoptosis antigen ligand / APTL / CD95 ligand / CD95-L / Fas antigen ligand / FasL


Mass: 17449.154 Da / Num. of mol.: 1 / Fragment: UNP residues 130-281
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FASLG, APT1LG1, CD95L, FASL, TNFSF6
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpB1_S (others)
References: UniProt: P48023
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 4.4 Å3/Da / Density % sol: 72.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M Sodium Acetate:Acetic Acid pH4.5; 1M Ammonium Phosphate Dibasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jan 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 3.1→50.01 Å / Num. obs: 11951 / % possible obs: 98.9 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 9.5
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.735 / Mean I/σ(I) obs: 3.33 / CC1/2: 0.812 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.8.0123refinement
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MSV

4msv


Resolution: 3.1→50.01 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.905 / SU B: 12.808 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.581 / ESU R Free: 0.317
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2226 570 4.8 %RANDOM
Rwork0.1779 ---
obs0.18 11245 98.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 161.72 Å2 / Biso mean: 58.229 Å2 / Biso min: 22.28 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å2-0.22 Å2-0 Å2
2---0.44 Å2-0 Å2
3---1.43 Å2
Refinement stepCycle: final / Resolution: 3.1→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2273 0 1 3 2277
Biso mean--34.01 30.82 -
Num. residues----291
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192345
X-RAY DIFFRACTIONr_bond_other_d0.0060.022112
X-RAY DIFFRACTIONr_angle_refined_deg21.9463182
X-RAY DIFFRACTIONr_angle_other_deg1.09734875
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8135287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.41722.547106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.69715368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9391519
X-RAY DIFFRACTIONr_chiral_restr0.1070.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212655
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02574
X-RAY DIFFRACTIONr_mcbond_it4.3895.5081160
X-RAY DIFFRACTIONr_mcbond_other4.3865.5091159
X-RAY DIFFRACTIONr_mcangle_it6.7848.2221443
LS refinement shellResolution: 3.099→3.179 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 39 -
Rwork0.252 831 -
all-870 -
obs--99.77 %

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