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- PDB-5l19: Crystal Structure of a human FasL mutant -

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Basic information

Entry
Database: PDB / ID: 5l19
TitleCrystal Structure of a human FasL mutant
ComponentsTumor necrosis factor ligand superfamily member 6
KeywordsAPOPTOSIS / FasL / CD95L / TNF ligand
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 / intracellular chloride ion homeostasis / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 ...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 / 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 / necroptotic signaling pathway / response to growth factor / 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 / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of endothelial cell apoptotic process / extrinsic apoptotic signaling pathway / lysosomal lumen / negative regulation of angiogenesis / cytokine activity / apoptotic signaling pathway / caveola / cellular response to type II interferon / positive regulation of neuron apoptotic process / cell-cell signaling / Interleukin-4 and Interleukin-13 signaling / response to lipopolysaccharide / positive regulation of canonical NF-kappaB signal transduction / positive regulation of apoptotic process / external side of plasma membrane / signaling receptor binding / apoptotic process / positive regulation of cell population proliferation / 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 / Tumour necrosis factor / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily ...Tumor necrosis factor ligand superfamily member 6 / Tumour necrosis factor / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tumor necrosis factor ligand superfamily member 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
DepositionJul 28, 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 9, 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: Tumor necrosis factor ligand superfamily member 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6113
Polymers17,4491
Non-polymers1612
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.690, 52.690, 87.385
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-455-

HOH

21A-461-

HOH

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Components

#1: 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
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.01 Å3/Da / Density % sol: 38.71 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Ammonium Sulfate, 0.1M Bis-Tris:HCl, pH6.5, 20% (W/V) PEG3350, 0.01M Zinc Chloride

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 9993 / % possible obs: 99.4 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 13.3
Reflection shellResolution: 2→2.03 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.942 / Mean I/σ(I) obs: 3.1 / CC1/2: 0.834 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
MOSFLMdata reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MSV

4msv


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.424 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.16 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21602 521 5.2 %RANDOM
Rwork0.16512 ---
obs0.16775 9414 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.706 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å2-0.48 Å20 Å2
2---0.95 Å2-0 Å2
3---3.1 Å2
Refinement stepCycle: 1 / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1176 0 6 61 1243
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191211
X-RAY DIFFRACTIONr_bond_other_d0.0060.021125
X-RAY DIFFRACTIONr_angle_refined_deg1.9991.9621636
X-RAY DIFFRACTIONr_angle_other_deg1.11132587
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3415149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00223.450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.19815205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.23155
X-RAY DIFFRACTIONr_chiral_restr0.1280.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021351
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02288
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6852.448599
X-RAY DIFFRACTIONr_mcbond_other2.6782.447598
X-RAY DIFFRACTIONr_mcangle_it4.2783.654747
X-RAY DIFFRACTIONr_mcangle_other4.2763.654748
X-RAY DIFFRACTIONr_scbond_it3.9532.647611
X-RAY DIFFRACTIONr_scbond_other3.9212.628608
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2913.814884
X-RAY DIFFRACTIONr_long_range_B_refined8.1918.6411303
X-RAY DIFFRACTIONr_long_range_B_other8.11318.5911292
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 44 -
Rwork0.221 675 -
obs--96.64 %

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