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- PDB-4msv: Crystal structure of FASL and DcR3 complex -

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Basic information

Entry
Database: PDB / ID: 4msv
TitleCrystal structure of FASL and DcR3 complex
Components
  • Tumor necrosis factor ligand superfamily member 6
  • Tumor necrosis factor receptor superfamily member 6B
KeywordsIMMUNE SYSTEM / FASL / DCR3 / TNF / TNFR / TNF6 / STRUCTURAL GENOMICS / PSI-BIOLOGY / NEW YORK STRUCTURAL GENOMICS / RESEARCH CONSORTIUM / NYSGRC / IMMUNITY / TNF SUPE CD95L / FAS LIGAND / MEMBRANE / ATOMS-TO-ANIMALS: THE IMMUNE FUNCTION NETWORK / IFN / JELLY-ROLL FOLD / BIND TNF RECEPTOR FAS / Protein Structure Initiative / New York Structural Genomics Research Consortium / CD95L / TNF SUPERFAMILY / SECRETED PROTEIN / CYTOKINE
Function / homology
Function and homology information


release of sequestered calcium ion into cytosol by endoplasmic reticulum / positive regulation of phosphatidylserine exposure on apoptotic cell surface / inflammatory cell apoptotic process / cytoplasmic vesicle lumen / FasL/ CD95L signaling / retinal cell programmed cell death / intracellular chloride ion homeostasis / TNFs bind their physiological receptors / Regulation by c-FLIP / CASP8 activity is inhibited ...release of sequestered calcium ion into cytosol by endoplasmic reticulum / positive regulation of phosphatidylserine exposure on apoptotic cell surface / inflammatory cell apoptotic process / cytoplasmic vesicle lumen / FasL/ CD95L signaling / retinal cell programmed cell death / intracellular chloride ion homeostasis / TNFs bind their physiological receptors / 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 / positive regulation of endothelial cell apoptotic process / tumor necrosis factor receptor binding / death receptor binding / positive regulation of epidermal growth factor receptor signaling pathway / RIPK1-mediated regulated necrosis / FOXO-mediated transcription of cell death genes / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / necroptotic process / extrinsic apoptotic signaling pathway via death domain receptors / extrinsic apoptotic signaling pathway / lysosomal lumen / negative regulation of angiogenesis / cytokine activity / caveola / apoptotic signaling pathway / cellular response to type II interferon / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of neuron apoptotic process / cell-cell signaling / signaling receptor activity / positive regulation of canonical NF-kappaB signal transduction / Interleukin-4 and Interleukin-13 signaling / response to lipopolysaccharide / positive regulation of apoptotic process / external side of plasma membrane / signaling receptor binding / apoptotic process / positive regulation of cell population proliferation / 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 / TNF family signature. / Tumour necrosis factor family. / TNF family profile. / TNF(Tumour Necrosis Factor) family ...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 / TNF family signature. / Tumour necrosis factor family. / TNF family profile. / TNF(Tumour Necrosis Factor) family / TNFR/NGFR family cysteine-rich region domain profile. / Tumour necrosis factor domain / 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 / Jelly Rolls - #40 / 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: 2.5 Å
AuthorsLiu, W. / Ramagopal, U.A. / Zhan, C. / Bonanno, J.B. / Bhosle, R.C. / Nathenson, S.G. / Almo, S.C. / Atoms-to-Animals: The Immune Function Network (IFN) / New York Structural Genomics Research Consortium (NYSGRC)
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
DepositionSep 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2014Group: Source and taxonomy
Revision 1.2Nov 16, 2016Group: Database references
Revision 1.3Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)36,5064
Polymers36,3892
Non-polymers1162
Water1,13563
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)109,51712
Polymers109,1686
Non-polymers3496
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area12750 Å2
ΔGint-99 kcal/mol
Surface area42810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.909, 126.909, 205.729
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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 / Plasmid: pMT-Bip-V5-His / Cell line (production host): S2 / 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 / Fas ligand / FasL / ...Apoptosis antigen ligand / APTL / CD95 ligand / CD95-L / Fas antigen ligand / Fas ligand / FasL / Tumor necrosis factor ligand superfamily member 6 / membrane form / Tumor necrosis factor ligand superfamily member 6 / soluble form / Receptor-binding FasL ectodomain / Soluble Fas ligand / sFasL / ADAM10-processed FasL form / APL / FasL intracellular domain / FasL ICD / SPPL2A-processed FasL form / SPA


Mass: 17344.959 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 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21phys / References: UniProt: P48023
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 1.46 Å3/Da / Density % sol: 15.86 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.09M Malonic Acid, 0.013M Ammonium Citr Tribasic, 0.006M Succinic Acid, 0.015M DL-Malic Acid, 0.02M Sodium Acetate, 0.025 M Sodium Formate, 0.008 M Ammonium Tartrate Dibasic, Final pH 7.0; ...Details: 0.09M Malonic Acid, 0.013M Ammonium Citr Tribasic, 0.006M Succinic Acid, 0.015M DL-Malic Acid, 0.02M Sodium Acetate, 0.025 M Sodium Formate, 0.008 M Ammonium Tartrate Dibasic, Final pH 7.0; 0.1M HEPES:NaOH pH 7.0, 10% (w/v) PEG MME 5000, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 22326 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.116 / Rsym value: 0.092 / Net I/σ(I): 14.9
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 7 % / Rmerge(I) obs: 0.826 / Mean I/σ(I) obs: 2 / Rsym value: 0.773 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4J6G

4j6g


Resolution: 2.5→48.52 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.487 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22075 1144 5.1 %RANDOM
Rwork0.18744 ---
obs0.18914 21164 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.065 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å2-0.34 Å20 Å2
2---0.34 Å20 Å2
3---1.1 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2332 0 7 63 2402
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0192419
X-RAY DIFFRACTIONr_bond_other_d0.0020.022208
X-RAY DIFFRACTIONr_angle_refined_deg2.0361.953287
X-RAY DIFFRACTIONr_angle_other_deg0.9693.0085067
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4685298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.48922.569109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.56515379
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6121520
X-RAY DIFFRACTIONr_chiral_restr0.130.2345
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212748
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02592
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.496→2.561 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 78 -
Rwork0.294 1436 -
obs--92.49 %

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