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- PDB-3k51: Crystal Structure of DcR3-TL1A complex -

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Basic information

Entry
Database: PDB / ID: 3k51
TitleCrystal Structure of DcR3-TL1A complex
Components
  • Decoy receptor 3
  • Tumor necrosis factor ligand superfamily member 15, secreted form
KeywordsIMMUNE SYSTEM / DcR3 / TL1A / TNF / TNFR / DECOY RECEPTOR / IMMUNITY / Cytokine / Disulfide bond / Glycoprotein / Membrane / Secreted / Signal-anchor / Transmembrane / Apoptosis / Receptor
Function / homology
Function and homology information


TNFs bind their physiological receptors / activation of NF-kappaB-inducing kinase activity / tumor necrosis factor receptor binding / cytokine activity / : / signaling receptor activity / immune response / signaling receptor binding / negative regulation of apoptotic process / apoptotic process ...TNFs bind their physiological receptors / activation of NF-kappaB-inducing kinase activity / tumor necrosis factor receptor binding / cytokine activity / : / signaling receptor activity / immune response / signaling receptor binding / negative regulation of apoptotic process / apoptotic process / signal transduction / extracellular space / extracellular region / membrane / plasma membrane
Similarity search - Function
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 family. / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region ...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 family. / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor (TNF) homology domain (THD) profile. / 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 ligand superfamily member 15 / Tumor necrosis factor receptor superfamily member 6B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 Å
AuthorsZhan, C. / Patskovsky, Y. / Yan, Q. / Li, Z. / Ramagopal, U.A. / Nathenson, S.G. / Almo, S.C.
CitationJournal: Structure / Year: 2011
Title: Decoy Strategies: The Structure of TL1A:DcR3 Complex.
Authors: Zhan, C. / Patskovsky, Y. / Yan, Q. / Li, Z. / Ramagopal, U. / Cheng, H. / Brenowitz, M. / Hui, X. / Nathenson, S.G. / Almo, S.C.
History
DepositionOct 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 27, 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 15, secreted form
B: Decoy receptor 3


Theoretical massNumber of molelcules
Total (without water)40,1662
Polymers40,1662
Non-polymers00
Water1,49583
1
A: Tumor necrosis factor ligand superfamily member 15, secreted form
B: Decoy receptor 3

A: Tumor necrosis factor ligand superfamily member 15, secreted form
B: Decoy receptor 3

A: Tumor necrosis factor ligand superfamily member 15, secreted form
B: Decoy receptor 3


Theoretical massNumber of molelcules
Total (without water)120,4986
Polymers120,4986
Non-polymers00
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 area11960 Å2
ΔGint-64 kcal/mol
Surface area44330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.890, 74.890, 143.125
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Tumor necrosis factor ligand superfamily member 15, secreted form / Vascular endothelial cell growth inhibitor / TNF ligand-related molecule 1 / Tumor necrosis factor ...Vascular endothelial cell growth inhibitor / TNF ligand-related molecule 1 / Tumor necrosis factor ligand superfamily member 15 / membrane form / Tumor necrosis factor ligand superfamily member 15 / secreted form


Mass: 20877.619 Da / Num. of mol.: 1 / Mutation: C95S,C135S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TL1, TNFSF15, VEGI / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI / References: UniProt: O95150
#2: Protein Decoy receptor 3 / Tumor necrosis factor receptor superfamily member 6B / Decoy receptor for Fas ligand / DcR3 / M68


Mass: 19288.488 Da / Num. of mol.: 1 / Fragment: TNFR cysteine rich domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCR3, TNFRSF6B, TR6, UNQ186/PRO212 / Plasmid: pMT/BiP/V5-His / Cell line (production host): S2 / Production host: DROSOPHILA (fruit flies) / References: UniProt: O95407
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.88 Å3/Da / Density % sol: 57.36 %
Crystal growTemperature: 290 K / pH: 6.5
Details: 0.1M MES pH6.5, 8% PEG 10K, 3% dextran sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 290.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 17791 / % possible obs: 99.9 % / Redundancy: 7.7 % / Biso Wilson estimate: 47.85 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 15.3
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 3.17 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QE3

2qe3


Resolution: 2.45→36.23 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.905 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 6.811 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.324 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: EXTRA ELECTRON DENSITY POSSIBLY CORRESPONDING TO N-GLYCAN IS OBSERVED CLOSE TO N173 IN CHAIN B. BECAUSE OF THE DYNAMIC STRUCTURAL FEATURES, THIS DENSITY IS TOO WEAK FOR ACCURATE MODELING OF GLYCANS.
RfactorNum. reflection% reflectionSelection details
Rfree0.262 566 3.2 %RANDOM
Rwork0.223 ---
obs0.224 17779 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 79.96 Å2
Baniso -1Baniso -2Baniso -3
1--3.27 Å2-1.63 Å20 Å2
2---3.27 Å20 Å2
3---4.9 Å2
Refinement stepCycle: LAST / Resolution: 2.45→36.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2339 0 0 83 2422
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222460
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.541.9473363
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2625313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.37522.909110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.11115370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1511519
X-RAY DIFFRACTIONr_chiral_restr0.0480.2362
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0221919
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1930.3970
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.51669
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.5222
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1360.362
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.511
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.19431543
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.90942499
X-RAY DIFFRACTIONr_scbond_it4.0265917
X-RAY DIFFRACTIONr_scangle_it5.976857
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.51 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 44 -
Rwork0.235 1227 -
obs--100 %

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