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- PDB-3mi8: The structure of TL1A-DCR3 COMPLEX -

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Basic information

Entry
Database: PDB / ID: 3mi8
TitleThe structure of TL1A-DCR3 COMPLEX
Components
  • TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 15, SECRETED FORM
  • Tumor necrosis factor receptor superfamily member 6B
KeywordsIMMUNE SYSTEM / DCR3 / TL1A / TNF / TNFR / DECOY RECEPTOR / IMMUNITY / DISULFIDE BOND / GLYCOPROTEIN / SECRETED / 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 / TNFR/NGFR family cysteine-rich region domain profile. / Tumour necrosis factor domain / 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 / 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 (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 / Resolution: 2.951 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
DepositionApr 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 15, SECRETED FORM
D: Tumor necrosis factor receptor superfamily member 6B


Theoretical massNumber of molelcules
Total (without water)40,1822
Polymers40,1822
Non-polymers00
Water724
1
A: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 15, SECRETED FORM
D: Tumor necrosis factor receptor superfamily member 6B

A: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 15, SECRETED FORM
D: Tumor necrosis factor receptor superfamily member 6B

A: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 15, SECRETED FORM
D: Tumor necrosis factor receptor superfamily member 6B


Theoretical massNumber of molelcules
Total (without water)120,5476
Polymers120,5476
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area11720 Å2
ΔGint-55 kcal/mol
Surface area35790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.080, 161.080, 161.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332

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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: 20893.684 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 72-251 / Mutation: 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 Tumor necrosis factor receptor superfamily member 6B / Decoy receptor for Fas ligand / Decoy receptor 3 / DcR3 / M68


Mass: 19288.488 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: DcR3, TNFRSF6B / 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.: 4 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.33 Å3/Da / Density % sol: 71.62 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.4M K/Na tartrate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 290.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. all: 15595 / Num. obs: 15595 / Redundancy: 20.9 % / Biso Wilson estimate: 91.4 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 36.6
Reflection shellResolution: 2.95→3 Å / Redundancy: 21.2 % / Rmerge(I) obs: 0.898 / Mean I/σ(I) obs: 3.9 / Num. unique all: 767

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3K51

3k51


Resolution: 2.951→25.16 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.921 / SU B: 10.413 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R: 0.377 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26096 764 5 %RANDOM
Rwork0.23225 ---
obs0.23367 14621 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 84.694 Å2
Refinement stepCycle: LAST / Resolution: 2.951→25.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1960 0 0 4 1964
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222020
X-RAY DIFFRACTIONr_angle_refined_deg1.1261.9412753
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8375249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.68923.07791
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.96615299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0781514
X-RAY DIFFRACTIONr_chiral_restr0.0830.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211565
X-RAY DIFFRACTIONr_mcbond_it2.72121265
X-RAY DIFFRACTIONr_mcangle_it4.89832033
X-RAY DIFFRACTIONr_scbond_it6.094755
X-RAY DIFFRACTIONr_scangle_it9.4916720
LS refinement shellResolution: 2.951→3.027 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 66 -
Rwork0.321 1048 -
obs--99.73 %

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