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- PDB-2zpx: TNF Receptor Subtype One-selective TNF Mutant with Antagonistic A... -

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Basic information

Entry
Database: PDB / ID: 2zpx
TitleTNF Receptor Subtype One-selective TNF Mutant with Antagonistic Activity; R1antTNF-T8
ComponentsTumor necrosis factor
KeywordsCYTOKINE / Tumor necrosis factor / Trimer / Antagonistic activity / TNFR1 specific / Phage display system / Cell membrane / Lipoprotein / Membrane / Myristate / Phosphoprotein / Polymorphism / Secreted / Signal-anchor / Transmembrane
Function / homology
Function and homology information


response to Gram-negative bacterium / negative regulation of L-glutamate import across plasma membrane / negative regulation of bile acid secretion / positive regulation of neutrophil activation / negative regulation of branching involved in lung morphogenesis / positive regulation of interleukin-33 production / positive regulation of fractalkine production / positive regulation of blood microparticle formation / positive regulation of chronic inflammatory response to antigenic stimulus / death receptor agonist activity ...response to Gram-negative bacterium / negative regulation of L-glutamate import across plasma membrane / negative regulation of bile acid secretion / positive regulation of neutrophil activation / negative regulation of branching involved in lung morphogenesis / positive regulation of interleukin-33 production / positive regulation of fractalkine production / positive regulation of blood microparticle formation / positive regulation of chronic inflammatory response to antigenic stimulus / death receptor agonist activity / response to 3,3',5-triiodo-L-thyronine / positive regulation of protein transport / positive regulation of vitamin D biosynthetic process / positive regulation of translational initiation by iron / : / chronic inflammatory response to antigenic stimulus / regulation of endothelial cell apoptotic process / response to macrophage colony-stimulating factor / regulation of branching involved in salivary gland morphogenesis / positive regulation of leukocyte adhesion to arterial endothelial cell / negative regulation of protein-containing complex disassembly / positive regulation of humoral immune response mediated by circulating immunoglobulin / response to gold nanoparticle / negative regulation of myelination / positive regulation of JUN kinase activity / reactive gliosis / negative regulation of vascular wound healing / negative regulation of amyloid-beta clearance / negative regulation of cytokine production involved in immune response / positive regulation of hair follicle development / inflammatory response to wounding / positive regulation of action potential / positive regulation of interleukin-18 production / response to resveratrol / TNF signaling / epithelial cell proliferation involved in salivary gland morphogenesis / response to quercetin / toll-like receptor 3 signaling pathway / vascular endothelial growth factor production / negative regulation of D-glucose import across plasma membrane / embryonic digestive tract development / positive regulation of fever generation / positive regulation of synoviocyte proliferation / positive regulation of calcineurin-NFAT signaling cascade / necroptotic signaling pathway / leukocyte tethering or rolling / positive regulation of hepatocyte proliferation / negative regulation of myoblast differentiation / positive regulation of mononuclear cell migration / regulation of establishment of endothelial barrier / response to fructose / endothelial cell apoptotic process / response to hydrogen sulfide / negative regulation of oxidative phosphorylation / positive regulation of protein-containing complex disassembly / positive regulation of protein localization to cell surface / positive regulation of osteoclast differentiation / cellular response to toxic substance / macrophage activation involved in immune response / tumor necrosis factor receptor binding / negative regulation of systemic arterial blood pressure / positive regulation of macrophage derived foam cell differentiation / positive regulation of cytokine production involved in inflammatory response / negative regulation of mitotic cell cycle / positive regulation of podosome assembly / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of programmed cell death / positive regulation of membrane protein ectodomain proteolysis / positive regulation of heterotypic cell-cell adhesion / regulation of fat cell differentiation / regulation of canonical NF-kappaB signal transduction / response to L-glutamate / positive regulation of leukocyte adhesion to vascular endothelial cell / positive regulation of extrinsic apoptotic signaling pathway / TNFR1-induced proapoptotic signaling / TNFR1-mediated ceramide production / regulation of reactive oxygen species metabolic process / positive regulation of DNA biosynthetic process / mRNA stabilization / negative regulation of heart rate / positive regulation of neuroinflammatory response / positive regulation of amyloid-beta formation / negative regulation of viral genome replication / negative regulation of bicellular tight junction assembly / positive regulation of immunoglobulin production / response to isolation stress / negative regulation of fat cell differentiation / negative regulation of endothelial cell proliferation / regulation of synapse organization / Interleukin-10 signaling / positive regulation of MAP kinase activity / humoral immune response / negative regulation of interleukin-6 production / histone H3K9ac reader activity / negative regulation of blood vessel endothelial cell migration / negative regulation of apoptotic signaling pathway / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of lipid storage / positive regulation of glial cell proliferation / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand
Similarity search - Function
Tumour necrosis factor alpha / 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 / Jelly Rolls - #40 / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Tumour necrosis factor-like domain superfamily ...Tumour necrosis factor alpha / 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 / Jelly Rolls - #40 / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Tumour necrosis factor-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tumor necrosis factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsMukai, Y. / Nakamura, T. / Yamagata, Y. / Tsutsumi, Y.
CitationJournal: J.Biochem. / Year: 2009
Title: Fast binding kinetics and conserved 3D structure underlie the antagonistic activity of mutant TNF: useful information for designing artificial proteo-antagonists
Authors: Mukai, Y. / Nakamura, T. / Yoshioka, Y. / Shibata, H. / Abe, Y. / Nomura, T. / Taniai, M. / Ohta, T. / Nakagawa, S. / Tsunoda, S. / Kamada, H. / Yamagata, Y. / Tsutsumi, Y.
History
DepositionJul 29, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 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 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 16, 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
B: Tumor necrosis factor
C: Tumor necrosis factor


Theoretical massNumber of molelcules
Total (without water)51,8503
Polymers51,8503
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6520 Å2
ΔGint-26.4 kcal/mol
Surface area17770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.586, 111.331, 75.382
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tumor necrosis factor / TNF-alpha / Tumor necrosis factor ligand superfamily member 2 / TNF-a / Cachectin / Antagonistic ...TNF-alpha / Tumor necrosis factor ligand superfamily member 2 / TNF-a / Cachectin / Antagonistic TNF mutant (R1antTNF-T8)


Mass: 17283.436 Da / Num. of mol.: 3 / Fragment: UNP residues 77-233
Mutation: K11M, K65S, A84T, V85P, S86A, Y87I, Q88N, T89R, K90P, K98R, K112N, K128P
Source method: isolated from a genetically manipulated source
Details: this mutant was created by phage display system / Source: (gene. exp.) Homo sapiens (human) / Strain: Human / Gene: TNF, TNFA, TNFSF2 / Plasmid: PYAS(MODIFIED FROM PUC18) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01375
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 38.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15% PEG1500, 0.2M Calcium Acetate, 0.1M Sodium Cacodylate, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Temp details: 15% PEG1500, 0.2M Calcium Acetate, 0.1M Sodium Cacodylate, pH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU
DetectorDetector: CCD / Date: Nov 6, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.8→55.67 Å / Num. obs: 10337 / % possible obs: 92.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 63.4 Å2 / Rmerge(I) obs: 0.244 / Net I/σ(I): 36.4
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.16 / % possible all: 85.6

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TNF

1tnf


Resolution: 2.83→50 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1361839.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.309 1009 10.3 %RANDOM
Rwork0.268 ---
obs0.268 9762 93.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 80.277 Å2 / ksol: 0.15 e/Å3
Displacement parametersBiso mean: 76.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.2 Å20 Å20 Å2
2--3.84 Å20 Å2
3----7.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.58 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.77 Å0.56 Å
Refinement stepCycle: LAST / Resolution: 2.83→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3312 0 0 7 3319
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.384 121 10 %
Rwork0.34 1084 -
obs--68.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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