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- PDB-2e7a: TNF Receptor Subtype One-selective TNF Mutant with Antagonistic A... -

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Basic information

Entry
Database: PDB / ID: 2e7a
TitleTNF Receptor Subtype One-selective TNF Mutant with Antagonistic Activity
ComponentsTumor necrosis factor
KeywordsCYTOKINE / Tumor necrosis factor / Trimer / antagonistic activity / TNFR1 specific / phage display system
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 interleukin-33 production / positive regulation of neutrophil activation / response to quercetin / negative regulation of branching involved in lung morphogenesis / positive regulation of fractalkine production / positive regulation of blood microparticle formation / response to 3,3',5-triiodo-L-thyronine ...response to Gram-negative bacterium / negative regulation of L-glutamate import across plasma membrane / negative regulation of bile acid secretion / positive regulation of interleukin-33 production / positive regulation of neutrophil activation / response to quercetin / negative regulation of branching involved in lung morphogenesis / positive regulation of fractalkine production / positive regulation of blood microparticle formation / response to 3,3',5-triiodo-L-thyronine / positive regulation of protein transport / positive regulation of vitamin D biosynthetic process / chronic inflammatory response to antigenic stimulus / regulation of endothelial cell apoptotic process / endothelial cell apoptotic process / response to macrophage colony-stimulating factor / negative regulation of myelination / positive regulation of leukocyte adhesion to arterial endothelial cell / response to gold nanoparticle / negative regulation of vascular wound healing / Differentiation of naive CD4+ T cells to T helper 1 cells (Th1 cells) / negative regulation of cytokine production involved in immune response / negative regulation of amyloid-beta clearance / positive regulation of podosome assembly / response to resveratrol / positive regulation of hair follicle development / inflammatory response to wounding / positive regulation of interleukin-18 production / positive regulation of hepatocyte proliferation / positive regulation of action potential / toll-like receptor 3 signaling pathway / TNF signaling / embryonic digestive tract development / negative regulation of D-glucose import across plasma membrane / vascular endothelial growth factor production / positive regulation of fever generation / positive regulation of calcineurin-NFAT signaling cascade / positive regulation of protein localization to cell surface / response to fructose / negative regulation of mitotic cell cycle / leukocyte tethering or rolling / necroptotic signaling pathway / positive regulation of synoviocyte proliferation / regulation of establishment of endothelial barrier / positive regulation of mononuclear cell migration / negative regulation of oxidative phosphorylation / macrophage activation involved in immune response / response to hydrogen sulfide / positive regulation of glial cell proliferation / positive regulation of protein-containing complex disassembly / positive regulation of osteoclast differentiation / cellular response to toxic substance / positive regulation of macrophage derived foam cell differentiation / regulation of fat cell differentiation / positive regulation of chemokine (C-X-C motif) ligand 2 production / tumor necrosis factor receptor binding / positive regulation of heterotypic cell-cell adhesion / positive regulation of membrane protein ectodomain proteolysis / negative regulation of systemic arterial blood pressure / response to L-glutamate / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of leukocyte adhesion to vascular endothelial cell / regulation of canonical NF-kappaB signal transduction / TNFR1-induced proapoptotic signaling / negative regulation of fat cell differentiation / regulation of reactive oxygen species metabolic process / positive regulation of cytokine production involved in inflammatory response / TNFR1-mediated ceramide production / positive regulation of programmed cell death / negative regulation of heart rate / negative regulation of viral genome replication / positive regulation of DNA biosynthetic process / positive regulation of neuroinflammatory response / positive regulation of amyloid-beta formation / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of endothelial cell proliferation / negative regulation of interleukin-6 production / positive regulation of immunoglobulin production / negative regulation of bicellular tight junction assembly / response to isolation stress / Interleukin-10 signaling / regulation of synapse organization / negative regulation of apoptotic signaling pathway / regulation of insulin secretion / histone H3K9ac reader activity / negative regulation of blood vessel endothelial cell migration / negative regulation of lipid storage / response to salt stress / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / detection of mechanical stimulus involved in sensory perception of pain / negative regulation of osteoblast differentiation / negative regulation of lipid catabolic process / extrinsic apoptotic signaling pathway / positive regulation of synaptic transmission / positive regulation of vascular associated smooth muscle cell proliferation / regulation of synaptic transmission, glutamatergic / cellular response to retinoic acid / cell surface receptor signaling pathway via JAK-STAT / positive regulation of chemokine production / phagocytic cup
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: 1.8 Å
AuthorsMukai, Y. / Yamagata, Y. / Tsutsumi, Y.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Creation and X-ray structure analysis of the tumor necrosis factor receptor-1-selective mutant of a tumor necrosis factor-alpha antagonist
Authors: Shibata, H. / Yoshioka, Y. / Ohkawa, A. / Minowa, K. / Mukai, Y. / Abe, Y. / Taniai, M. / Nomura, T. / Kayamuro, H. / Nabeshi, H. / Sugita, T. / Imai, S. / Nagano, K. / Yoshikawa, T. / ...Authors: Shibata, H. / Yoshioka, Y. / Ohkawa, A. / Minowa, K. / Mukai, Y. / Abe, Y. / Taniai, M. / Nomura, T. / Kayamuro, H. / Nabeshi, H. / Sugita, T. / Imai, S. / Nagano, K. / Yoshikawa, T. / Fujita, T. / Nakagawa, S. / Yamamoto, A. / Ohta, T. / Hayakawa, T. / Mayumi, T. / Vandenabeele, P. / Aggarwal, B.B. / Nakamura, T. / Yamagata, Y. / Tsunoda, S. / Kamada, H. / Tsutsumi, Y.
History
DepositionJan 9, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2007Provider: 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 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 23, 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)51,8983
Polymers51,8983
Non-polymers00
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6330 Å2
ΔGint-34.6 kcal/mol
Surface area17730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.560, 66.970, 103.560
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


Mass: 17299.348 Da / Num. of mol.: 3
Mutation: K11M, K65S, A84S, V85T, S86T, Y87H, Q88N, T89Q, K90P, K98R, K112N, K128P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: This mutant was created by phage display system
Plasmid: pYas(modified from pUC18) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01375
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.16 Å3/Da / Density % sol: 42.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.05M HEPES pH7.5, 1.5%(w/v) 1,2,3-Heptanetriol, 12.5% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU
DetectorDetector: CCD / Date: Mar 25, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 42227 / % possible obs: 99.6 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.063
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 2.71 / Num. unique all: 4031 / % possible all: 96.1

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Processing

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

1tnf


Resolution: 1.8→41 Å /
RfactorNum. reflection
Rfree0.239 -
Rwork0.198 -
obs-42155
Refinement stepCycle: LAST / Resolution: 1.8→41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3387 0 0 237 3624

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