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- PDB-5tsw: HIGH RESOLUTION CRYSTAL STRUCTURE OF A HUMAN TNF-ALPHA MUTANT -

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Basic information

Entry
Database: PDB / ID: 5tsw
TitleHIGH RESOLUTION CRYSTAL STRUCTURE OF A HUMAN TNF-ALPHA MUTANT
ComponentsPROTEIN (TUMOR NECROSIS FACTOR-ALPHA)
KeywordsLYMPHOKINE / LOW SYSTEMIC TOXICITY / MUTANT
Function / homology
Function and homology information


negative regulation of L-glutamate import across plasma membrane / negative regulation of bile acid secretion / response to Gram-negative bacterium / positive regulation of neutrophil activation / positive regulation of fractalkine production / negative regulation of branching involved in lung morphogenesis / positive regulation of interleukin-33 production / positive regulation of blood microparticle formation / positive regulation of chronic inflammatory response to antigenic stimulus / response to 3,3',5-triiodo-L-thyronine ...negative regulation of L-glutamate import across plasma membrane / negative regulation of bile acid secretion / response to Gram-negative bacterium / positive regulation of neutrophil activation / positive regulation of fractalkine production / negative regulation of branching involved in lung morphogenesis / positive regulation of interleukin-33 production / positive regulation of blood microparticle formation / positive regulation of chronic inflammatory response to antigenic stimulus / response to 3,3',5-triiodo-L-thyronine / positive regulation of protein transport / positive regulation of leukocyte adhesion to arterial endothelial cell / positive regulation of vitamin D biosynthetic process / positive regulation of translational initiation by iron / regulation of membrane lipid metabolic process / regulation of endothelial cell apoptotic process / chronic inflammatory response to antigenic stimulus / response to macrophage colony-stimulating factor / regulation of branching involved in salivary gland morphogenesis / negative regulation of protein-containing complex disassembly / positive regulation of humoral immune response mediated by circulating immunoglobulin / positive regulation of hair follicle development / negative regulation of myelination / response to gold nanoparticle / negative regulation of vascular wound healing / negative regulation of cytokine production involved in immune response / negative regulation of amyloid-beta clearance / positive regulation of interleukin-18 production / inflammatory response to wounding / death receptor agonist activity / positive regulation of action potential / TNF signaling / epithelial cell proliferation involved in salivary gland morphogenesis / toll-like receptor 3 signaling pathway / embryonic digestive tract development / negative regulation of D-glucose import / leukocyte migration involved in inflammatory response / vascular endothelial growth factor production / positive regulation of fever generation / response to fructose / positive regulation of neuroinflammatory response / positive regulation of synoviocyte proliferation / positive regulation of calcineurin-NFAT signaling cascade / necroptotic signaling pathway / positive regulation of mononuclear cell migration / leukocyte tethering or rolling / positive regulation of hepatocyte proliferation / negative regulation of myoblast differentiation / positive regulation of protein-containing complex disassembly / regulation of establishment of endothelial barrier / endothelial cell apoptotic process / negative regulation of oxidative phosphorylation / cellular response to toxic substance / positive regulation of protein localization to cell surface / macrophage activation involved in immune response / negative regulation of systemic arterial blood pressure / positive regulation of osteoclast differentiation / tumor necrosis factor receptor binding / positive regulation of heterotypic cell-cell adhesion / positive regulation of macrophage derived foam cell differentiation / positive regulation of cytokine production involved in inflammatory response / regulation of immunoglobulin production / TNFR1-mediated ceramide production / negative regulation of mitotic cell cycle / positive regulation of programmed cell death / positive regulation of podosome assembly / positive regulation of membrane protein ectodomain proteolysis / positive regulation of chemokine (C-X-C motif) ligand 2 production / regulation of fat cell differentiation / regulation of canonical NF-kappaB signal transduction / response to L-glutamate / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of leukocyte adhesion to vascular endothelial cell / TNFR1-induced proapoptotic signaling / negative regulation of bicellular tight junction assembly / regulation of metabolic process / regulation of reactive oxygen species metabolic process / positive regulation of DNA biosynthetic process / negative regulation of heart rate / positive regulation of amyloid-beta formation / negative regulation of viral genome replication / response to isolation stress / negative regulation of fat cell differentiation / regulation of synapse organization / negative regulation of endothelial cell proliferation / positive regulation of JUN kinase activity / positive regulation of MAP kinase activity / Interleukin-10 signaling / negative regulation of interleukin-6 production / humoral immune response / negative regulation of apoptotic signaling pathway / negative regulation of blood vessel endothelial cell migration / negative regulation of lipid storage / positive regulation of glial cell proliferation / extrinsic apoptotic signaling pathway via death domain receptors / cell surface receptor signaling pathway via JAK-STAT / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / skeletal muscle contraction / negative regulation of osteoblast differentiation / detection of mechanical stimulus involved in sensory perception of pain
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 / Resolution: 2.5 Å
AuthorsCha, S.-S. / Kim, J.-S. / Cho, H.-S. / Oh, B.-H.
Citation
Journal: J.Biol.Chem. / Year: 1998
Title: High resolution crystal structure of a human tumor necrosis factor-alpha mutant with low systemic toxicity.
Authors: Cha, S.S. / Kim, J.S. / Cho, H.S. / Shin, N.K. / Jeong, W. / Shin, H.C. / Kim, Y.J. / Hahn, J.H. / Oh, B.H.
#1: Journal: J.Biol.Chem. / Year: 1989
Title: The Structure of Tumor Necrosis Factor-Alpha at 2.6 A Resolution. Implications for Receptor Binding
Authors: Eck, M.J. / Sprang, S.R.
History
DepositionApr 22, 1999Deposition site: RCSB / Processing site: RCSB
SupersessionApr 30, 1999ID: 4TSW
Revision 1.0May 7, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Nov 3, 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 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.6Nov 13, 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: PROTEIN (TUMOR NECROSIS FACTOR-ALPHA)
B: PROTEIN (TUMOR NECROSIS FACTOR-ALPHA)
C: PROTEIN (TUMOR NECROSIS FACTOR-ALPHA)
D: PROTEIN (TUMOR NECROSIS FACTOR-ALPHA)
E: PROTEIN (TUMOR NECROSIS FACTOR-ALPHA)
F: PROTEIN (TUMOR NECROSIS FACTOR-ALPHA)


Theoretical massNumber of molelcules
Total (without water)99,4736
Polymers99,4736
Non-polymers00
Water6,413356
1
A: PROTEIN (TUMOR NECROSIS FACTOR-ALPHA)
B: PROTEIN (TUMOR NECROSIS FACTOR-ALPHA)
C: PROTEIN (TUMOR NECROSIS FACTOR-ALPHA)


Theoretical massNumber of molelcules
Total (without water)49,7363
Polymers49,7363
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-35 kcal/mol
Surface area17970 Å2
MethodPISA
2
D: PROTEIN (TUMOR NECROSIS FACTOR-ALPHA)
E: PROTEIN (TUMOR NECROSIS FACTOR-ALPHA)
F: PROTEIN (TUMOR NECROSIS FACTOR-ALPHA)


Theoretical massNumber of molelcules
Total (without water)49,7363
Polymers49,7363
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-38 kcal/mol
Surface area18220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.170, 94.560, 95.890
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
PROTEIN (TUMOR NECROSIS FACTOR-ALPHA)


Mass: 16578.797 Da / Num. of mol.: 6
Mutation: DELETION OF N-TERMINAL SEVEN RESIDUES, L29S, S52I, Y56F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / 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.: 356 / 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: 2.14 Å3/Da / Density % sol: 42.65 %
Crystal growpH: 6.8
Details: 20% POLYETHYLENEGLYCOL 4000, 0.1 M SODIUM CITRATE PH 5.6, pH 6.8
Crystal grow
*PLUS
Temperature: 24 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
210 mMHEPES1drop
325 %PEG40001reservoir
40.1 Msodium citrate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE M18X / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Dec 1, 1995
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→10 Å / Num. obs: 41282 / % possible obs: 92.5 % / Observed criterion σ(I): 1 / Rsym value: 0.04
Reflection
*PLUS
Rmerge(I) obs: 0.0721

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.01refinement
RefinementResolution: 2.5→8 Å / σ(F): 1
RfactorNum. reflection% reflection
Rfree0.299 -10 %
Rwork0.207 --
obs-41282 92.5 %
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8190 0 0 1068 9258
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.992
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.01 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 800 Å / σ(F): 1 / % reflection Rfree: 10 % / Rfactor obs: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS

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