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- PDB-1tnf: THE STRUCTURE OF TUMOR NECROSIS FACTOR-ALPHA AT 2.6 ANGSTROMS RES... -

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Basic information

Entry
Database: PDB / ID: 1tnf
TitleTHE STRUCTURE OF TUMOR NECROSIS FACTOR-ALPHA AT 2.6 ANGSTROMS RESOLUTION. IMPLICATIONS FOR RECEPTOR BINDING
ComponentsTUMOR NECROSIS FACTOR-ALPHA
KeywordsLYMPHOKINE
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 / 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 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 / response to 3,3',5-triiodo-L-thyronine / : / death receptor agonist activity / positive regulation of protein transport / positive regulation of vitamin D biosynthetic process / positive regulation of translational initiation by iron / regulation of endothelial cell apoptotic process / regulation of branching involved in salivary gland morphogenesis / chronic inflammatory response to antigenic stimulus / response to macrophage colony-stimulating factor / negative regulation of protein-containing complex disassembly / positive regulation of humoral immune response mediated by circulating immunoglobulin / positive regulation of leukocyte adhesion to arterial endothelial cell / response to gold nanoparticle / negative regulation of myelination / positive regulation of JUN kinase activity / negative regulation of vascular wound healing / negative regulation of amyloid-beta clearance / negative regulation of cytokine production involved in immune response / reactive gliosis / positive regulation of hair follicle development / positive regulation of interleukin-18 production / inflammatory response to wounding / response to resveratrol / positive regulation of action potential / epithelial cell proliferation involved in salivary gland morphogenesis / response to quercetin / TNF signaling / 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 / leukocyte tethering or rolling / necroptotic signaling pathway / negative regulation of myoblast differentiation / positive regulation of mononuclear cell migration / positive regulation of hepatocyte proliferation / response to fructose / regulation of establishment of endothelial barrier / endothelial cell apoptotic process / negative regulation of oxidative phosphorylation / response to hydrogen sulfide / 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 / positive regulation of macrophage derived foam cell differentiation / negative regulation of mitotic cell cycle / negative regulation of systemic arterial blood pressure / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of cytokine production involved in inflammatory response / positive regulation of podosome assembly / regulation of fat cell differentiation / positive regulation of heterotypic cell-cell adhesion / positive regulation of programmed cell death / positive regulation of membrane protein ectodomain proteolysis / regulation of canonical NF-kappaB signal transduction / response to L-glutamate / positive regulation of leukocyte adhesion to vascular endothelial cell / TNFR1-induced proapoptotic signaling / TNFR1-mediated ceramide production / positive regulation of extrinsic apoptotic signaling pathway / mRNA stabilization / regulation of reactive oxygen species metabolic process / negative regulation of heart rate / positive regulation of DNA biosynthetic process / positive regulation of amyloid-beta formation / positive regulation of neuroinflammatory response / negative regulation of viral genome replication / positive regulation of immunoglobulin production / negative regulation of bicellular tight junction assembly / negative regulation of fat cell differentiation / response to isolation stress / negative regulation of endothelial cell proliferation / positive regulation of MAP kinase activity / Interleukin-10 signaling / regulation of synapse organization / regulation of insulin secretion / 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 / negative regulation of lipid storage / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of glial cell proliferation
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: 2.6 Å
AuthorsEck, M.J. / Sprang, S.R.
Citation
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.
#1: Journal: J.Biol.Chem. / Year: 1988
Title: Crystallization of Trimeric Recombinant Human Tumor Necrosis Factor (Cachectin)
Authors: Eck, M.J. / Beutler, B. / Kuo, G. / Merryweather, J.P. / Sprang, S.R.
History
DepositionAug 25, 1989Processing site: BNL
Revision 1.0Jan 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 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-ALPHA
B: TUMOR NECROSIS FACTOR-ALPHA
C: TUMOR NECROSIS FACTOR-ALPHA


Theoretical massNumber of molelcules
Total (without water)52,1063
Polymers52,1063
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7040 Å2
ΔGint-37 kcal/mol
Surface area18400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.000, 95.000, 117.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Atom site foot note1: SEE REMARK 4. / 2: SEE REMARK 5.
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.04046, -0.10575, 0.99357), (-0.98065, 0.18643, 0.05978), (-0.19155, -0.97676, -0.09616)-16.17, 57.43, 96.33
2given(-0.02896, -0.99271, -0.11699), (-0.20202, 0.12044, -0.97195), (0.97895, -0.00451, -0.20404)74.4, 87.33, 28.89
3given(-0.01202, -0.16346, 0.98646), (-0.98656, 0.16273, 0.01494), (-0.16297, -0.97304, -0.16322)-11.46, 60.62, 97.89
DetailsTHE MOLECULE EXISTS AS A TRIMER IN WHICH THE THREE SUBUNITS ARE RELATED BY APPROXIMATE THREE-FOLD SYMMETRY. THE THREE SUBUNITS HAVE BEEN ASSIGNED CHAIN INDICATORS A, B, AND C. THE TRANSFORMATION PRESENTED ON *MTRIX 1* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN B WHEN APPLIED TO CHAIN A. THE TRANSFORMATION PRESENTED ON *MTRIX 2* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN C WHEN APPLIED TO CHAIN A. THE TRANSFORMATION PRESENTED ON *MTRIX 3* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN C WHEN APPLIED TO CHAIN B.

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Components

#1: Protein TUMOR NECROSIS FACTOR-ALPHA


Mass: 17368.729 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P01375
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.41 %
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 5.5 / Method: unknown
Components of the solutions
*PLUS
Conc.: 2.6 M / Common name: magnesium sulfate

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Data collection

Reflection
*PLUS
Highest resolution: 2.6 Å / Num. obs: 17097 / % possible obs: 72.1 % / Observed criterion σ(I): 2 / Num. measured all: 126662 / Rmerge(I) obs: 0.065

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementRfactor Rwork: 0.23 / Highest resolution: 2.6 Å
Refinement stepCycle: LAST / Highest resolution: 2.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3552 0 0 0 3552
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg4.1
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 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_angle_d4.1

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