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- PDB-2tnf: 1.4 A RESOLUTION STRUCTURE OF MOUSE TUMOR NECROSIS FACTOR, TOWARD... -

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Basic information

Entry
Database: PDB / ID: 2tnf
Title1.4 A RESOLUTION STRUCTURE OF MOUSE TUMOR NECROSIS FACTOR, TOWARDS MODULATION OF ITS SELECTIVITY AND TRIMERISATION
ComponentsPROTEIN (TUMOR NECROSIS FACTOR ALPHA)
KeywordsCYTOKINE / LYMPHOKINE / CYTOTOXIN / TRANSMEMBRANE / GLYCOPROTEIN / SIGNAL-ANCHOR
Function / homology
Function and homology information


TNF signaling / TNFR1-mediated ceramide production / TNFR1-induced proapoptotic signaling / positive regulation of amide metabolic process / TNFR1-induced NF-kappa-B signaling pathway / cellular extravasation / Regulation of TNFR1 signaling / negative regulation of branching involved in lung morphogenesis / positive regulation of interleukin-33 production / positive regulation of lipid metabolic process ...TNF signaling / TNFR1-mediated ceramide production / TNFR1-induced proapoptotic signaling / positive regulation of amide metabolic process / TNFR1-induced NF-kappa-B signaling pathway / cellular extravasation / Regulation of TNFR1 signaling / negative regulation of branching involved in lung morphogenesis / positive regulation of interleukin-33 production / positive regulation of lipid metabolic process / positive regulation of blood microparticle formation / positive regulation of chronic inflammatory response to antigenic stimulus / positive regulation of protein transport / positive regulation of leukocyte adhesion to arterial endothelial cell / positive regulation of vitamin D biosynthetic process / TNFR2 non-canonical NF-kB pathway / 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 / 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 vascular wound healing / negative regulation of cytokine production involved in immune response / negative regulation of amyloid-beta clearance / inflammatory response to wounding / death receptor agonist activity / epithelial cell proliferation involved in salivary gland morphogenesis / embryonic digestive tract development / negative regulation of D-glucose import / vascular endothelial growth factor production / regulation of osteoclast differentiation / positive regulation of fever generation / positive regulation of synoviocyte proliferation / positive regulation of calcineurin-NFAT signaling cascade / necroptotic signaling pathway / leukocyte tethering or rolling / negative regulation of myoblast differentiation / positive regulation of protein-containing complex disassembly / regulation of establishment of endothelial barrier / endothelial cell apoptotic process / positive regulation of protein localization to cell surface / macrophage activation involved in immune response / 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 / negative regulation of mitotic cell cycle / positive regulation of podosome assembly / positive regulation of membrane protein ectodomain proteolysis / positive regulation of chemokine (C-X-C motif) ligand 2 production / negative regulation of bicellular tight junction assembly / regulation of metabolic process / regulation of reactive oxygen species metabolic process / leukocyte migration / negative regulation of viral genome replication / positive regulation of amyloid-beta formation / regulation of protein secretion / regulation of synapse organization / negative regulation of endothelial cell proliferation / positive regulation of JUN kinase activity / positive regulation of MAP kinase activity / negative regulation of interleukin-6 production / humoral immune response / negative regulation of blood vessel endothelial cell migration / positive regulation of glial cell proliferation / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of osteoblast differentiation / positive regulation of synaptic transmission / phagocytic cup / negative regulation of lipid catabolic process / positive regulation of vascular associated smooth muscle cell proliferation / extrinsic apoptotic signaling pathway / JNK cascade / extracellular matrix organization / antiviral innate immune response / regulation of insulin secretion / negative regulation of insulin receptor signaling pathway / response to glucocorticoid / osteoclast differentiation / secretory granule / animal organ morphogenesis / positive regulation of interleukin-1 beta production / cytokine activity / tumor necrosis factor-mediated signaling pathway / cellular response to ionizing radiation / protein localization to plasma membrane / positive regulation of interleukin-8 production / positive regulation of protein localization to plasma membrane / positive regulation of JNK cascade / cellular response to amino acid stimulus / apoptotic signaling pathway / phosphatidylinositol 3-kinase/protein kinase B signal transduction / microglial cell activation / positive regulation of non-canonical NF-kappaB signal transduction
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
ISOPROPYL ALCOHOL / Tumor necrosis factor
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsBaeyens, K.J. / De Bondt, H.L. / Raeymaekers, A. / Fiers, W. / De Ranter, C.J.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: The structure of mouse tumour-necrosis factor at 1.4 A resolution: towards modulation of its selectivity and trimerization.
Authors: Baeyens, K.J. / De Bondt, H.L. / Raeymaekers, A. / Fiers, W. / De Ranter, C.J.
#1: 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.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Crystallization and Preliminary X-Ray Studies of Mouse Tumor Necrosis Factor
Authors: Baeyens, K.J. / De Bondt, H.L. / Raeymaekers, A. / De Ranter, C.J. / Fiers, W.
#3: Journal: Protein Eng. / Year: 1997
Title: Crystal Structure of Tnf-Alpha Mutant R31D with Greater Affinity for Receptor R1 Compared with R2
Authors: Reed, C. / Fu, Z.Q. / Wu, J. / Xue, Y.N. / Harrison, R.W. / Chen, M.J. / Weber, I.T.
#4: Journal: J.Biol.Chem. / Year: 1989
Title: The Structure of Tumor Necrosis Factor-Alpha at 2.6 Angstroms Resolution. Implications for Receptor Binding
Authors: Eck, M.J. / Sprang, S.R.
#5: Journal: Nature / Year: 1989
Title: Structure of Tumor Necrosis Factor
Authors: Jones, E.Y. / Stuart, D.I. / Walker, N.P.C.
History
DepositionOct 12, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 12, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0005
Polymers51,8173
Non-polymers1822
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6320 Å2
ΔGint-26 kcal/mol
Surface area18960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.214, 48.300, 51.095
Angle α, β, γ (deg.)114.81, 103.65, 91.05
Int Tables number1
Space group name H-MP1

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Components

#1: Protein PROTEIN (TUMOR NECROSIS FACTOR ALPHA) / TNF-ALPHA / CACHECTIN


Mass: 17272.494 Da / Num. of mol.: 3 / Fragment: RESIDUES 80-235
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P06804
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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 Å3/Da / Density % sol: 38.4 %
Crystal growpH: 8.5
Details: EQUAL VOLUMES OF RESERVOIR SOLUTION, CONTAINING 7 % ISOPROP, pH 8.5
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 277 K / pH: 6.8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17 %2-propanol1reservoir
230 %PEGME20001reservoir
30.1 MTris-HCl1reservoir
40.5 %1dropNaCl
511 mg/mlprotain1drop
610 mMHEPES1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 1.1024
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1997 / Details: RHODIUM COATED PRE-MIRROR, SEGMENTED MIRROR
RadiationMonochromator: BENT SINGLE-CRYSTAL GERMANIUM TRIANGULAR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1024 Å / Relative weight: 1
ReflectionResolution: 1.4→20 Å / Num. obs: 72552 / % possible obs: 90.9 % / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.029 / Net I/σ(I): 19
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.148 / Mean I/σ(I) obs: 5.7 / % possible all: 85.5
Reflection
*PLUS
Num. measured all: 128698
Reflection shell
*PLUS
% possible obs: 85.5 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.843refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TNF

1tnf


Resolution: 1.4→8 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.235 6871 10.1 %RANDOM
Rwork0.201 ---
obs0.201 67767 85.8 %-
Displacement parametersBiso mean: 19.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3477 0 8 244 3729
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.39
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.481.5
X-RAY DIFFRACTIONx_mcangle_it2.592
X-RAY DIFFRACTIONx_scbond_it1.982
X-RAY DIFFRACTIONx_scangle_it2.992.5
LS refinement shellResolution: 1.4→1.49 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.274 962 10 %
Rwork0.264 8666 -
obs--73 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH11.WAT
X-RAY DIFFRACTION3IPA.PARIPA.TOP
X-RAY DIFFRACTION4TRS.PARTRS.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 10.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 19.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.39
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.274 / % reflection Rfree: 10 % / Rfactor Rwork: 0.264

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