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- PDB-5uui: Crystal Structure of Spin-Labeled T77C TNFa -

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Basic information

Entry
Database: PDB / ID: 5uui
TitleCrystal Structure of Spin-Labeled T77C TNFa
ComponentsTumor necrosis factor
KeywordsIMMUNE SYSTEM / T77C / TNFa / TNF alpha / cytokine
Function / homology
Function and homology information


response to Gram-negative bacterium / negative regulation of L-glutamate import across plasma membrane / positive regulation of chronic inflammatory response to antigenic stimulus / negative regulation of bile acid secretion / positive regulation of interleukin-33 production / positive regulation of neutrophil activation / negative regulation of branching involved in lung morphogenesis / positive regulation of fractalkine production / positive regulation of blood microparticle formation / : ...response to Gram-negative bacterium / negative regulation of L-glutamate import across plasma membrane / positive regulation of chronic inflammatory response to antigenic stimulus / negative regulation of bile acid secretion / positive regulation of interleukin-33 production / positive regulation of neutrophil activation / 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 / death receptor agonist activity / positive regulation of translational initiation by iron / positive regulation of protein transport / positive regulation of vitamin D biosynthetic process / regulation of branching involved in salivary gland morphogenesis / regulation of endothelial cell apoptotic process / chronic inflammatory response to antigenic stimulus / negative regulation of protein-containing complex disassembly / response to macrophage colony-stimulating factor / 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 / negative regulation of vascular wound healing / positive regulation of JUN kinase activity / 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 / epithelial cell proliferation involved in salivary gland morphogenesis / positive regulation of action potential / response to quercetin / TNF signaling / toll-like receptor 3 signaling pathway / negative regulation of D-glucose import across plasma membrane / vascular endothelial growth factor production / embryonic digestive tract development / positive regulation of fever generation / positive regulation of calcineurin-NFAT signaling cascade / necroptotic signaling pathway / positive regulation of synoviocyte proliferation / leukocyte tethering or rolling / negative regulation of myoblast differentiation / positive regulation of mononuclear cell migration / response to fructose / positive regulation of hepatocyte proliferation / 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 / positive regulation of macrophage derived foam cell differentiation / tumor necrosis factor receptor binding / negative regulation of mitotic cell cycle / 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 / negative regulation of systemic arterial blood pressure / response to L-glutamate / positive regulation of leukocyte adhesion to vascular endothelial cell / TNFR1-induced proapoptotic signaling / positive regulation of extrinsic apoptotic signaling pathway / TNFR1-mediated ceramide production / regulation of reactive oxygen species metabolic process / mRNA stabilization / 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 / negative regulation of endothelial cell proliferation / response to isolation stress / positive regulation of MAP kinase activity / Interleukin-10 signaling / regulation of synapse organization / regulation of insulin secretion / negative regulation of interleukin-6 production / humoral immune response / histone H3K9ac reader activity / negative regulation of blood vessel endothelial cell migration / negative regulation of lipid storage / negative regulation of apoptotic signaling pathway / 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
Chem-MTN / Tumor necrosis factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsHoranyi, P.S. / Dranow, D.M. / Ceska, T.
CitationJournal: Biophys. J. / Year: 2017
Title: Natural Conformational Sampling of Human TNF alpha Visualized by Double Electron-Electron Resonance.
Authors: Carrington, B. / Myers, W.K. / Horanyi, P. / Calmiano, M. / Lawson, A.D.G.
History
DepositionFeb 16, 2017Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 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: Tumor necrosis factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7242
Polymers17,4601
Non-polymers2641
Water93752
1
A: Tumor necrosis factor
hetero molecules

A: Tumor necrosis factor
hetero molecules

A: Tumor necrosis factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1726
Polymers52,3793
Non-polymers7933
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area5240 Å2
ΔGint-38 kcal/mol
Surface area16320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.660, 65.660, 84.090
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-351-

HOH

21A-352-

HOH

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Components

#1: Protein Tumor necrosis factor / Cachectin / TNF-alpha / Tumor necrosis factor ligand superfamily member 2 / TNF-a


Mass: 17459.775 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MTSL / Source: (gene. exp.) Homo sapiens (human) / Gene: TNF, TNFA, TNFSF2 / Production host: Escherichia coli (E. coli) / References: UniProt: P01375
#2: Chemical ChemComp-MTN / S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate / MTSL


Mass: 264.385 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C10H18NO3S2 / Details: MTSL / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 38.44 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: TNFa (VCID10616, B114005) at 10 mg/ml (in 10 mM HEPES, pH = 7.5, 150 mM NaCl) was mixed with an equal volume of protein solution and a solution containing 24% (w/v) PEG-4000, 0.24 M MgCl2, 0. ...Details: TNFa (VCID10616, B114005) at 10 mg/ml (in 10 mM HEPES, pH = 7.5, 150 mM NaCl) was mixed with an equal volume of protein solution and a solution containing 24% (w/v) PEG-4000, 0.24 M MgCl2, 0.05% DDM, and 0.1 M HEPES/NaOH, pH=8.5. Crystals were produced by sitting drop vapor diffusion at 16 degrees Celsius. Crystals were then soaked with the same solution supplemented with 10% MTSL for one week and harvested with paraffin oil.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 2, 2016
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.4→32.83 Å / Num. obs: 26091 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 3.78 % / CC1/2: 0.997 / Rsym value: 0.074 / Net I/σ(I): 12.71
Reflection shellResolution: 1.4→1.43 Å / Redundancy: 3.02 % / Num. unique obs: 1816 / CC1/2: 0.608 / Rsym value: 0.572 / % possible all: 91.8

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Processing

Software
NameVersionClassification
PHENIX(dev_2356: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1tnf

1tnf


Resolution: 1.4→32.83 Å / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 17.05
RfactorNum. reflection% reflection
Rfree0.17 2115 8.2 %
Rwork0.1393 --
obs0.1478 26091 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.4→32.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1018 0 0 52 1070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111051
X-RAY DIFFRACTIONf_angle_d1.2741441
X-RAY DIFFRACTIONf_dihedral_angle_d18.184368
X-RAY DIFFRACTIONf_chiral_restr0.093166
X-RAY DIFFRACTIONf_plane_restr0.005184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4005-1.4330.27041450.24961477X-RAY DIFFRACTION83
1.433-1.46870.23381320.23651643X-RAY DIFFRACTION92
1.4687-1.50830.22951380.21351618X-RAY DIFFRACTION92
1.5083-1.55250.19541660.18791600X-RAY DIFFRACTION90
1.5525-1.60250.20061620.18471602X-RAY DIFFRACTION91
1.6025-1.65950.17791720.1831569X-RAY DIFFRACTION90
1.6595-1.72560.20771260.17111652X-RAY DIFFRACTION93
1.7256-1.80370.14921000.17021650X-RAY DIFFRACTION93
1.8037-1.89820.18871380.16211606X-RAY DIFFRACTION91
1.8982-2.01620.191590.15861579X-RAY DIFFRACTION89
2.0162-2.17040.18081500.15741601X-RAY DIFFRACTION90
2.1704-2.38620.19921570.15281565X-RAY DIFFRACTION89
2.3862-2.72530.151160.14181611X-RAY DIFFRACTION91
2.7253-3.41080.15611310.1231574X-RAY DIFFRACTION89
3.4108-10.0030.14311240.09371555X-RAY DIFFRACTION88
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.0587-0.1275-2.14522.9478-0.60384.26390.16530.08230.0414-0.0912-0.0723-0.2793-0.24970.4102-0.11690.046-0.0073-0.02180.1332-0.0380.121250.754757.817815.4305
22.6318-1.31811.2444.37111.85672.2453-0.0872-0.06740.34010.09440.1223-0.2935-0.060.1633-0.01280.0744-0.00880.0010.1205-0.0250.131351.038861.142720.0789
31.29140.2488-0.28551.1344-0.55782.6520.0264-0.0025-0.0899-0.01460.0325-0.11480.130.034-0.070.05810.0003-0.01370.0701-0.01290.098244.326950.58914.6831
42.45080.8623-1.07931.49550.57292.5401-0.06710.069-0.26010.05440.0467-0.21130.2940.04350.14190.10850.0153-0.00520.0781-0.02390.149541.702844.46279.7795
51.18610.2446-0.91622.0677-1.94495.27180.060.0870.0433-0.01410.076-0.018-0.0762-0.1735-0.14670.05540.0021-0.00280.0819-0.0140.081938.085354.11399.4442
61.1214-0.20540.00153.2907-2.89193.18510.0873-0.0754-0.2935-0.0464-0.0583-0.16270.49880.52430.31290.15180.0194-0.05970.15960.01520.147346.484644.464421.2047
70.3875-0.5774-0.26771.27371.48593.66990.055-0.00040.0545-0.10280.0245-0.1077-0.10090.11-0.07020.0397-0.01180.00490.1004-0.01640.102145.552956.82989.2038
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 27 )
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 38 )
3X-RAY DIFFRACTION3chain 'A' and (resid 39 through 83 )
4X-RAY DIFFRACTION4chain 'A' and (resid 84 through 112 )
5X-RAY DIFFRACTION5chain 'A' and (resid 113 through 126 )
6X-RAY DIFFRACTION6chain 'A' and (resid 127 through 135 )
7X-RAY DIFFRACTION7chain 'A' and (resid 136 through 157 )

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