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- PDB-8kb6: Crystal Structure of Canine TNF-alpha -

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Basic information

Entry
Database: PDB / ID: 8kb6
TitleCrystal Structure of Canine TNF-alpha
ComponentsTumor necrosis factor
KeywordsCYTOKINE / immune system / inflammatory
Function / homology
Function and homology information


TNFR1-induced proapoptotic signaling / Regulation of TNFR1 signaling / TNFR1-induced NF-kappa-B signaling pathway / TNFR1-mediated ceramide production / TNFR2 non-canonical NF-kB pathway / TNF signaling / negative regulation of branching involved in lung morphogenesis / positive regulation of blood microparticle formation / positive regulation of protein transport / positive regulation of vitamin D biosynthetic process ...TNFR1-induced proapoptotic signaling / Regulation of TNFR1 signaling / TNFR1-induced NF-kappa-B signaling pathway / TNFR1-mediated ceramide production / TNFR2 non-canonical NF-kB pathway / TNF signaling / negative regulation of branching involved in lung morphogenesis / positive regulation of blood microparticle formation / positive regulation of protein transport / positive regulation of vitamin D biosynthetic process / regulation of endothelial cell apoptotic process / chronic inflammatory response to antigenic stimulus / positive regulation of leukocyte adhesion to arterial endothelial cell / negative regulation of vascular wound healing / negative regulation of amyloid-beta clearance / negative regulation of cytokine production involved in immune response / positive regulation of hair follicle development / inflammatory response to wounding / vascular endothelial growth factor production / embryonic digestive tract development / positive regulation of fever generation / necroptotic signaling pathway / leukocyte tethering or rolling / regulation of establishment of endothelial barrier / endothelial cell apoptotic process / positive regulation of protein-containing complex disassembly / positive regulation of protein localization to cell surface / positive regulation of osteoclast differentiation / 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 podosome assembly / positive regulation of heterotypic cell-cell adhesion / positive regulation of membrane protein ectodomain proteolysis / positive regulation of extrinsic apoptotic signaling pathway / regulation of reactive oxygen species metabolic process / positive regulation of amyloid-beta formation / negative regulation of viral genome replication / negative regulation of bicellular tight junction assembly / negative regulation of endothelial cell proliferation / regulation of synapse organization / regulation of insulin secretion / negative regulation of interleukin-6 production / negative regulation of blood vessel endothelial cell migration / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of glial cell proliferation / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of lipid catabolic process / negative regulation of osteoblast differentiation / positive regulation of synaptic transmission / positive regulation of vascular associated smooth muscle cell proliferation / phagocytic cup / antiviral innate immune response / response to glucocorticoid / cytokine activity / tumor necrosis factor-mediated signaling pathway / positive regulation of interleukin-8 production / positive regulation of interleukin-1 beta production / cellular response to ionizing radiation / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / microglial cell activation / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to nicotine / recycling endosome / positive regulation of interleukin-6 production / positive regulation of JNK cascade / cellular response to type II interferon / positive regulation of nitric oxide biosynthetic process / positive regulation of neuron apoptotic process / protease binding / positive regulation of canonical NF-kappaB signal transduction / transcription cis-regulatory region binding / immune response / positive regulation of apoptotic process / membrane raft / external side of plasma membrane / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / : / identical protein binding
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 / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Tumour necrosis factor-like domain superfamily
Similarity search - Domain/homology
Tumor necrosis factor
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85016596237 Å
AuthorsLee, C.C. / Wang, A.H.-J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Protein Sci. / Year: 2024
Title: Structure-based development of a canine TNF-alpha-specific antibody using adalimumab as a template.
Authors: Lee, C.C. / Kuo, W.C. / Chang, Y.W. / Hsu, S.F. / Wu, C.H. / Chen, Y.W. / Chang, J.J. / Wang, A.H.
History
DepositionAug 3, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 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


Theoretical massNumber of molelcules
Total (without water)16,7901
Polymers16,7901
Non-polymers00
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.119, 67.119, 79.024
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Components on special symmetry positions
IDModelComponents
11A-343-

HOH

21A-365-

HOH

31A-398-

HOH

41A-406-

HOH

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Components

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


Mass: 16789.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Gene: TNF, TNFA, TNFSF2 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P51742
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.04 Å3/Da / Density % sol: 39.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 1.6 M MgSO4, 100 mM MES, pH 5.6.

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Data collection

DiffractionMean temperature: 98 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→18 Å / Num. obs: 11257 / % possible obs: 99.4 % / Redundancy: 4.7 % / Biso Wilson estimate: 15.9585259751 Å2 / CC1/2: 0.98 / CC star: 0.99 / Rmerge(I) obs: 0.03 / Net I/σ(I): 44.9
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 5.9 / Num. unique obs: 1128 / CC1/2: 0.96 / CC star: 0.99 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
HKL-3000data scaling
REFMACphasing
Cootmodel building
PHENIX1.1.4refinement
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85016596237→16.77975 Å / SU ML: 0.180697152146 / Cross valid method: FREE R-VALUE / σ(F): 1.99610631886 / Phase error: 21.5966776056
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.214920291661 598 5.31225015546 %
Rwork0.16826326764 10659 -
obs0.170531742474 11257 99.4083362769 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.7522334178 Å2
Refinement stepCycle: LAST / Resolution: 1.85016596237→16.77975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1154 0 0 109 1263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008405029688381182
X-RAY DIFFRACTIONf_angle_d0.9991529487911612
X-RAY DIFFRACTIONf_chiral_restr0.0613873775527182
X-RAY DIFFRACTIONf_plane_restr0.00648584587226209
X-RAY DIFFRACTIONf_dihedral_angle_d8.00080125573703
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8502-2.03610.2075683859521610.1710808853242692X-RAY DIFFRACTION100
2.0361-2.330.2236011208581900.1675362984892628X-RAY DIFFRACTION100
2.33-2.9330.2551430057331150.190340375712711X-RAY DIFFRACTION99.9646268129
2.933-16.779750.1977163086041320.1567055171672628X-RAY DIFFRACTION97.6645435244
Refinement TLS params.Method: refined / Origin x: 11.5572636834 Å / Origin y: 4.67301487418 Å / Origin z: 1.7794117503 Å
111213212223313233
T0.0342399311127 Å2-0.026488838963 Å20.0190212182917 Å2-0.0733099209563 Å20.00617056037921 Å2--0.080413751964 Å2
L0.823854419493 °2-0.129578986453 °20.0484137952944 °2-0.416613660011 °20.257382418654 °2--0.540051226939 °2
S0.0779017592693 Å °-0.0136777044061 Å °0.149807865728 Å °0.0315168716349 Å °0.0839090132621 Å °-0.218743528752 Å °-0.0627941322794 Å °0.132817261195 Å °0.472933337026 Å °
Refinement TLS groupSelection details: all

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