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- PDB-7kpa: asymmetric hTNF-alpha -

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Basic information

Entry
Database: PDB / ID: 7kpa
Titleasymmetric hTNF-alpha
ComponentsTumor necrosis factor
KeywordsCYTOKINE / TNF / Receptor / TNFR1 / symmetric
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 / : / chronic inflammatory response to antigenic stimulus / regulation of endothelial cell apoptotic process / 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 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 / inflammatory response to wounding / positive regulation of action potential / positive regulation of interleukin-18 production / response to resveratrol / epithelial cell proliferation involved in salivary gland morphogenesis / TNF signaling / response to quercetin / 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 / necroptotic signaling pathway / leukocyte tethering or rolling / positive regulation of hepatocyte proliferation / negative regulation of myoblast differentiation / positive regulation of mononuclear cell migration / regulation of establishment of endothelial barrier / response to fructose / response to hydrogen sulfide / endothelial cell apoptotic process / negative regulation of oxidative phosphorylation / 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 systemic arterial blood pressure / negative regulation of mitotic cell cycle / positive regulation of cytokine production involved in inflammatory response / positive regulation of podosome assembly / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of heterotypic cell-cell adhesion / positive regulation of programmed cell death / regulation of fat cell differentiation / regulation of canonical NF-kappaB signal transduction / positive regulation of membrane protein ectodomain proteolysis / 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 / mRNA stabilization / regulation of reactive oxygen species metabolic process / negative regulation of heart rate / positive regulation of DNA biosynthetic process / positive regulation of neuroinflammatory response / positive regulation of amyloid-beta formation / negative regulation of viral genome replication / negative regulation of bicellular tight junction assembly / positive regulation of immunoglobulin production / response to isolation stress / negative regulation of fat cell differentiation / negative regulation of endothelial cell proliferation / regulation of synapse organization / positive regulation of MAP kinase activity / Interleukin-10 signaling / 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 / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of lipid storage / 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 / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Tumour necrosis factor-like domain superfamily
Similarity search - Domain/homology
Chem-D84 / Tumor necrosis factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFox III, D. / Lukacs, C.M. / Ceska, T.
CitationJournal: Nat Commun / Year: 2021
Title: A conformation-selective monoclonal antibody against a small molecule-stabilised signalling-deficient form of TNF.
Authors: Lightwood, D.J. / Munro, R.J. / Porter, J. / McMillan, D. / Carrington, B. / Turner, A. / Scott-Tucker, A. / Hickford, E.S. / Schmidt, A. / Fox III, D. / Maloney, A. / Ceska, T. / Bourne, T. ...Authors: Lightwood, D.J. / Munro, R.J. / Porter, J. / McMillan, D. / Carrington, B. / Turner, A. / Scott-Tucker, A. / Hickford, E.S. / Schmidt, A. / Fox III, D. / Maloney, A. / Ceska, T. / Bourne, T. / O'Connell, J. / Lawson, A.D.G.
History
DepositionNov 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 29, 2022Group: Database references / Structure summary / Category: citation_author / database_2 / struct
Item: _citation_author.name / _database_2.pdbx_DOI ..._citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title
Revision 1.3Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tumor necrosis factor
B: Tumor necrosis factor
C: Tumor necrosis factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9304
Polymers52,3733
Non-polymers5571
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-29 kcal/mol
Surface area17800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.130, 82.130, 93.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 17457.736 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNF, TNFA, TNFSF2 / Plasmid: PEMB54 / Production host: Escherichia coli (E. coli) / Variant (production host): Top10 / References: UniProt: P01375
#2: Chemical ChemComp-D84 / 5-(1-{[2-(difluoromethoxy)phenyl]methyl}-2-{[3-(2-oxopyrrolidin-1-yl)phenoxy]methyl}-1H-benzimidazol-6-yl)pyridin-2(1H)-one


Mass: 556.559 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H26F2N4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 39.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7 / Details: 24.4% PEG 3350, 100 mM HEPES, pH7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 18973 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 5.53 % / Biso Wilson estimate: 36.002 Å2 / Rmerge(I) obs: 0.117 / Net I/av σ(I): 11.77 / Net I/σ(I): 11.77
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsDiffraction-ID% possible all
2.3-2.360.6742.61375199.6
2.36-2.420.59531377199.6
2.42-2.490.4933.51319199.6
2.49-2.570.4433.81299199.5
2.57-2.660.3624.61258199.2
2.66-2.750.2756.11216199.2
2.75-2.850.2546.61158199
2.85-2.970.2147.81115198.9
2.97-3.10.15710.21087198.1
3.1-3.250.12712.61027198.6
3.25-3.430.10115.1984197.8
3.43-3.640.09715.8927197.3
3.64-3.890.09217.9858195.9
3.89-4.20.05823.6808197.3
4.2-4.60.04727.3757196.8
4.6-5.140.04728.9676195.8
5.14-5.940.05125.5604195.7
5.94-7.270.04726.7514194.3
7.27-10.290.04130.3399193
10.29-500.04534215183

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
PDB_EXTRACT3.004data extraction
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: unpublished structure

Resolution: 2.3→27.03 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2622 1897 10 %RANDOM
Rwork0.2163 18965 --
obs0.221 18965 97.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.686 Å2
Refinement stepCycle: LAST / Resolution: 2.3→27.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3169 0 41 63 3273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093295
X-RAY DIFFRACTIONf_angle_d1.0754517
X-RAY DIFFRACTIONf_dihedral_angle_d13.1711945
X-RAY DIFFRACTIONf_chiral_restr0.063519
X-RAY DIFFRACTIONf_plane_restr0.006585
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.35750.32691320.27371188X-RAY DIFFRACTION99
2.3575-2.42120.34821370.26191230X-RAY DIFFRACTION100
2.4212-2.49240.29271360.26641216X-RAY DIFFRACTION100
2.4924-2.57280.31181350.25941213X-RAY DIFFRACTION100
2.5728-2.66470.31411350.25521219X-RAY DIFFRACTION99
2.6647-2.77130.29361360.25661227X-RAY DIFFRACTION99
2.7713-2.89730.33881350.25751215X-RAY DIFFRACTION99
2.8973-3.04980.31191340.25241205X-RAY DIFFRACTION99
3.0498-3.24060.29841360.23981229X-RAY DIFFRACTION98
3.2406-3.49030.27741340.23161211X-RAY DIFFRACTION98
3.4903-3.84070.26231340.20791206X-RAY DIFFRACTION96
3.8407-4.39440.19121370.16921220X-RAY DIFFRACTION97
4.3944-5.52870.19881370.161236X-RAY DIFFRACTION96
5.5287-27.030.21791390.18861253X-RAY DIFFRACTION93

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