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- PDB-2zjc: TNFR1 selectve TNF mutant; R1-6 -

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Basic information

Entry
Database: PDB / ID: 2zjc
TitleTNFR1 selectve TNF mutant; R1-6
ComponentsTumor necrosis factor
KeywordsCYTOKINE / phage display system / TNFR1 selectivity / TNF / agonist / mutant / Lipoprotein / Membrane / Myristate / Phosphoprotein / Secreted / Signal-anchor / Transmembrane
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 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 / positive regulation of protein transport ...response to Gram-negative bacterium / negative regulation of L-glutamate import across plasma membrane / 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 / positive regulation of protein transport / positive regulation of vitamin D biosynthetic process / chronic inflammatory response to antigenic stimulus / regulation of endothelial cell apoptotic process / response to macrophage colony-stimulating factor / negative regulation of myelination / positive regulation of leukocyte adhesion to arterial endothelial cell / response to gold nanoparticle / response to quercetin / Differentiation of naive CD4+ T cells to T helper 1 cells (Th1 cells) / negative regulation of vascular wound healing / negative regulation of amyloid-beta clearance / negative regulation of cytokine production involved in immune response / positive regulation of podosome assembly / positive regulation of hair follicle development / inflammatory response to wounding / response to resveratrol / positive regulation of interleukin-18 production / positive regulation of hepatocyte proliferation / positive regulation of action potential / toll-like receptor 3 signaling pathway / TNF signaling / negative regulation of D-glucose import across plasma membrane / embryonic digestive tract development / vascular endothelial growth factor production / positive regulation of fever generation / positive regulation of calcineurin-NFAT signaling cascade / response to fructose / positive regulation of protein localization to cell surface / negative regulation of mitotic cell cycle / leukocyte tethering or rolling / endothelial cell apoptotic process / necroptotic signaling pathway / positive regulation of synoviocyte proliferation / regulation of establishment of endothelial barrier / positive regulation of mononuclear cell migration / negative regulation of oxidative phosphorylation / macrophage activation involved in immune response / response to hydrogen sulfide / positive regulation of protein-containing complex disassembly / positive regulation of osteoclast differentiation / cellular response to toxic substance / positive regulation of macrophage derived foam cell differentiation / positive regulation of chemokine (C-X-C motif) ligand 2 production / regulation of fat cell differentiation / tumor necrosis factor receptor binding / positive regulation of heterotypic cell-cell adhesion / positive regulation of membrane protein ectodomain proteolysis / negative regulation of systemic arterial blood pressure / response to L-glutamate / positive regulation of extrinsic apoptotic signaling pathway / regulation of reactive oxygen species metabolic process / positive regulation of leukocyte adhesion to vascular endothelial cell / regulation of canonical NF-kappaB signal transduction / TNFR1-induced proapoptotic signaling / negative regulation of fat cell differentiation / positive regulation of cytokine production involved in inflammatory response / positive regulation of programmed cell death / TNFR1-mediated ceramide production / negative regulation of heart rate / negative regulation of viral genome replication / positive regulation of DNA biosynthetic process / positive regulation of amyloid-beta formation / positive regulation of neuroinflammatory response / negative regulation of endothelial cell proliferation / negative regulation of interleukin-6 production / positive regulation of immunoglobulin production / negative regulation of bicellular tight junction assembly / extrinsic apoptotic signaling pathway via death domain receptors / response to isolation stress / Interleukin-10 signaling / regulation of synapse organization / regulation of insulin secretion / histone H3K9ac reader activity / negative regulation of apoptotic signaling pathway / negative regulation of blood vessel endothelial cell migration / negative regulation of lipid storage / positive regulation of glial cell proliferation / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / detection of mechanical stimulus involved in sensory perception of pain / negative regulation of lipid catabolic process / extrinsic apoptotic signaling pathway / negative regulation of osteoblast differentiation / positive regulation of synaptic transmission / cellular response to retinoic acid / positive regulation of vascular associated smooth muscle cell proliferation / cell surface receptor signaling pathway via JAK-STAT / regulation of synaptic transmission, glutamatergic / positive regulation of chemokine production / phagocytic cup / skeletal muscle contraction
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMukai, Y. / Yamagata, Y. / Tsutsumi, Y.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structure-Function Relationship of Tumor Necrosis Factor (TNF) and Its Receptor Interaction Based on 3D Structural Analysis of a Fully Active TNFR1-Selective TNF Mutant
Authors: Mukai, Y. / Shibata, H. / Nakamura, T. / Yoshioka, Y. / Abe, Y. / Nomura, T. / Taniai, M. / Ohta, T. / Ikemizu, S. / Nakagawa, S. / Tsunoda, S. / Kamada, H. / Yamagata, Y. / Tsutsumi, Y.
History
DepositionMar 5, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)51,3354
Polymers51,2433
Non-polymers921
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7180 Å2
ΔGint-38 kcal/mol
Surface area17010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.873, 135.873, 58.023
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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


Mass: 17081.131 Da / Num. of mol.: 3 / Fragment: R1-6, UNP residues 77-233
Mutation: K11M, K65S, L29K, R31A, R32G, K90P, K98R, K112N, K128P, E146S, S147T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNF, TNFA, TNFSF2 / Plasmid: pYas(modifed from pUC vector) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01375
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.01 Å3/Da / Density % sol: 38.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU
DetectorType: ADSC / Detector: CCD / Date: Dec 13, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 13445 / % possible obs: 99.9 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 28.9
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 4.2 / Num. unique all: 1173 / % possible all: 85.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TNF

1tnf


Resolution: 2.5→25.67 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.9 / Rfactor Rfree error: 0.008 / SU B: 30.501 / SU ML: 0.329 / TLS residual ADP flag: LIKELY RESIDUAL / Data cutoff high absF: 2548521.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.378 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27222 1373 10.2 %RANDOM
Rwork0.20146 ---
obs0.20881 12060 97.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK / Bsol: 106.48 Å2 / ksol: 0.1 e/Å3
Displacement parametersBiso mean: 19.696 Å2
Baniso -1Baniso -2Baniso -3
1-1.17 Å20.59 Å20 Å2
2--1.17 Å20 Å2
3----1.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.62 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.5→25.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3338 0 6 59 3403
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223429
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2711.9644696
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7885430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.48524.805154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.60515500
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3081516
X-RAY DIFFRACTIONr_chiral_restr0.0890.2530
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022666
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.21488
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22260
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2141
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.263
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4251.52219
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.76623506
X-RAY DIFFRACTIONr_scbond_it0.93831374
X-RAY DIFFRACTIONr_scangle_it1.4834.51190
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.498→2.563 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 67 9.5 %
Rwork0.318 798 -
obs--84.23 %
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)
17.2741-0.73180.49935.0031-0.27572.12150.10490.4883-0.7046-0.44880.021-0.14290.0590.0964-0.1259-0.0303-0.00720.0522-0.1278-0.07440.69650.50619.777-2.451
28.45630.34462.61442.56950.34062.5998-0.0378-0.6922-0.72460.29250.0528-0.18980.1934-0.0944-0.015-0.03910.06650.08670.05570.15080.6702-8.04122.05217.324
34.69710.05980.02822.8298-0.41222.2781-0.087-0.15540.36280.01940.0632-0.1324-0.1994-0.03710.0238-0.03770.0347-0.0158-0.0837-0.03480.6419-3.92439.8215.167
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 157
2X-RAY DIFFRACTION2B6 - 157
3X-RAY DIFFRACTION3C8 - 157
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3gol.paramgol.top

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