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- PDB-7kp7: asymmetric mTNF-alpha hTNFR1 complex -

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Basic information

Entry
Database: PDB / ID: 7kp7
Titleasymmetric mTNF-alpha hTNFR1 complex
Components
  • Tumor necrosis factor
  • Tumor necrosis factor receptor superfamily member 1A
KeywordsCYTOKINE / Tumour necrosis factor alpha / TNF / Receptor / TNFR1 / asymmetric / protein-protein inhibitor
Function / homology
Function and homology information


TNF signaling / TNFR1-mediated ceramide production / TNFR1-induced proapoptotic signaling / positive regulation of amide metabolic process / tumor necrosis factor receptor superfamily complex / pulmonary valve development / TNFR1-induced NF-kappa-B signaling pathway / cellular extravasation / Regulation of TNFR1 signaling / negative regulation of branching involved in lung morphogenesis ...TNF signaling / TNFR1-mediated ceramide production / TNFR1-induced proapoptotic signaling / positive regulation of amide metabolic process / tumor necrosis factor receptor superfamily complex / pulmonary valve development / 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 blood microparticle formation / positive regulation of chronic inflammatory response to antigenic stimulus / aortic valve development / tumor necrosis factor receptor activity / positive regulation of lipid metabolic process / positive regulation of leukocyte adhesion to arterial endothelial cell / negative regulation of extracellular matrix constituent secretion / positive regulation of vitamin D biosynthetic process / positive regulation of protein transport / positive regulation of translational initiation by iron / positive regulation of apoptotic process involved in morphogenesis / TNFR2 non-canonical NF-kB pathway / 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 / TNFs bind their physiological receptors / negative regulation of cytokine production involved in immune response / negative regulation of vascular wound healing / tumor necrosis factor binding / negative regulation of amyloid-beta clearance / negative regulation of cardiac muscle hypertrophy / inflammatory response to wounding / death receptor agonist activity / TNF signaling / epithelial cell proliferation involved in salivary gland morphogenesis / regulation of osteoclast differentiation / embryonic digestive tract development / negative regulation of D-glucose import / vascular endothelial growth factor production / positive regulation of synoviocyte proliferation / necroptotic signaling pathway / positive regulation of calcineurin-NFAT signaling cascade / leukocyte tethering or rolling / positive regulation of fever generation / negative regulation of myoblast differentiation / positive regulation of protein-containing complex disassembly / regulation of establishment of endothelial barrier / endothelial cell apoptotic process / regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of protein localization to cell surface / positive regulation of osteoclast differentiation / macrophage activation involved in immune response / tumor necrosis factor receptor binding / positive regulation of heterotypic cell-cell adhesion / positive regulation of cytokine production involved in inflammatory response / positive regulation of macrophage derived foam cell differentiation / regulation of immunoglobulin production / TNFR1-mediated ceramide production / positive regulation of membrane protein ectodomain proteolysis / positive regulation of podosome assembly / positive regulation of chemokine (C-X-C motif) ligand 2 production / TNFR1-induced proapoptotic signaling / negative regulation of bicellular tight junction assembly / regulation of metabolic process / regulation of reactive oxygen species metabolic process / prostaglandin metabolic process / leukocyte migration / positive regulation of amyloid-beta formation / negative regulation of viral genome replication / regulation of synapse organization / regulation of protein secretion / negative regulation of endothelial cell proliferation / Interleukin-10 signaling / positive regulation of JUN kinase activity / negative regulation of interleukin-6 production / humoral immune response / negative regulation of blood vessel endothelial cell migration / negative regulation of mitotic cell cycle / positive regulation of execution phase of apoptosis / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of osteoblast differentiation / cell surface receptor signaling pathway via JAK-STAT / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of synaptic transmission / positive regulation of MAP kinase activity / negative regulation of lipid catabolic process / phagocytic cup / positive regulation of vascular associated smooth muscle cell proliferation / tumor necrosis factor-mediated signaling pathway / extrinsic apoptotic signaling pathway / JNK cascade / positive regulation of glial cell proliferation / TNFR1-induced NF-kappa-B signaling pathway / extracellular matrix organization / antiviral innate immune response
Similarity search - Function
Tumour necrosis factor receptor 1A / Tumor necrosis factor receptor 1A, N-terminal / Tumor necrosis factor receptor 1A, death domain / : / Tumour necrosis factor alpha / Tumour necrosis factor / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / TNFR/NGFR family cysteine-rich region domain profile. ...Tumour necrosis factor receptor 1A / Tumor necrosis factor receptor 1A, N-terminal / Tumor necrosis factor receptor 1A, death domain / : / Tumour necrosis factor alpha / Tumour necrosis factor / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNF(Tumour Necrosis Factor) family / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Tumour necrosis factor-like domain superfamily / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily
Similarity search - Domain/homology
Tumor necrosis factor / Tumor necrosis factor receptor superfamily member 1A
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å
AuthorsArakaki, T.L. / Fox III, D. / Edwards, T.E. / Foley, A. / Ceska, T.
CitationJournal: Nat Commun / Year: 2021
Title: Structural insights into the disruption of TNF-TNFR1 signalling by small molecules stabilising a distorted TNF.
Authors: McMillan, D. / Martinez-Fleites, C. / Porter, J. / Fox 3rd, D. / Davis, R. / Mori, P. / Ceska, T. / Carrington, B. / Lawson, A. / Bourne, T. / O'Connell, J.
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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 3, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 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

Downloads & links

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Assembly

Deposited unit
B: Tumor necrosis factor
A: Tumor necrosis factor
C: Tumor necrosis factor
E: Tumor necrosis factor receptor superfamily member 1A
D: Tumor necrosis factor receptor superfamily member 1A
F: Tumor necrosis factor receptor superfamily member 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,81141
Polymers97,8236
Non-polymers3,98835
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19710 Å2
ΔGint-385 kcal/mol
Surface area39610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.220, 139.220, 138.340
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 16411.596 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tnf, Tnfa, Tnfsf2 / Plasmid: pEMB54 / Production host: Escherichia coli (E. coli) / Strain (production host): Top10 / References: UniProt: P06804
#2: Protein Tumor necrosis factor receptor superfamily member 1A / Tumor necrosis factor receptor 1 / TNF-R1 / Tumor necrosis factor receptor type I / TNFR-I / p55 / p60


Mass: 16196.158 Da / Num. of mol.: 3 / Mutation: N25D, C153S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF1A, TNFAR, TNFR1 / Plasmid: pEMB50 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P19438
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: SO4
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.98 Å3/Da / Density % sol: 69.07 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 2.0M Ammonium sulfate, 0.1M BisTris pH5.5, and cryo-protected with paraffin oil; Vapor diffusion, sitting drop, temperature 289K.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 11, 2014
RadiationMonochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 43935 / % possible obs: 99.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 49.2 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 19.98
Reflection shellResolution: 2.65→2.72 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 2.83 / Num. unique obs: 3238 / % possible all: 99.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation8.16 Å49.07 Å
Translation8.16 Å49.07 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: unpublished structure

Resolution: 2.65→49.07 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.923 / SU B: 9.446 / SU ML: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.366 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.227 2045 4.7 %RANDOM
Rwork0.193 41890 --
obs0.195 43935 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.464 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20.22 Å2-0 Å2
2--0.45 Å2-0 Å2
3----1.46 Å2
Refinement stepCycle: LAST / Resolution: 2.65→49.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6486 0 225 225 6936
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196875
X-RAY DIFFRACTIONr_bond_other_d0.0050.026016
X-RAY DIFFRACTIONr_angle_refined_deg1.4261.9799397
X-RAY DIFFRACTIONr_angle_other_deg0.941313847
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5625855
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.22524.832298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.237151014
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8521524
X-RAY DIFFRACTIONr_chiral_restr0.070.21060
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217803
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021572
X-RAY DIFFRACTIONr_mcbond_it3.24.8083426
X-RAY DIFFRACTIONr_mcbond_other3.24.8073425
X-RAY DIFFRACTIONr_mcangle_it4.967.1974273
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 134 -
Rwork0.33 3086 -
all-3220 -
obs--99.44 %

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