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- PDB-7ta3: Trimer-to-Monomer Disruption of Tumor Necrosis Factor-alpha (TNF-... -

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Basic information

Entry
Database: PDB / ID: 7ta3
TitleTrimer-to-Monomer Disruption of Tumor Necrosis Factor-alpha (TNF-alpha) by alpha-peptide-3
Components
  • Alpha-peptide-3
  • Tumor necrosis factor
KeywordsSIGNALING PROTEIN / tumor necrosis factor-alpha / signaling
Function / homology
Function and homology information


negative regulation of L-glutamate import across plasma membrane / negative regulation of branching involved in lung morphogenesis / negative regulation of bile acid secretion / response to Gram-negative bacterium / positive regulation of interleukin-33 production / positive regulation of neutrophil activation / positive regulation of blood microparticle formation / negative regulation of signaling receptor activity / positive regulation of chronic inflammatory response to antigenic stimulus / positive regulation of fractalkine production ...negative regulation of L-glutamate import across plasma membrane / negative regulation of branching involved in lung morphogenesis / negative regulation of bile acid secretion / response to Gram-negative bacterium / positive regulation of interleukin-33 production / positive regulation of neutrophil activation / positive regulation of blood microparticle formation / negative regulation of signaling receptor activity / positive regulation of chronic inflammatory response to antigenic stimulus / positive regulation of fractalkine production / positive regulation of leukocyte adhesion to arterial endothelial cell / positive regulation of vitamin D biosynthetic process / positive regulation of translational initiation by iron / response to macrophage colony-stimulating factor / 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 / response to 3,3',5-triiodo-L-thyronine / response to gold nanoparticle / positive regulation of humoral immune response mediated by circulating immunoglobulin / positive regulation of hair follicle development / negative regulation of myelination / negative regulation of bicellular tight junction assembly / negative regulation of cytokine production involved in immune response / negative regulation of vascular wound healing / : / negative regulation of amyloid-beta clearance / response to isolation stress / positive regulation of action potential / inflammatory response to wounding / positive regulation of interleukin-18 production / death receptor agonist activity / positive regulation of protein transport / TNF signaling / epithelial cell proliferation involved in salivary gland morphogenesis / toll-like receptor 3 signaling pathway / embryonic digestive tract development / vascular endothelial growth factor production / leukocyte migration involved in inflammatory response / necroptotic signaling pathway / response to fructose / positive regulation of neuroinflammatory response / positive regulation of synoviocyte proliferation / positive regulation of calcineurin-NFAT signaling cascade / leukocyte tethering or rolling / positive regulation of mononuclear cell migration / positive regulation of fever generation / negative regulation of myoblast differentiation / cellular response to toxic substance / regulation of establishment of endothelial barrier / endothelial cell apoptotic process / negative regulation of D-glucose import / negative regulation of oxidative phosphorylation / positive regulation of protein localization to cell surface / macrophage activation involved in immune response / positive regulation of osteoclast differentiation / tumor necrosis factor receptor binding / positive regulation of protein-containing complex disassembly / negative regulation of systemic arterial blood pressure / 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 programmed cell death / positive regulation of hepatocyte proliferation / positive regulation of membrane protein ectodomain proteolysis / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of podosome assembly / regulation of canonical NF-kappaB signal transduction / regulation of fat cell differentiation / TNFR1-induced proapoptotic signaling / positive regulation of leukocyte adhesion to vascular endothelial cell / regulation of metabolic process / regulation of reactive oxygen species metabolic process / negative regulation of heart rate / positive regulation of amyloid-beta formation / positive regulation of DNA biosynthetic process / negative regulation of viral genome replication / response to L-glutamate / negative regulation of fat cell differentiation / regulation of synapse organization / Interleukin-10 signaling / negative regulation of endothelial cell proliferation / negative regulation of interleukin-6 production / negative regulation of blood vessel endothelial cell migration / humoral immune response / negative regulation of apoptotic signaling pathway / negative regulation of lipid storage / negative regulation of mitotic cell cycle / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of JUN kinase activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / cell surface receptor signaling pathway via JAK-STAT / phagocytic cup / negative regulation of osteoblast differentiation / positive regulation of synaptic transmission
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 speciesHomo sapiens (human)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsNiu, J. / Bingman, C.A. / Gellman, S.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM056414 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: Trimer-to-Monomer Disruption Mechanism for a Potent, Protease-Resistant Antagonist of Tumor Necrosis Factor-alpha Signaling.
Authors: Niu, J. / Cederstrand, A.J. / Eddinger, G.A. / Yin, B. / Checco, J.W. / Bingman, C.A. / Outlaw, V.K. / Gellman, S.H.
History
DepositionDec 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 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
A: Alpha-peptide-3
B: Tumor necrosis factor
C: Alpha-peptide-3
D: Tumor necrosis factor


Theoretical massNumber of molelcules
Total (without water)42,1244
Polymers42,1244
Non-polymers00
Water23413
1
A: Alpha-peptide-3
B: Tumor necrosis factor


Theoretical massNumber of molelcules
Total (without water)21,0622
Polymers21,0622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-13 kcal/mol
Surface area9460 Å2
MethodPISA
2
C: Alpha-peptide-3
D: Tumor necrosis factor


Theoretical massNumber of molelcules
Total (without water)21,0622
Polymers21,0622
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.560, 86.560, 143.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein/peptide Alpha-peptide-3


Mass: 3604.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)
#2: Protein Tumor necrosis factor / Cachectin / TNF-alpha / Tumor necrosis factor ligand superfamily member 2 / TNF-a


Mass: 17457.736 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNF, TNFA, TNFSF2 / Production host: Escherichia coli (E. coli) / References: UniProt: P01375
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 3.2 Å3/Da / Density % sol: 61.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 1.5M ammonium sulfate, 0.1 M tris HCL pH 8.5, 12% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12713 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12713 Å / Relative weight: 1
ReflectionResolution: 2.5→43.28 Å / Num. obs: 19636 / % possible obs: 99.9 % / Redundancy: 26.4 % / Biso Wilson estimate: 69.58 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.111 / Rrim(I) all: 0.113 / Χ2: 1.046 / Net I/σ(I): 20.51 / Num. measured all: 518383 / Scaling rejects: 24
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.5-2.5726.5431.851.4637770142314230.8681.886100
2.57-2.6427.91.5071.9838251137213710.931.53599.9
2.64-2.7127.7941.0682.9837856136213620.9571.087100
2.71-2.827.7120.9173.5536331131113110.9760.934100
2.8-2.8927.5990.8074.235216127612760.9710.822100
2.89-2.9927.3280.5585.9333422122312230.9860.568100
2.99-3.127.0310.4248.0432005118411840.9920.432100
3.1-3.2326.5870.30710.9430814116011590.9940.31399.9
3.23-3.3726.0450.21614.9228519109510950.9960.221100
3.37-3.5423.5290.16519.3124658105110480.9970.16999.7
3.54-3.7325.5260.11726.9626088102210220.9980.119100
3.73-3.9527.5750.10632.05266939689680.9990.108100
3.95-4.2327.130.08140.97246079079070.9990.083100
4.23-4.5626.820.06550.07228248518510.9990.067100
4.56-526.1630.06150.372043378178110.063100
5-5.5925.5740.06647.38186697307300.9990.067100
5.59-6.4623.5930.06546.71151706436430.9990.067100
6.46-7.9122.1360.05252.72122415585530.9990.05499.1
7.91-11.1825.1880.03969.031136045145110.04100
11.18-43.2819.6260.04254.84545628627810.04397.2

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Processing

Software
NameVersionClassification
XDSMar 15, 2019data reduction
XSCALEMar 15, 2019data scaling
PHENIX1.19.2refinement
PDB_EXTRACT3.27data extraction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TNF_A

Resolution: 2.5→43.28 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 34.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2767 1934 9.91 %
Rwork0.2459 17589 -
obs0.249 19523 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 226.36 Å2 / Biso mean: 98.6984 Å2 / Biso min: 54.84 Å2
Refinement stepCycle: final / Resolution: 2.5→43.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2758 0 0 13 2771
Biso mean---70.55 -
Num. residues----355
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.560.4495950.40031267136299
2.56-2.630.39241930.36261150134399
2.63-2.710.3711970.338512891386100
2.71-2.80.33611920.33111162135499
2.8-2.90.4371970.342712711368100
2.9-3.010.383960.33521260135699
3.01-3.150.36271940.301911891383100
3.15-3.320.3228970.287112841381100
3.32-3.520.31221940.260511891383100
3.52-3.80.3126970.241413051402100
3.8-4.180.25671460.218212601406100
4.18-4.780.24571450.184312761421100
4.78-6.020.2541970.223213401437100
6.02-43.280.21641940.23561347154199
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)
10.36590.1530.21980.17670.11070.18390.1323-0.3429-0.266-0.96350.10760.8336-1.9939-0.1370.00291.1050.04960.02280.8479-0.05560.8658-6.034-52.6812-21.6957
20.0480.00660.00250.0216-0.0433-0.0270.6824-0.35241.04820.7463-1.5802-1.2599-0.9290.8144-0.00460.9555-0.0626-0.14951.12960.09480.9885.3481-58.0916-25.0202
31.40151.48230.71382.1533-0.15581.31620.00480.8676-0.06361.4804-0.3688-0.8416-0.5271-0.6037-0.0021.1211-0.1427-0.1090.71870.00630.8525-1.122-60.1081-15.204
41.52740.009-0.48784.0166-0.10782.81360.06620.1488-0.19920.00920.01480.0050.0111-0.0519-00.6535-0.03110.00350.6277-0.0570.7299-10.4588-65.3435-28.1643
54.04690.41650.80950.32350.24632.60910.0609-0.3789-0.22230.60720.0867-0.67840.2138-0.549-0.00040.7672-0.02130.08550.6617-0.04180.7014-21.7684-67.96-21.5036
63.4908-1.97510.692.2345-0.78492.20630.07420.08170.18330.1883-0.0586-0.0510.0042-0.22730.00040.7915-0.02670.03960.6297-0.03330.6935-15.798-60.2568-25.6709
70.32330.32420.26851.0746-0.10540.45780.9762-0.3985-1.70340.26250.35190.63430.39460.1769-0.00080.95510.0397-0.04010.8278-0.06161.0047-36.9646-86.7105-9.9183
80.27620.0590.0160.2834-0.16580.22420.94-0.19351.04921.40850.501-0.3926-1.19530.7529-0.00310.9437-0.17010.22541.7993-0.08240.919-44.9213-84.1321-0.2023
91.25241.3030.78981.75-0.36941.41580.6828-0.93840.21140.8982-0.0988-0.37380.1747-0.73520.00181.1149-0.15950.08790.8634-0.02020.7838-33.5327-80.1104-2.1138
102.891-0.4637-0.88262.6364-1.68031.29460.52610.12230.25160.31980.04150.7871-0.6918-0.6516-0.00360.82430.0410.15370.77270.03570.9223-44.7802-75.4036-14.8067
110.12410.11450.30590.35120.36210.76511.2017-0.6093-0.35070.2742-0.41631.98141.1248-1.7030.03051.049-0.01430.09041.2202-0.02731.4571-48.0191-75.9643-10.0836
121.2041.7853-0.941.8889-0.33981.00450.088-0.22830.3863-0.27930.17110.679-0.6965-0.016100.85390.12220.09160.7659-0.06520.8006-38.3854-71.0884-13.452
131.48571.9220.04951.1094-0.28062.7251-0.00310.20630.2210.2030.11270.3880.0078-0.20470.00040.71280.01570.05470.63860.02160.7482-32.0885-73.6458-26.0177
140.9416-0.00550.06990.2867-0.35640.3288-1.00250.5195-0.2636-1.05220.2469-0.71640.6290.39380.00071.3333-0.02670.040.9410.05680.9682-29.4119-94.3526-36.4386
150.5234-0.9125-1.25421.47210.80381.10120.13040.0320.3421-0.1541-0.19480.5033-0.0022-0.4046-0.00020.87060.00910.03390.77940.01360.7929-36.501-76.9438-18.5186
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 10 )A1 - 10
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 16 )A11 - 16
3X-RAY DIFFRACTION3chain 'A' and (resid 17 through 31 )A17 - 31
4X-RAY DIFFRACTION4chain 'B' and (resid 8 through 74 )B8 - 74
5X-RAY DIFFRACTION5chain 'B' and (resid 75 through 99 )B75 - 99
6X-RAY DIFFRACTION6chain 'B' and (resid 100 through 157 )B100 - 157
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 11 )C1 - 11
8X-RAY DIFFRACTION8chain 'C' and (resid 12 through 16 )C12 - 16
9X-RAY DIFFRACTION9chain 'C' and (resid 17 through 31 )C17 - 31
10X-RAY DIFFRACTION10chain 'D' and (resid 9 through 27 )D9 - 27
11X-RAY DIFFRACTION11chain 'D' and (resid 28 through 38 )D28 - 38
12X-RAY DIFFRACTION12chain 'D' and (resid 39 through 66 )D39 - 66
13X-RAY DIFFRACTION13chain 'D' and (resid 67 through 98 )D67 - 98
14X-RAY DIFFRACTION14chain 'D' and (resid 99 through 113 )D99 - 113
15X-RAY DIFFRACTION15chain 'D' and (resid 114 through 157 )D114 - 157

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