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- PDB-1a8m: TUMOR NECROSIS FACTOR ALPHA, R31D MUTANT -

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Basic information

Entry
Database: PDB / ID: 1a8m
TitleTUMOR NECROSIS FACTOR ALPHA, R31D MUTANT
ComponentsTUMOR NECROSIS FACTOR ALPHA
KeywordsLYMPHOKINE / CYTOKINE / CYTOTOXIN
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 / response to quercetin / 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 ...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 / response to quercetin / 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 / 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 / negative regulation of vascular wound healing / Differentiation of naive CD4+ T cells to T helper 1 cells (Th1 cells) / negative regulation of cytokine production involved in immune response / negative regulation of amyloid-beta clearance / positive regulation of podosome assembly / response to resveratrol / positive regulation of hair follicle development / inflammatory response to wounding / positive regulation of interleukin-18 production / positive regulation of hepatocyte proliferation / positive regulation of action potential / toll-like receptor 3 signaling pathway / TNF signaling / embryonic digestive tract development / negative regulation of D-glucose import across plasma membrane / vascular endothelial growth factor production / positive regulation of fever generation / positive regulation of calcineurin-NFAT signaling cascade / positive regulation of protein localization to cell surface / response to fructose / negative regulation of mitotic cell cycle / leukocyte tethering or rolling / 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 glial cell proliferation / 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 / regulation of fat cell differentiation / positive regulation of chemokine (C-X-C motif) ligand 2 production / 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 / 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 / regulation of reactive oxygen species metabolic process / positive regulation of cytokine production involved in inflammatory response / TNFR1-mediated ceramide production / positive regulation of programmed cell death / negative regulation of heart rate / negative regulation of viral genome replication / positive regulation of DNA biosynthetic process / positive regulation of neuroinflammatory response / positive regulation of amyloid-beta formation / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of endothelial cell proliferation / negative regulation of interleukin-6 production / positive regulation of immunoglobulin production / negative regulation of bicellular tight junction assembly / response to isolation stress / Interleukin-10 signaling / regulation of synapse organization / negative regulation of apoptotic signaling pathway / regulation of insulin secretion / histone H3K9ac reader activity / negative regulation of blood vessel endothelial cell migration / negative regulation of lipid storage / response to salt stress / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / detection of mechanical stimulus involved in sensory perception of pain / negative regulation of osteoblast differentiation / negative regulation of lipid catabolic process / extrinsic apoptotic signaling pathway / positive regulation of synaptic transmission / positive regulation of vascular associated smooth muscle cell proliferation / regulation of synaptic transmission, glutamatergic / cellular response to retinoic acid / cell surface receptor signaling pathway via JAK-STAT / positive regulation of chemokine production / phagocytic cup
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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsReed, C. / Fu, Z.-Q. / Wu, J. / Xue, Y.-N. / Harrison, R.W. / Chen, M.-J. / Weber, I.T.
Citation
Journal: Protein Eng. / Year: 1997
Title: Crystal structure of TNF-alpha mutant R31D with greater affinity for receptor R1 compared with R2.
Authors: Reed, C. / Fu, Z.Q. / Wu, J. / Xue, Y.N. / Harrison, R.W. / Chen, M.J. / Weber, I.T.
#1: Journal: Protein Eng. / Year: 1995
Title: Model Complexes of Tumor Necrosis Factor-Alpha with Receptors R1 and R2
Authors: Fu, Z.Q. / Harrison, R.W. / Reed, C. / Wu, J. / Xue, Y.N. / Chen, M.J. / Weber, I.T.
History
DepositionMar 27, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Aug 2, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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 ALPHA
B: TUMOR NECROSIS FACTOR ALPHA
C: TUMOR NECROSIS FACTOR ALPHA


Theoretical massNumber of molelcules
Total (without water)51,9863
Polymers51,9863
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7470 Å2
ΔGint-38 kcal/mol
Surface area17930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.700, 94.700, 117.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.04046, -0.10575, 0.99357), (-0.98065, 0.18643, 0.05978), (-0.19155, -0.97676, -0.09616)-16.17, 57.43, 96.33
2given(-0.02896, -0.99271, -0.11699), (-0.20202, 0.12044, -0.97195), (0.97895, -0.00451, -0.20404)74.4, 87.33, 28.89
3given(-0.01202, -0.16346, 0.98646), (-0.98656, 0.16273, 0.01494), (-0.16297, -0.97304, -0.16322)-11.46, 60.62, 97.89

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Components

#1: Protein TUMOR NECROSIS FACTOR ALPHA / TNF-ALPHA


Mass: 17328.551 Da / Num. of mol.: 3 / Mutation: R31D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01375
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.6 Å3/Da / Density % sol: 48.8 %
Crystal growpH: 5.5
Details: CRYSTALLIZED FROM 88% MGSO4, 1-2% PEG 400, 0.2 M MES, PH 5.5.
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
20.15 M1dropNaCl
30.02 MTris-HCl1drop
50.2 MMES1reservoir
61-2 %PEG4001reservoir
4magnesium sulfate1drop

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jul 1, 1994
RadiationMonochromator: NI / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→10 Å / Num. obs: 21396 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 7.8
Reflection shellResolution: 2.3→2.4 Å / Mean I/σ(I) obs: 1.8
Reflection
*PLUS
Num. measured all: 85815

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Processing

Software
NameVersionClassification
PROCESSdata collection
PROCESSdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
PROCESSdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TNF

1tnf


Resolution: 2.3→10 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1171 8 %RANDOM
Rwork0.218 ---
obs0.218 21396 97.3 %-
Displacement parametersBiso mean: 38 Å2
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4347 0 0 69 4416
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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