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- PDB-2tun: CONFORMATIONAL CHANGES IN THE (ALA-84-VAL) MUTANT OF TUMOR NECROS... -

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Basic information

Entry
Database: PDB / ID: 2tun
TitleCONFORMATIONAL CHANGES IN THE (ALA-84-VAL) MUTANT OF TUMOR NECROSIS FACTOR
ComponentsTUMOR NECROSIS FACTOR-ALPHA
KeywordsLYMPHOKINE
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 / regulation of endothelial cell apoptotic process / regulation of branching involved in salivary gland morphogenesis / chronic inflammatory response to antigenic stimulus / response to macrophage colony-stimulating factor / 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 / positive regulation of interleukin-18 production / inflammatory response to wounding / response to resveratrol / positive regulation of action potential / epithelial cell proliferation involved in salivary gland morphogenesis / response to quercetin / TNF signaling / 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 / leukocyte tethering or rolling / necroptotic signaling pathway / negative regulation of myoblast differentiation / positive regulation of mononuclear cell migration / positive regulation of hepatocyte proliferation / response to fructose / regulation of establishment of endothelial barrier / endothelial cell apoptotic process / negative regulation of oxidative phosphorylation / response to hydrogen sulfide / 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 mitotic cell cycle / negative regulation of systemic arterial blood pressure / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of cytokine production involved in inflammatory response / positive regulation of podosome assembly / regulation of fat cell differentiation / positive regulation of heterotypic cell-cell adhesion / positive regulation of programmed cell death / positive regulation of membrane protein ectodomain proteolysis / regulation of canonical NF-kappaB signal transduction / 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 amyloid-beta formation / positive regulation of neuroinflammatory response / negative regulation of viral genome replication / positive regulation of immunoglobulin production / negative regulation of bicellular tight junction assembly / negative regulation of fat cell differentiation / response to isolation stress / negative regulation of endothelial cell proliferation / positive regulation of MAP kinase activity / Interleukin-10 signaling / regulation of synapse organization / 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 / negative regulation of lipid storage / extrinsic apoptotic signaling pathway via death domain receptors / 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 / 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 / Resolution: 3.1 Å
AuthorsSaludjian, P. / Prange, T.
Citation
Journal: To be Published
Title: Conformational Changes in the (Ala-84-Val) Mutant of Tumor Necrosis Factor
Authors: Saludjian, P. / Prange, T. / Kahn, R. / Fourme, R. / Tavernier, J. / Van-Oostade, X. / Fiers, W. / Navaza, G.
#1: Journal: Acta Crystallogr.,Sect.A / Year: 1991
Title: Methodology Employed for the Structure Determination of Tumor Necrosis Factor, a Case of High Non-Crystallographic Symmetry
Authors: Jones, E.Y. / Walker, N.P. / Stuart, D.I.
#2: Journal: J.Biol.Chem. / Year: 1989
Title: The Structure of Tumor Necrosis Factor-Alpha at 2.6 Angstroms Resolution. Implications for Receptor Binding
Authors: Eck, M.J. / Sprang, S.R.
#3: Journal: Nature / Year: 1989
Title: Structure of Tumor Necrosis Factor
Authors: Jones, E.Y. / Stuart, D.I. / Walker, N.P.
#4: Journal: J.Mol.Biol. / Year: 1988
Title: Structure of Tumor Necrosis Factor by X-Ray Solution Scattering and Preliminary Studies by Single Crystal X-Ray Diffraction
Authors: Lewitt-Bentley, A. / Fourme, R. / Kahn, R. / Prange, T. / Vachette, P. / Tavernier, J. / Hauquier, G. / Fiers, W.
History
DepositionOct 6, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 19, 2013Group: Other
Revision 1.4Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TUMOR NECROSIS FACTOR-ALPHA
B: TUMOR NECROSIS FACTOR-ALPHA
C: TUMOR NECROSIS FACTOR-ALPHA
D: TUMOR NECROSIS FACTOR-ALPHA
E: TUMOR NECROSIS FACTOR-ALPHA
F: TUMOR NECROSIS FACTOR-ALPHA


Theoretical massNumber of molelcules
Total (without water)104,3816
Polymers104,3816
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
D: TUMOR NECROSIS FACTOR-ALPHA
E: TUMOR NECROSIS FACTOR-ALPHA
F: TUMOR NECROSIS FACTOR-ALPHA


Theoretical massNumber of molelcules
Total (without water)52,1903
Polymers52,1903
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-38 kcal/mol
Surface area18470 Å2
MethodPISA
3
A: TUMOR NECROSIS FACTOR-ALPHA
B: TUMOR NECROSIS FACTOR-ALPHA
C: TUMOR NECROSIS FACTOR-ALPHA


Theoretical massNumber of molelcules
Total (without water)52,1903
Polymers52,1903
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7010 Å2
ΔGint-35 kcal/mol
Surface area18070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.000, 166.000, 93.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Atom site foot note1: CIS PROLINE - PRO B 8
2: THR C 7 - PRO C 8 OMEGA =210.32 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: THR D 7 - PRO D 8 OMEGA = 84.95 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

#1: Protein
TUMOR NECROSIS FACTOR-ALPHA


Mass: 17396.781 Da / Num. of mol.: 6 / Mutation: A84V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P01375
Has protein modificationY
Sequence detailsPROTEIN DATA BANK ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY ...PROTEIN DATA BANK ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: TNFA_HUMAN SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE ASP 220 LEU 137

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.57 Å3/Da / Density % sol: 65.53 %

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Processing

Software
NameClassification
SHARPphasing
PROLSQrefinement
RefinementResolution: 3.1→9 Å / σ(F): 3
Details: THE STRUCTURE WAS SOLVED BY MOLECULAR REPLACEMENT (PROGRAM *AMORE*) STARTING FROM THE COORDINATES IN PROTEIN DATA BANK ENTRY 1TNF. ONLY FAINT ELECTRON DENSITY IS OBSERVED FOR RESIDUES 1 - 6 ...Details: THE STRUCTURE WAS SOLVED BY MOLECULAR REPLACEMENT (PROGRAM *AMORE*) STARTING FROM THE COORDINATES IN PROTEIN DATA BANK ENTRY 1TNF. ONLY FAINT ELECTRON DENSITY IS OBSERVED FOR RESIDUES 1 - 6 AT THE N-TERMINUS OF EACH CHAIN AND, THEREFORE, NO COORDINATES FOR THESE RESIDUES ARE PRESENT IN THIS ENTRY. ELECTRON DENSITY FOR THE LOOP 103 - 110 IS ALSO RATHER WEAK IN CHAINS A, B, D, AND F. SEVERE DISTORSIONS ARE ALSO OBSERVED IN THE SEGMENTS 7-9
RfactorNum. reflection
obs0.198 15325
Refinement stepCycle: LAST / Resolution: 3.1→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7086 0 0 0 7086
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.02
X-RAY DIFFRACTIONp_angle_d0.0370.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.070.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.8072
X-RAY DIFFRACTIONp_mcangle_it3.213
X-RAY DIFFRACTIONp_scbond_it1.8372
X-RAY DIFFRACTIONp_scangle_it3.3013
X-RAY DIFFRACTIONp_plane_restr0.0070.01
X-RAY DIFFRACTIONp_chiral_restr0.050.03
X-RAY DIFFRACTIONp_singtor_nbd0.230.3
X-RAY DIFFRACTIONp_multtor_nbd0.290.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.180.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor7.32
X-RAY DIFFRACTIONp_staggered_tor17.710
X-RAY DIFFRACTIONp_orthonormal_tor3110
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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