[English] 日本語
Yorodumi
- PDB-2tun: CONFORMATIONAL CHANGES IN THE (ALA-84-VAL) MUTANT OF TUMOR NECROS... -

+
Open data


ID or keywords:

Loading...

-
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


negative regulation of L-glutamate import across plasma membrane / negative regulation of bile acid secretion / response to Gram-negative bacterium / positive regulation of neutrophil activation / 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 / positive regulation of fractalkine production / : ...negative regulation of L-glutamate import across plasma membrane / negative regulation of bile acid secretion / response to Gram-negative bacterium / positive regulation of neutrophil activation / 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 / positive regulation of fractalkine production / : / positive regulation of vitamin D biosynthetic process / response to macrophage colony-stimulating factor / positive regulation of leukocyte adhesion to arterial endothelial cell / positive regulation of translational initiation by iron / response to 3,3',5-triiodo-L-thyronine / regulation of membrane lipid metabolic process / regulation of endothelial cell apoptotic process / regulation of branching involved in salivary gland morphogenesis / chronic inflammatory response to antigenic stimulus / negative regulation of protein-containing complex disassembly / response to gold nanoparticle / positive regulation of humoral immune response mediated by circulating immunoglobulin / negative regulation of myosin-light-chain-phosphatase activity / positive regulation of hair follicle development / negative regulation of myelination / death receptor agonist activity / response to isolation stress / negative regulation of vascular wound healing / negative regulation of bicellular tight junction assembly / negative regulation of amyloid-beta clearance / negative regulation of cytokine production involved in immune response / inflammatory response to wounding / cellular response to toxic substance / positive regulation of calcidiol 1-monooxygenase activity / positive regulation of I-kappaB phosphorylation / sequestering of triglyceride / positive regulation of interleukin-18 production / positive regulation of action potential / TNF signaling / positive regulation of protein transport / epithelial cell proliferation involved in salivary gland morphogenesis / toll-like receptor 3 signaling pathway / embryonic digestive tract development / positive regulation of superoxide dismutase activity / leukocyte migration involved in inflammatory response / necroptotic signaling pathway / vascular endothelial growth factor production / positive regulation of calcineurin-NFAT signaling cascade / positive regulation of neuroinflammatory response / leukocyte tethering or rolling / positive regulation of synoviocyte proliferation / response to fructose / positive regulation of fever generation / positive regulation of mononuclear cell migration / negative regulation of myoblast differentiation / negative regulation of glucose import / regulation of establishment of endothelial barrier / endothelial cell apoptotic process / macrophage activation involved in immune response / positive regulation of protein localization to cell surface / TNFR1-mediated ceramide production / negative regulation of oxidative phosphorylation / positive regulation of osteoclast differentiation / positive regulation of cytokine production involved in inflammatory response / tumor necrosis factor receptor binding / negative regulation of systemic arterial blood pressure / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of programmed cell death / regulation of immunoglobulin production / positive regulation of hepatocyte proliferation / positive regulation of heterotypic cell-cell adhesion / positive regulation of protein-containing complex disassembly / positive regulation of podosome assembly / positive regulation of membrane protein ectodomain proteolysis / regulation of canonical NF-kappaB signal transduction / regulation of reactive oxygen species metabolic process / TNFR1-induced proapoptotic signaling / regulation of fat cell differentiation / positive regulation of leukocyte adhesion to vascular endothelial cell / response to L-glutamate / cortical actin cytoskeleton organization / negative regulation of heart rate / positive regulation of amyloid-beta formation / positive regulation of DNA biosynthetic process / negative regulation of viral genome replication / regulation of synapse organization / negative regulation of fat cell differentiation / negative regulation of endothelial cell proliferation / Interleukin-10 signaling / regulation of insulin secretion / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / negative regulation of interleukin-6 production / phagocytic cup / antiviral innate immune response / negative regulation of apoptotic signaling pathway / humoral immune response / negative regulation of blood vessel endothelial cell migration / negative regulation of lipid storage / 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 / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Jelly Rolls - #40 / 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 / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Jelly Rolls - #40 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more