[English] 日本語
Yorodumi
- PDB-2tnf: 1.4 A RESOLUTION STRUCTURE OF MOUSE TUMOR NECROSIS FACTOR, TOWARD... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2tnf
Title1.4 A RESOLUTION STRUCTURE OF MOUSE TUMOR NECROSIS FACTOR, TOWARDS MODULATION OF ITS SELECTIVITY AND TRIMERISATION
ComponentsPROTEIN (TUMOR NECROSIS FACTOR ALPHA)
KeywordsCYTOKINE / LYMPHOKINE / CYTOTOXIN / TRANSMEMBRANE / GLYCOPROTEIN / SIGNAL-ANCHOR
Function / homology
Function and homology information


TNF signaling / TNFR1-mediated ceramide production / TNFR1-induced proapoptotic signaling / positive regulation of amide metabolic process / 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 ...TNF signaling / TNFR1-mediated ceramide production / TNFR1-induced proapoptotic signaling / positive regulation of amide metabolic process / 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 / positive regulation of lipid metabolic process / positive regulation of leukocyte adhesion to arterial endothelial cell / positive regulation of vitamin D biosynthetic process / positive regulation of protein transport / positive regulation of translational initiation by iron / 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 / negative regulation of cytokine production involved in immune response / negative regulation of vascular wound healing / negative regulation of amyloid-beta clearance / inflammatory response to wounding / death receptor agonist activity / 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 / 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 / positive regulation of membrane protein ectodomain proteolysis / positive regulation of podosome assembly / positive regulation of chemokine (C-X-C motif) ligand 2 production / negative regulation of bicellular tight junction assembly / regulation of metabolic process / regulation of reactive oxygen species 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 / 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 / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of osteoblast differentiation / 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 / extracellular matrix organization / antiviral innate immune response / cellular response to ionizing radiation / negative regulation of insulin receptor signaling pathway / regulation of insulin secretion / response to glucocorticoid / osteoclast differentiation / secretory granule / animal organ morphogenesis / positive regulation of interleukin-1 beta production / cytokine activity / protein localization to plasma membrane / positive regulation of interleukin-8 production / positive regulation of protein localization to plasma membrane / cellular response to amino acid stimulus / positive regulation of JNK cascade / phosphatidylinositol 3-kinase/protein kinase B signal transduction / apoptotic signaling pathway / microglial cell activation / positive regulation of non-canonical NF-kappaB signal transduction
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
ISOPROPYL ALCOHOL / Tumor necrosis factor
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsBaeyens, K.J. / De Bondt, H.L. / Raeymaekers, A. / Fiers, W. / De Ranter, C.J.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: The structure of mouse tumour-necrosis factor at 1.4 A resolution: towards modulation of its selectivity and trimerization.
Authors: Baeyens, K.J. / De Bondt, H.L. / Raeymaekers, A. / Fiers, W. / De Ranter, C.J.
#1: Journal: J.Biol.Chem. / Year: 1998
Title: High Resolution Crystal Structure of a Human Tumor Necrosis Factor-Alpha Mutant with Low Systemic Toxicity
Authors: Cha, S.-S. / Kim, J.-S. / Cho, H.-S. / Shin, N.-K. / Jeong, W. / Shin, H.-C. / Kim, Y.J. / Hahn, J.H. / Oh, B.-H.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Crystallization and Preliminary X-Ray Studies of Mouse Tumor Necrosis Factor
Authors: Baeyens, K.J. / De Bondt, H.L. / Raeymaekers, A. / De Ranter, C.J. / Fiers, W.
#3: 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.
#4: 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.
#5: Journal: Nature / Year: 1989
Title: Structure of Tumor Necrosis Factor
Authors: Jones, E.Y. / Stuart, D.I. / Walker, N.P.C.
History
DepositionOct 12, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 12, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (TUMOR NECROSIS FACTOR ALPHA)
B: PROTEIN (TUMOR NECROSIS FACTOR ALPHA)
C: PROTEIN (TUMOR NECROSIS FACTOR ALPHA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0005
Polymers51,8173
Non-polymers1822
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6320 Å2
ΔGint-26 kcal/mol
Surface area18960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.214, 48.300, 51.095
Angle α, β, γ (deg.)114.81, 103.65, 91.05
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein PROTEIN (TUMOR NECROSIS FACTOR ALPHA) / TNF-ALPHA / CACHECTIN


Mass: 17272.494 Da / Num. of mol.: 3 / Fragment: RESIDUES 80-235
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P06804
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.4 %
Crystal growpH: 8.5
Details: EQUAL VOLUMES OF RESERVOIR SOLUTION, CONTAINING 7 % ISOPROP, pH 8.5
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 277 K / pH: 6.8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17 %2-propanol1reservoir
230 %PEGME20001reservoir
30.1 MTris-HCl1reservoir
40.5 %1dropNaCl
511 mg/mlprotain1drop
610 mMHEPES1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 1.1024
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1997 / Details: RHODIUM COATED PRE-MIRROR, SEGMENTED MIRROR
RadiationMonochromator: BENT SINGLE-CRYSTAL GERMANIUM TRIANGULAR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1024 Å / Relative weight: 1
ReflectionResolution: 1.4→20 Å / Num. obs: 72552 / % possible obs: 90.9 % / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.029 / Net I/σ(I): 19
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.148 / Mean I/σ(I) obs: 5.7 / % possible all: 85.5
Reflection
*PLUS
Num. measured all: 128698
Reflection shell
*PLUS
% possible obs: 85.5 %

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.843refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TNF

1tnf


Resolution: 1.4→8 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.235 6871 10.1 %RANDOM
Rwork0.201 ---
obs0.201 67767 85.8 %-
Displacement parametersBiso mean: 19.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3477 0 8 244 3729
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.39
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.481.5
X-RAY DIFFRACTIONx_mcangle_it2.592
X-RAY DIFFRACTIONx_scbond_it1.982
X-RAY DIFFRACTIONx_scangle_it2.992.5
LS refinement shellResolution: 1.4→1.49 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.274 962 10 %
Rwork0.264 8666 -
obs--73 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH11.WAT
X-RAY DIFFRACTION3IPA.PARIPA.TOP
X-RAY DIFFRACTION4TRS.PARTRS.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 10.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 19.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.39
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.274 / % reflection Rfree: 10 % / Rfactor Rwork: 0.264

+
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://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