2TNF

1.4 A RESOLUTION STRUCTURE OF MOUSE TUMOR NECROSIS FACTOR, TOWARDS MODULATION OF ITS SELECTIVITY AND TRIMERISATION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The structure of mouse tumour-necrosis factor at 1.4 A resolution: towards modulation of its selectivity and trimerization.

Baeyens, K.J.De Bondt, H.L.Raeymaekers, A.Fiers, W.De Ranter, C.J.

(1999) Acta Crystallogr.,Sect.D 55: 772-778


  • PubMed Abstract: 
  • The 1.4 A resolution structure of recombinant mouse tumour-necrosis factor alpha (mTNF) at 100 K has been determined. The crystals are triclinic, space group P1, with unit-cell parameters a = 48.06, b = 48.18, c = 51.01 A, alpha = 114.8, beta = 103.6 ...

    The 1.4 A resolution structure of recombinant mouse tumour-necrosis factor alpha (mTNF) at 100 K has been determined. The crystals are triclinic, space group P1, with unit-cell parameters a = 48.06, b = 48.18, c = 51.01 A, alpha = 114.8, beta = 103.6, gamma = 91.1 degrees. The structure was refined to a final crystallographic R value of 19.7% (Rfree = 23.3%), including 3477 protein atoms, one 2-propanol molecule, one Tris molecule and 240 water molecules. Throughout the crystal lattice, the trimers are differently packed compared with human TNF, which was crystallized in the tetragonal space group P41212 and refined to 2.6 A resolution. The structures of mTNF and human TNF are very similar, diverging mainly in regions that are either flexible and/or involved in crystal packing. Some loops in mTNF which contain residues important for receptor binding are better resolved than in human TNF, such as the surface-exposed loops 30-34 and 144-147, which are also important for receptor specificity. Compared with human TNFs, the channel formed by the three monomers in mTNF is narrower. One 2-propanol molecule trapped in the trimeric channel could be a lead compound for the design of TNF inhibitors.


    Related Citations: 
    • Crystal Structure of Tnf-Alpha Mutant R31D with Greater Affinity for Receptor R1 Compared with R2
      Reed, C.,Fu, Z.Q.,Wu, J.,Xue, Y.N.,Harrison, R.W.,Chen, M.J.,Weber, I.T.
      (1997) Protein Eng. 10: 1101
    • The Structure of Tumor Necrosis Factor-Alpha at 2.6 Angstroms Resolution. Implications for Receptor Binding
      Eck, M.J.,Sprang, S.R.
      (1989) J.Biol.Chem. 264: 17595
    • High Resolution Crystal Structure of a Human Tumor Necrosis Factor-Alpha Mutant with Low Systemic Toxicity
      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.
      (1998) J.Biol.Chem. 273: 2153
    • Crystallization and Preliminary X-Ray Studies of Mouse Tumor Necrosis Factor
      Baeyens, K.J.,De Bondt, H.L.,Raeymaekers, A.,De Ranter, C.J.,Fiers, W.
      (1997) Acta Crystallogr.,Sect.D 53: 329
    • Structure of Tumor Necrosis Factor
      Jones, E.Y.,Stuart, D.I.,Walker, N.P.C.
      (1989) Nature 338: 225


    Organizational Affiliation

    Laboratorium voor Analytische Chemie en Medicinale Fysicochemie, E. Van Evenstraat 4, B-3000 Leuven, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (TUMOR NECROSIS FACTOR ALPHA)
A, B, C
156Mus musculusMutation(s): 0 
Gene Names: Tnf (Tnfa, Tnfsf2)
Find proteins for P06804 (Mus musculus)
Go to UniProtKB:  P06804
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IPA
Query on IPA

Download SDF File 
Download CCD File 
B
ISOPROPYL ALCOHOL
2-PROPANOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.201 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 48.214α = 114.81
b = 48.300β = 103.65
c = 51.095γ = 91.05
Software Package:
Software NamePurpose
X-PLORmodel building
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-10-12
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Structure summary