PDBsum entry 1a8m

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protein Protein-protein interface(s) links
Lymphokine PDB id
Protein chains
152 a.a. *
Waters ×69
* Residue conservation analysis
PDB id:
Name: Lymphokine
Title: Tumor necrosis factor alpha, r31d mutant
Structure: Tumor necrosis factor alpha. Chain: a, b, c. Synonym: tnf-alpha. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Trimer (from PDB file)
2.30Å     R-factor:   0.218     R-free:   0.240
Authors: C.Reed,Z.-Q.Fu,J.Wu,Y.-N.Xue,R.W.Harrison,M.-J.Chen, I.T.Weber
Key ref: C.Reed et al. (1997). Crystal structure of TNF-alpha mutant R31D with greater affinity for receptor R1 compared with R2. Protein Eng, 10, 1101-1107. PubMed id: 9488135
27-Mar-98     Release date:   17-Jun-98    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P01375  (TNFA_HUMAN) -  Tumor necrosis factor
233 a.a.
152 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   1 term 
  Biological process     immune response   1 term 
  Biochemical function     tumor necrosis factor receptor binding     1 term  


Protein Eng 10:1101-1107 (1997)
PubMed id: 9488135  
Crystal structure of TNF-alpha mutant R31D with greater affinity for receptor R1 compared with R2.
C.Reed, Z.Q.Fu, J.Wu, Y.N.Xue, R.W.Harrison, M.J.Chen, I.T.Weber.
Crystal structures have been determined of recombinant human tumor necrosis factor-alpha (TNF-alpha) and its R31D mutant that preferentially binds to TNF receptor R1 with more than seven times the relative affinity of binding to receptor R2. Crystals of the wild-type TNF were of space group P4(1)2(1)2 and had unit cell dimensions of a = b = 94.7 and c = 117.4 A. Refinement of the structure gave an R-factor of 22.3% at 2.5 A resolution. The crystals of TNF R31D mutant diffracted to 2.3 A resolution, and were of identical space group to the wild type with unit cell dimensions of a = b = 95.4 and c = 116.2 A, and the structure was refined to an R-factor of 21.8%. The trimer structures of the wild-type and mutant TNF were similar with a root mean square (r.m.s.) deviation of 0.56 A for Calpha atoms; however, the subunits within each trimer were more variable with an average r.m.s. deviation of 1.00 A on Calpha atoms for pairwise comparison of subunits. Model complexes of TNF with receptors R1 and R2 have been used to predict TNF-receptor interactions. Arg31 in all three subunits of wild-type TNF is predicted to form an ionic interaction with the equivalent glutamic acid in both receptors R1 and R2. Asp31 of the TNF R31D mutant is predicted to interact differently with the two receptors. The side chain of Asp31 in two subunits of the TNF mutant is predicted to form hydrogen bond interactions with Ser59 or Cys70 of R1, while it has no predicted interactions with R2. The loss of three strong ionic interactions of Arg31 and the electrostatic repulsion of Asp31 with Glu in the receptors is consistent with the reduced binding of the R31D mutant to both receptors relative to wild-type TNF. The replacement of these ionic interactions by two weaker hydrogen bond interactions between Asp31 of the R31D mutant and R1, compared with no interactions with R2, is in agreement with the observed preferential binding of the R31D mutant to R1 over R2. Analysis of the structure and function of receptor-discriminating mutants of TNF will help understand the biological role of TNF and facilitate its use as an antitumor agent.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20111721 J.Dong, Y.Gao, Y.Liu, J.Shi, J.Feng, Z.Li, H.Pan, Y.Xue, C.Liu, B.Shen, N.Shao, and G.Yang (2010).
The protective antibodies induced by a novel epitope of human TNF-alpha could suppress the development of collagen-induced arthritis.
  PLoS One, 5, e8920.  
20303167 S.Yachamaneni, G.Yushin, S.H.Yeon, Y.Gogotsi, C.Howell, S.Sandeman, G.Phillips, and S.Mikhalovsky (2010).
Mesoporous carbide-derived carbon for cytokine removal from blood plasma.
  Biomaterials, 31, 4789-4794.  
20140191 T.Yang, Z.Wang, F.Wu, J.Tan, Y.Shen, E.Li, J.Dai, R.Shen, G.Li, J.Wu, L.Wang, H.Wang, and Y.Liu (2010).
A variant of TNFR2-Fc fusion protein exhibits improved efficacy in treating experimental rheumatoid arthritis.
  PLoS Comput Biol, 6, e1000669.  
  19255488 Y.Mukai, T.Nakamura, Y.Yoshioka, S.Tsunoda, H.Kamada, S.Nakagawa, Y.Yamagata, and Y.Tsutsumi (2009).
Crystallization and preliminary X-ray analysis of the tumour necrosis factor alpha-tumour necrosis factor receptor type 2 complex.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 295-298.  
16806458 C.A.Howell, S.R.Sandeman, G.J.Phillips, A.W.Lloyd, J.G.Davies, S.V.Mikhalovsky, S.R.Tennison, A.P.Rawlinson, O.P.Kozynchenko, H.L.Owen, J.D.Gaylor, J.J.Rouse, and J.M.Courtney (2006).
The in vitro adsorption of cytokines by polymer-pyrolysed carbon.
  Biomaterials, 27, 5286-5291.  
16914195 G.Yushin, E.N.Hoffman, M.W.Barsoum, Y.Gogotsi, C.A.Howell, S.R.Sandeman, G.J.Phillips, A.W.Lloyd, and S.V.Mikhalovsky (2006).
Mesoporous carbide-derived carbon with porosity tuned for efficient adsorption of cytokines.
  Biomaterials, 27, 5755-5762.  
15981250 A.Berchanski, D.Segal, and M.Eisenstein (2005).
Modeling oligomers with Cn or Dn symmetry: application to CAPRI target 10.
  Proteins, 60, 202-206.  
11679718 J.M.Petock, I.Y.Torshin, Y.F.Wang, G.C.Du Bois, C.M.Croce, R.W.Harrison, and I.T.Weber (2001).
Structure of murine Tcl1 at 2.5 A resolution and implications for the TCL oncogene family.
  Acta Crystallogr D Biol Crystallogr, 57, 1545-1551.
PDB code: 1jnp
10891884 H.T.Idriss, and J.H.Naismith (2000).
TNF alpha and the TNF receptor superfamily: structure-function relationship(s).
  Microsc Res Tech, 50, 184-195.  
10089307 K.J.Baeyens, H.L.De Bondt, A.Raeymaekers, W.Fiers, and C.J.De Ranter (1999).
The structure of mouse tumour-necrosis factor at 1.4 A resolution: towards modulation of its selectivity and trimerization.
  Acta Crystallogr D Biol Crystallogr, 55, 772-778.
PDB code: 2tnf
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