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PDBsum entry 2fjg
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protein ligands Protein-protein interface(s) links
Hormone/growth factor/immune system PDB id
2fjg

 

 

 

 

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Contents
Protein chains
95 a.a. *
211 a.a. *
218 a.a. *
Ligands
SO4 ×7
* Residue conservation analysis
PDB id:
2fjg
Name: Hormone/growth factor/immune system
Title: Structure of the g6 fab, a phage derived fab fragment, in complex with vegf
Structure: Vascular endothelial growth factor a. Chain: v, w. Fragment: receptor binding domain (residues 34-135). Synonym: vegf-a, vascular permeability factor, vpf. Engineered: yes. Fab light chain. Chain: l, a. Engineered: yes. Fab heavy chain.
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dodecamer (from PQS)
Resolution:
2.80Å     R-factor:   0.201     R-free:   0.239
Authors: C.Wiesmann
Key ref:
G.Fuh et al. (2006). Structure-function studies of two synthetic anti-vascular endothelial growth factor Fabs and comparison with the Avastin Fab. J Biol Chem, 281, 6625-6631. PubMed id: 16373345 DOI: 10.1074/jbc.M507783200
Date:
02-Jan-06     Release date:   07-Feb-06    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P15692  (VEGFA_HUMAN) -  Vascular endothelial growth factor A, long form from Homo sapiens
Seq:
Struc: 		395 a.a.
95 a.a.
Protein chains
No UniProt id for this chain
Struc: 211 a.a.
Protein chains
No UniProt id for this chain
Struc: 218 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
DOI no: 10.1074/jbc.M507783200 J Biol Chem 281:6625-6631 (2006)
PubMed id: 16373345  
 
 
Structure-function studies of two synthetic anti-vascular endothelial growth factor Fabs and comparison with the Avastin Fab.
G.Fuh, P.Wu, W.C.Liang, M.Ultsch, C.V.Lee, B.Moffat, C.Wiesmann.
 
  ABSTRACT  
 
In the quest to discover new research tools and to develop better agents in the fight against cancer, two antibodies, G6 and B20-4, were isolated from synthetic antibody phage libraries. Unlike the AVASTINtrade mark antibody, a recently approved agent for the treatment of patients with colorectal cancer, B20-4 and G6 bind and block both human and murine vascular endothelial growth factor (VEGF). Here we have analyzed and compared the binding epitopes on VEGF for these three antibodies using alanine-scanning mutagenesis and structural analyses. The epitopes recognized by both synthetic antibodies are conserved between human and mouse VEGF, and they match closely to the receptor epitopes both structurally and functionally. In contrast, the Avastin epitope overlaps minimally with the receptor binding surface and centers around a residue that is not conserved in mouse. Our structural and functional analyses elucidate the cross-species reactivity of all three antibodies and emphasize the potential advantages of antibody generation using phage display as the resulting antibodies do not depend on sequence differences across species and preferentially target natural protein-protein interaction surfaces.
 
  Selected figure(s)  
 
Figure 4.
FIGURE 4. G6 bound to VEGF (shown in red) and G6 in its unbound form (green) superimposed on a number of Fab fragments in two different views. Shown are B20-4 (yellow), the Avastin-Fab (blue), and 4D5 (Protein Data Bank code 1FVC, in white), which adopt canonical conformations, as well as a selection of Fabs that have non-canonical conformations in CDR-H2 (Protein Data Bank codes 1IND, 1BBJ, 1FIG, 6FAB, all shown in white). Note the significant conformational shift of the G6 CDR-H2 upon VEGF binding. 		Figure 5.
FIGURE 5. Common hot spot of VEGF for binding of VEGFR1, G6, and B20-4. Depicted is the surface of VEGF. All residues that form contacts with VEGFR1, G6, and B20-4 are colored yellow, and all residues that when exchanged to alanine cause a loss in binding affinity of >4-fold in all three complexes are colored red. All residues that differ in the sequence between mouse and human VEGF are green. Only 5 of the 10 residues that differ in the receptor binding domain of human and murine VEGF are labeled; the remaining 5 residues are disordered in the crystal structure of the VEGF or more distant from the binding interface of the molecules investigated here.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 6625-6631) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20454698 B.Guo, Y.Wang, Y.Hui, X.Yang, and Q.Fan (2010).
Effects of anti-VEGF agents on rat retinal Müller glial cells.
  Mol Vis, 16, 793-799.  
19944970 C.W.Kanaly, D.Ding, A.B.Heimberger, and J.H.Sampson (2010).
Clinical applications of a peptide-based vaccine for glioblastoma.
  Neurosurg Clin N Am, 21, 95.  
  20165696 F.G.Blankenberg, Z.Levashova, S.K.Sarkar, J.Pizzonia, M.V.Backer, and J.M.Backer (2010).
Noninvasive assessment of tumor VEGF receptors in response to treatment with pazopanib: a molecular imaging study.
  Transl Oncol, 3, 56-64.  
20424732 I.C.Chen, C.M.Yu, Y.C.Lee, Y.J.Huang, H.J.Hsu, and A.S.Yang (2010).
Signal sequence as a determinant in expressing disulfide-stabilized single chain antibody variable fragments (sc-dsFv) against human VEGF.
  Mol Biosyst, 6, 1307-1315.  
20373131 K.L.Lan, F.Ou-Yang, S.H.Yen, H.L.Shih, and K.H.Lan (2010).
Cationic liposome coupled endostatin gene for treatment of peritoneal colon cancer.
  Clin Exp Metastasis, 27, 307-318.  
20495549 M.Singh, A.Lima, R.Molina, P.Hamilton, A.C.Clermont, V.Devasthali, J.D.Thompson, J.H.Cheng, H.Bou Reslan, C.C.Ho, T.C.Cao, C.V.Lee, M.A.Nannini, G.Fuh, R.A.Carano, H.Koeppen, R.X.Yu, W.F.Forrest, G.D.Plowman, and L.Johnson (2010).
Assessing therapeutic responses in Kras mutant cancers using genetically engineered mouse models.
  Nat Biotechnol, 28, 585-593.  
20501651 S.Iyer, P.I.Darley, and K.R.Acharya (2010).
Structural insights into the binding of vascular endothelial growth factor-B by VEGFR-1(D2): recognition and specificity.
  J Biol Chem, 285, 23779-23789.
PDB code: 2xac
19644699 S.Saati, R.N.Agrawal, S.Louie, G.J.Chader, and M.S.Humayun (2010).
Effect of multiple injections of small divided doses vs single injection of intravitreal bevacizumab on retinal neovascular model in rabbits.
  Graefes Arch Clin Exp Ophthalmol, 248, 457-466.  
20068035 Y.J.Huang, I.C.Chen, C.M.Yu, Y.C.Lee, H.J.Hsu, A.T.Ching, H.J.Chang, and A.S.Yang (2010).
Engineering anti-vascular endothelial growth factor single chain disulfide-stabilized antibody variable fragments (sc-dsFv) with phage-displayed sc-dsFv libraries.
  J Biol Chem, 285, 7880-7891.  
20140208 Y.Yu, P.Lee, Y.Ke, Y.Zhang, Q.Yu, J.Lee, M.Li, J.Song, J.Chen, J.Dai, F.J.Do Couto, Z.An, W.Zhu, and G.L.Yu (2010).
A humanized anti-VEGF rabbit monoclonal antibody inhibits angiogenesis and blocks tumor growth in xenograft models.
  PLoS One, 5, e9072.  
18781316 F.Lu, and R.A.Adelman (2009).
Are intravitreal bevacizumab and ranibizumab effective in a rat model of choroidal neovascularization?
  Graefes Arch Clin Exp Ophthalmol, 247, 171-177.  
19368895 H.J.Chang, H.J.Hsu, C.F.Chang, H.P.Peng, Y.K.Sun, H.M.Yu, H.C.Shih, C.Y.Song, Y.T.Lin, C.C.Chen, C.H.Wang, and A.S.Yang (2009).
Molecular evolution of cystine-stabilized miniproteins as stable proteinaceous binders.
  Structure, 17, 620-631.  
19299620 J.Bostrom, S.F.Yu, D.Kan, B.A.Appleton, C.V.Lee, K.Billeci, W.Man, F.Peale, S.Ross, C.Wiesmann, and G.Fuh (2009).
Variants of the antibody herceptin that interact with HER2 and VEGF at the antigen binding site.
  Science, 323, 1610-1614.
PDB codes: 3bdy 3be1
19296866 L.N.Johnson (2009).
Protein kinase inhibitors: contributions from structure to clinical compounds.
  Q Rev Biophys, 42, 1.  
19409041 T.H.Stollman, M.G.Scheer, G.M.Franssen, K.N.Verrijp, W.J.Oyen, T.J.Ruers, W.P.Leenders, and O.C.Boerman (2009).
Tumor accumulation of radiolabeled bevacizumab due to targeting of cell- and matrix-associated VEGF-A isoforms.
  Cancer Biother Radiopharm, 24, 195-200.  
  19816603 X.Yuan, and K.R.Wilhelmus (2009).
Corneal neovascularization during experimental fungal keratitis.
  Mol Vis, 15, 1988-1996.  
18411193 I.G.Muñoz, F.J.Blanco, and G.Montoya (2008).
On the relevance of defining protein structures in cancer research.
  Clin Transl Oncol, 10, 204-212.  
17475701 A.Iriyama, Y.N.Chen, Y.Tamaki, and Y.Yanagi (2007).
Effect of anti-VEGF antibody on retinal ganglion cells in rats.
  Br J Ophthalmol, 91, 1230-1233.  
17989695 B.A.Appleton, P.Wu, J.Maloney, J.Yin, W.C.Liang, S.Stawicki, K.Mortara, K.K.Bowman, J.M.Elliott, W.Desmarais, J.F.Bazan, A.Bagri, M.Tessier-Lavigne, A.W.Koch, Y.Wu, R.J.Watts, and C.Wiesmann (2007).
Structural studies of neuropilin/antibody complexes provide insights into semaphorin and VEGF binding.
  EMBO J, 26, 4902-4912.
PDB codes: 2qqi 2qqj 2qqk 2qql 2qqm 2qqn 2qqo
17150020 G.Fuh (2007).
Synthetic antibodies as therapeutics.
  Expert Opin Biol Ther, 7, 73-87.  
17360669 H.P.Gerber, X.Wu, L.Yu, C.Wiesmann, X.H.Liang, C.V.Lee, G.Fuh, C.Olsson, L.Damico, D.Xie, Y.G.Meng, J.Gutierrez, R.Corpuz, B.Li, L.Hall, L.Rangell, R.Ferrando, H.Lowman, F.Peale, and N.Ferrara (2007).
Mice expressing a humanized form of VEGF-A may provide insights into the safety and efficacy of anti-VEGF antibodies.
  Proc Natl Acad Sci U S A, 104, 3478-3483.  
17108986 S.S.Sidhu, and F.A.Fellouse (2006).
Synthetic therapeutic antibodies.
  Nat Chem Biol, 2, 682-688.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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