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PDBsum entry 3be1
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protein ligands Protein-protein interface(s) links
Transferase PDB id
3be1

 

 

 

 

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JSmol PyMol  
Contents
Protein chains
583 a.a. *
213 a.a. *
216 a.a. *
Ligands
NAG ×2
MES
* Residue conservation analysis
PDB id:
3be1
Name: Transferase
Title: Dual specific bh1 fab in complex with the extracellular domain of her2/erbb-2
Structure: Receptor tyrosine-protein kinase erbb-2. Chain: a. Fragment: sequence database residues 23-646. Synonym: p185erbb2, c-erbb-2, neu proto-oncogene, tyrosine kinase- type cell surface receptor her2, mln 19, cd340 antigen. Engineered: yes. Fab fragment-heavy chain. Chain: h. Engineered: yes.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: erbb2, her2, neu, ngl. Expressed in: cricetulus griseus. Expression_system_taxid: 10029. Expression_system_cell_line: chinese hamster ovary. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.90Å     R-factor:   0.222     R-free:   0.277
Authors: J.M.Bostrom,C.Wiesmann,B.A.Appleton
Key ref:
J.Bostrom et al. (2009). Variants of the antibody herceptin that interact with HER2 and VEGF at the antigen binding site. Science, 323, 1610-1614. PubMed id: 19299620 DOI: 10.1126/science.1165480
Date:
15-Nov-07     Release date:   18-Nov-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P04626  (ERBB2_HUMAN) -  Receptor tyrosine-protein kinase erbB-2 from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		1255 a.a.
583 a.a.
Protein chain
No UniProt id for this chain
Struc: 213 a.a.
Protein chain
No UniProt id for this chain
Struc: 216 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chain A: E.C.2.7.10.1  - receptor protein-tyrosine kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-tyrosyl-[protein] + ATP = O-phospho-L-tyrosyl-[protein] + ADP + H+
L-tyrosyl-[protein]
 + ATP
 = O-phospho-L-tyrosyl-[protein]
Bound ligand (Het Group name = NAG)
matches with 41.38% similarity 		+ ADP
 + H(+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added reference    
 
 
DOI no: 10.1126/science.1165480 Science 323:1610-1614 (2009)
PubMed id: 19299620  
 
 
Variants of the antibody herceptin that interact with HER2 and VEGF at the antigen binding site.
J.Bostrom, S.F.Yu, D.Kan, B.A.Appleton, C.V.Lee, K.Billeci, W.Man, F.Peale, S.Ross, C.Wiesmann, G.Fuh.
 
  ABSTRACT  
 
The interface between antibody and antigen is often depicted as a lock and key, suggesting that an antibody surface can accommodate only one antigen. Here, we describe an antibody with an antigen binding site that binds two distinct proteins with high affinity. We isolated a variant of Herceptin, a therapeutic monoclonal antibody that binds the human epidermal growth factor receptor 2 (HER2), on the basis of its ability to simultaneously interact with vascular endothelial growth factor (VEGF). Crystallographic and mutagenesis studies revealed that distinct amino acids of this antibody, called bH1, engage HER2 and VEGF energetically, but there is extensive overlap between the antibody surface areas contacting the two antigens. An affinity-improved version of bH1 inhibits both HER2- and VEGF-mediated cell proliferation in vitro and tumor progression in mouse models. Such "two-in-one" antibodies challenge the monoclonal antibody paradigm of one binding site, one antigen. They could also provide new opportunities for antibody-based therapy.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. The crystal structures of bH1 Fab bound to HER2 or VEGF. (A) The bH1 Fab (gray)/HER2 (gold) superimposed on to the Herceptin (pink)/HER2 (red) complex (left), and bH1 Fab (light blue)/VEGF (green, teal) complex (right). (B) Fab surface residues are colored according to the extent buried in the complex (red, >75%; orange, >50 to 75%; yellow, >25 to 50%). The underlined amino acids differ between bH1 and Herceptin. The white dotted line separates the LC and HC. (C) Superposition of the CDR loops of VEGF and HER2-bound bH1 (blue, gray) and HER2-bound Herceptin (pink) in the same orientation as in (B). (D) CDR-L1 regions of the two bH1 complexes shown in the same orientation. The residues with temperature factors higher than average are shown in red and orange. VEGF would clash with Tyr32 of bH1 in its HER2-bound conformation. 		Figure 2.
Fig. 2. The distinct interactions of bH1 with HER2 and VEGF. (A) The G values (y axis, kilocalories per mole) of each mutation to alanine (black) or a homologous amino acid (white) for VEGF or HER2 binding based on shotgun scanning mutagenesis (10). The extent of the bH1 residues buried upon VEGF or HER2 complex formation is indicated (single asterisk, >25 to 50% buried; double asterisk, >50 to 75%; triple asterisk, >75%). The dagger symbol represents a lower limit (table S7). (B) The residues that make structural contacts (>25% buried) or energetic interaction ( G > 10% total binding energy) with HER2 (pink), VEGF (green), or both (shared, blue) are mapped on the surface of HER2-bound bH1.
 
  The above figures are reprinted by permission from the AAAs: Science (2009, 323, 1610-1614) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21390033 A.R.Bradbury, S.Sidhu, S.Dübel, and J.McCafferty (2011).
Beyond natural antibodies: the power of in vitro display technologies.
  Nat Biotechnol, 29, 245-254.  
21415364 C.J.Tape, S.H.Willems, S.L.Dombernowsky, P.L.Stanley, M.Fogarasi, W.Ouwehand, J.McCafferty, and G.Murphy (2011).
Cross-domain inhibition of TACE ectodomain.
  Proc Natl Acad Sci U S A, 108, 5578-5583.  
21151137 H.Wang, Z.Y.Li, Y.Liu, J.Persson, I.Beyer, T.Möller, D.Koyuncu, M.R.Drescher, R.Strauss, X.B.Zhang, J.K.Wahl, N.Urban, C.Drescher, A.Hemminki, P.Fender, and A.Lieber (2011).
Desmoglein 2 is a receptor for adenovirus serotypes 3, 7, 11 and 14.
  Nat Med, 17, 96.  
21081901 I.Beyer, Z.Li, J.Persson, Y.Liu, R.van Rensburg, R.Yumul, X.B.Zhang, M.C.Hung, and A.Lieber (2011).
Controlled extracellular matrix degradation in breast cancer tumors improves therapy by trastuzumab.
  Mol Ther, 19, 479-489.  
21227701 T.Kaneko, S.S.Sidhu, and S.S.Li (2011).
Evolving specificity from variability for protein interaction domains.
  Trends Biochem Sci, 36, 183-190.  
20414207 A.Beck, T.Wurch, C.Bailly, and N.Corvaia (2010).
Strategies and challenges for the next generation of therapeutic antibodies.
  Nat Rev Immunol, 10, 345-352.  
20414204 A.C.Chan, and P.J.Carter (2010).
Therapeutic antibodies for autoimmunity and inflammation.
  Nat Rev Immunol, 10, 301-316.  
20882002 A.Plückthun (2010).
HIV: Antibodies with a split personality.
  Nature, 467, 537-538.  
20696930 C.Eigenbrot, M.Ultsch, A.Dubnovitsky, L.Abrahmsén, and T.Härd (2010).
Structural basis for high-affinity HER2 receptor binding by an engineered protein.
  Proc Natl Acad Sci U S A, 107, 15039-15044.
PDB codes: 2kzi 2kzj 3mzw
20199124 D.Müller, and R.E.Kontermann (2010).
Bispecific antibodies for cancer immunotherapy: Current perspectives.
  BioDrugs, 24, 89-98.  
20299542 J.H.Davis, C.Aperlo, Y.Li, E.Kurosawa, Y.Lan, K.M.Lo, and J.S.Huston (2010).
SEEDbodies: fusion proteins based on strand-exchange engineered domain (SEED) CH3 heterodimers in an Fc analogue platform for asymmetric binders or immunofusions and bispecific antibodies.
  Protein Eng Des Sel, 23, 195-202.  
20444694 J.Jackman, Y.Chen, A.Huang, B.Moffat, J.M.Scheer, S.R.Leong, W.P.Lee, J.Zhang, N.Sharma, Y.Lu, S.Iyer, R.L.Shields, N.Chiang, M.C.Bauer, D.Wadley, M.Roose-Girma, R.Vandlen, D.G.Yansura, Y.Wu, and L.C.Wu (2010).
Development of a two-part strategy to identify a therapeutic human bispecific antibody that inhibits IgE receptor signaling.
  J Biol Chem, 285, 20850-20859.  
20669044 L.Gibiansky, and E.Gibiansky (2010).
Target-mediated drug disposition model for drugs that bind to more than one target.
  J Pharmacokinet Pharmacodyn, 37, 323-346.  
20412054 M.Umetsu, T.Nakanishi, R.Asano, T.Hattori, and I.Kumagai (2010).
Protein-protein interactions and selection: generation of molecule-binding proteins on the basis of tertiary structural information.
  FEBS J, 277, 2006-2014.  
20704569 R.Ganesan, C.Eigenbrot, and D.Kirchhofer (2010).
Structural and mechanistic insight into how antibodies inhibit serine proteases.
  Biochem J, 430, 179-189.  
20706783 S.Zahler, J.Liebl, R.Fürst, and A.M.Vollmar (2010).
Anti-angiogenic potential of small molecular inhibitors of cyclin dependent kinases in vitro.
  Angiogenesis, 13, 239-249.  
21149738 V.R.Doppalapudi, J.Huang, D.Liu, P.Jin, B.Liu, L.Li, J.Desharnais, C.Hagen, N.J.Levin, M.J.Shields, M.Parish, R.E.Murphy, J.Del Rosario, B.D.Oates, J.Y.Lai, M.J.Matin, Z.Ainekulu, A.Bhat, C.W.Bradshaw, G.Woodnutt, R.A.Lerner, and R.W.Lappe (2010).
Chemical generation of bispecific antibodies.
  Proc Natl Acad Sci U S A, 107, 22611-22616.  
19497721 A.Lanzavecchia, and F.Sallusto (2009).
Human B cell memory.
  Curr Opin Immunol, 21, 298-304.  
19853060 G.G.Bornstein, S.L.Klakamp, L.Andrews, W.J.Boyle, and M.Tabrizi (2009).
Surrogate approaches in development of monoclonal antibodies.
  Drug Discov Today, 14, 1159-1165.  
20636020 I.G.Valladares, and L.R.Espinoza (2009).
Designing two-in-one antibodies.
  Immunotherapy, 1, 749-751.  
19530116 P.D.Griffiths (2009).
An antibody which behaves like a man with a wife and a mistress.
  Rev Med Virol, 19, 181-183.  
19610073 S.S.Hall, and P.S.Daugherty (2009).
Quantitative specificity-based display library screening identifies determinants of antibody-epitope binding specificity.
  Protein Sci, 18, 1926-1934.  
19711313 T.Winckler (2009).
[In Process Citation]
  Pharm Unserer Zeit, 38, 395-396.  
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 codes are shown on the right.

 

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