PDBsum entry 2b2x

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protein metals Protein-protein interface(s) links
Immune system PDB id
Protein chains
188 a.a. *
210 a.a. *
210 a.a. *
176 a.a. *
_MG ×2
Waters ×226
* Residue conservation analysis
PDB id:
Name: Immune system
Title: Vla1 rdeltah i-domain complexed with a quadruple mutant of t fab
Structure: Integrin alpha-1. Chain: a, b. Fragment: i domain r delta h. Synonym: laminin and collagen receptor, vla-1, cd49a. Engineered: yes. Mutation: yes. Antibody aqc2 fab. Chain: h, i. Fragment: aqc2 fab heavy chain.
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116. Gene: itga1. Expressed in: escherichia coli. Expression_system_taxid: 562. Mus musculus. House mouse. Organism_taxid: 10090.
Biol. unit: Trimer (from PQS)
2.20Å     R-factor:   0.241     R-free:   0.272
Authors: L.A.Clark,P.A.Boriack-Sjodin,J.Eldredge,C.Fitch,B.Friedman,K M.Jarpe,S.F.Liparoto,Y.Li,A.Lugovskoy
Key ref:
L.A.Clark et al. (2006). Affinity enhancement of an in vivo matured therapeutic antibody using structure-based computational design. Protein Sci, 15, 949-960. PubMed id: 16597831 DOI: 10.1110/ps.052030506
19-Sep-05     Release date:   18-Apr-06    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P18614  (ITA1_RAT) -  Integrin alpha-1
1180 a.a.
188 a.a.*
Protein chains
No UniProt id for this chain
Struc: 210 a.a.
Protein chains
No UniProt id for this chain
Struc: 210 a.a.
Protein chain
Pfam   ArchSchema ?
P18614  (ITA1_RAT) -  Integrin alpha-1
1180 a.a.
176 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 8 residue positions (black crosses)


DOI no: 10.1110/ps.052030506 Protein Sci 15:949-960 (2006)
PubMed id: 16597831  
Affinity enhancement of an in vivo matured therapeutic antibody using structure-based computational design.
L.A.Clark, P.A.Boriack-Sjodin, J.Eldredge, C.Fitch, B.Friedman, K.J.Hanf, M.Jarpe, S.F.Liparoto, Y.Li, A.Lugovskoy, S.Miller, M.Rushe, W.Sherman, K.Simon, H.Van Vlijmen.
Improving the affinity of a high-affinity protein-protein interaction is a challenging problem that has practical applications in the development of therapeutic biomolecules. We used a combination of structure-based computational methods to optimize the binding affinity of an antibody fragment to the I-domain of the integrin VLA1. Despite the already high affinity of the antibody (Kd approximately 7 nM) and the moderate resolution (2.8 A) of the starting crystal structure, the affinity was increased by an order of magnitude primarily through a decrease in the dissociation rate. We determined the crystal structure of a high-affinity quadruple mutant complex at 2.2 A. The structure shows that the design makes the predicted contacts. Structural evidence and mutagenesis experiments that probe a hydrogen bond network illustrate the importance of satisfying hydrogen bonding requirements while seeking higher-affinity mutations. The large and diverse set of interface mutations allowed refinement of the mutant binding affinity prediction protocol and improvement of the single-mutant success rate. Our results indicate that structure-based computational design can be successfully applied to further improve the binding of high-affinity antibodies.
  Selected figure(s)  
Figure 3.
Visualization of the quadruple mutant crystal structure (dark gray) near side chain repacking mutants. (A) Comparison to the predicted structure (light gray) in the vicinity of the S28Q mutation in the light chain. The predicted structure forms a similar stacking-like interaction between Tyr264 on antigen and the glutamine. The electron density (2F[o] [minus sign] F[c], [sigma] = 1.1) indicates that the tyrosine has swung inward toward the bulk of the antigen. (B) Comparison of the wild-type (light gray) and quadruple mutant crystal (dark gray) structures in the vicinity of the N52Y mutation in the light chain.
Figure 5.
Comparison of the wild-type (light gray) and quadruple mutant (dark gray) crystal structures in the vicinity of the H:T50V mutation. The wild-type threonine hydrogen bonds with the tryptophan. When substituted with a valine, the local environment rearranges to eliminate an unsatisfied hydrogen bond.
  The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (2006, 15, 949-960) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21365678 O.Sharabi, A.Dekel, and J.M.Shifman (2011).
Triathlon for energy functions: Who is the winner for design of protein-protein interactions?
  Proteins, 79, 1487-1498.  
20007707 B.Li, L.Zhao, C.Wang, H.Guo, L.Wu, X.Zhang, W.Qian, H.Wang, and Y.Guo (2010).
The protein-protein interface evolution acts in a similar way to antibody affinity maturation.
  J Biol Chem, 285, 3865-3871.  
20847101 R.J.Pantazes, and C.D.Maranas (2010).
OptCDR: a general computational method for the design of antibody complementarity determining regions for targeted epitope binding.
  Protein Eng Des Sel, 23, 849-858.  
19458157 A.Sircar, E.T.Kim, and J.J.Gray (2009).
RosettaAntibody: antibody variable region homology modeling server.
  Nucleic Acids Res, 37, W474-W479.  
19062174 A.Sivasubramanian, A.Sircar, S.Chaudhury, and J.J.Gray (2009).
Toward high-resolution homology modeling of antibody Fv regions and application to antibody-antigen docking.
  Proteins, 74, 497-514.  
19477127 C.J.Farady, B.D.Sellers, M.P.Jacobson, and C.S.Craik (2009).
Improving the species cross-reactivity of an antibody using computational design.
  Bioorg Med Chem Lett, 19, 3744-3747.  
18767161 J.N.Haidar, B.Pierce, Y.Yu, W.Tong, M.Li, and Z.Weng (2009).
Structure-based design of a T-cell receptor leads to nearly 100-fold improvement in binding affinity for pepMHC.
  Proteins, 74, 948-960.  
19074157 L.A.Clark, P.A.Boriack-Sjodin, E.Day, J.Eldredge, C.Fitch, M.Jarpe, S.Miller, Y.Li, K.Simon, and H.W.van Vlijmen (2009).
An antibody loop replacement design feasibility study and a loop-swapped dimer structure.
  Protein Eng Des Sel, 22, 93.
PDB code: 3eot
19643977 O.Sharabi, Y.Peleg, E.Mashiach, E.Vardy, Y.Ashani, I.Silman, J.L.Sussman, and J.M.Shifman (2009).
Design, expression and characterization of mutants of fasciculin optimized for interaction with its target, acetylcholinesterase.
  Protein Eng Des Sel, 22, 641-648.  
17671962 A.Sivasubramanian, J.A.Maynard, and J.J.Gray (2008).
Modeling the structure of mAb 14B7 bound to the anthrax protective antigen.
  Proteins, 70, 218-230.  
18514737 F.E.Boas, and P.B.Harbury (2008).
Design of protein-ligand binding based on the molecular-mechanics energy model.
  J Mol Biol, 380, 415-424.  
17910054 L.A.Clark, and H.W.van Vlijmen (2008).
A knowledge-based forcefield for protein-protein interface design.
  Proteins, 70, 1540-1550.  
18574150 R.Barderas, J.Desmet, P.Timmerman, R.Meloen, and J.I.Casal (2008).
Affinity maturation of antibodies assisted by in silico modeling.
  Proc Natl Acad Sci U S A, 105, 9029-9034.  
18275813 S.Li, P.Kussie, and K.M.Ferguson (2008).
Structural basis for EGF receptor inhibition by the therapeutic antibody IMC-11F8.
  Structure, 16, 216-227.
PDB codes: 3b2u 3b2v
18384529 W.Sherman, and B.Tidor (2008).
Novel method for probing the specificity binding profile of ligands: applications to HIV protease.
  Chem Biol Drug Des, 71, 387-407.  
17895381 A.S.Gardberg, L.T.Dice, S.Ou, R.L.Rich, E.Helmbrecht, J.Ko, R.Wetzel, D.G.Myszka, P.H.Patterson, and C.Dealwis (2007).
Molecular basis for passive immunotherapy of Alzheimer's disease.
  Proc Natl Acad Sci U S A, 104, 15659-15664.
PDB codes: 2ipt 2ipu 2iq9 2iqa 2r0w 2r0z
17603074 D.W.Sammond, Z.M.Eletr, C.Purbeck, R.J.Kimple, D.P.Siderovski, and B.Kuhlman (2007).
Structure-based protocol for identifying mutations that enhance protein-protein binding affinities.
  J Mol Biol, 371, 1392-1404.
PDB code: 2om2
17387014 F.E.Boas, and P.B.Harbury (2007).
Potential energy functions for protein design.
  Curr Opin Struct Biol, 17, 199-204.  
18074396 R.L.Rich, and D.G.Myszka (2007).
Survey of the year 2006 commercial optical biosensor literature.
  J Mol Recognit, 20, 300-366.  
17644370 S.M.Lippow, and B.Tidor (2007).
Progress in computational protein design.
  Curr Opin Biotechnol, 18, 305-311.  
17891135 S.M.Lippow, K.D.Wittrup, and B.Tidor (2007).
Computational design of antibody-affinity improvement beyond in vivo maturation.
  Nat Biotechnol, 25, 1171-1176.  
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.