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protein ligands metals Protein-protein interface(s) links
Immune system PDB id
1lp1
Jmol
Contents
Protein chains
55 a.a. *
54 a.a. *
Ligands
SO4 ×4
Metals
_MG
Waters ×182
* Residue conservation analysis
PDB id:
1lp1
Name: Immune system
Title: Protein z in complex with an in vitro selected affibody
Structure: Affibody binding protein z. Chain: a. Fragment: in vitro selected binding protein. Engineered: yes. Immunoglobulin g binding protein a. Chain: b. Fragment: residues 2-58. Engineered: yes. Mutation: yes
Source: Staphylococcus aureus. Organism_taxid: 1280. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
2.30Å     R-factor:   0.224     R-free:   0.256
Authors: M.Hogbom,M.Eklund,P.A.Nygren,P.Nordlund
Key ref:
M.Högbom et al. (2003). Structural basis for recognition by an in vitro evolved affibody. Proc Natl Acad Sci U S A, 100, 3191-3196. PubMed id: 12604795 DOI: 10.1073/pnas.0436100100
Date:
07-May-02     Release date:   18-Mar-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
No UniProt id for this chain
Protein chain
Pfam   ArchSchema ?
P38507  (SPA_STAAU) -  Immunoglobulin G-binding protein A
Seq:
Struc: 		508 a.a.
54 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!
  Biological process     pathogenesis   1 term 
  Biochemical function     protein binding     2 terms  

 

 
DOI no: 10.1073/pnas.0436100100 Proc Natl Acad Sci U S A 100:3191-3196 (2003)
PubMed id: 12604795  
 
 
Structural basis for recognition by an in vitro evolved affibody.
M.Högbom, M.Eklund, P.A.Nygren, P.Nordlund.
 
  ABSTRACT  
 
The broad binding repertoire of antibodies has permitted their use in a wide range of applications. However, some uses of antibodies are precluded due to limitations in the efficiency of antibody generation. In vitro evolved binding proteins, selected from combinatorial libraries generated around various alternative structural scaffolds, are promising alternatives to antibodies. We have solved the crystal structure of a complex of an all alpha-helical in vitro selected binding protein (affibody) bound to protein Z, an IgG Fc-binding domain derived from staphylococcal protein A. The structure of the complex reveals an extended and complementary binding surface with similar properties to protein-antibody interactions. The surface region of protein Z recognized by the affibody is strikingly similar to the one used for IgG(1) Fc binding, suggesting that this surface contains potential hot-spots for binding. The implications of the selected affibody binding-mode for its application as a universal binding protein are discussed.
 
  Selected figure(s)  
 
Figure 1.
Fig 1. Structure of the in vitro evolved complex. (a) Structure of the complex, the Z[SPA-1] affibody in blue and protein Z in green. The ordered sulfate ions with partial occupancy and putative magnesium ion from the mother liquor are also shown; however, they do not seem to influence the interaction surface. (b) Superposition of the two molecules. Notice the shift of helix 1 in the affibody (blue) compared with protein Z (green). (c) Electron density (2 F[obs] - F[calc] map contoured at 1 ) for all 13 mutated residues in the affibody; for clarity, only the electron density around the side chains is displayed. 		Figure 2.
Fig 2. The interaction between protein Z and the Z[SPA-1] affibody. (a) Ligplot (21) representation of the interaction, Z[SPA-1] affibody on the left in blue and protein Z on the right in green. H bonding residues are drawn out, and residues that contribute hydrophobic interactions are indicated. Mutated residues in the affibody are underlined in red. There is one peripheral water molecule (H[2]O77) contributing H bonds to both proteins. (b) Stereo view of the interaction; the Z[SPA-1] affibody helices 1 and 2 over the surface of protein Z. The beginning of helix 1 is indicated. Closely interacting residues are drawn out; nonmutated residues are in brown. A small cavity is shown in yellow; the cavity is very hydrophobic and no electron density is seen inside. (c) The complex is opened up to show the electrostatics of the interaction surface. Red is negative, and blue is positive. Z[SPA-1] affibody is on the left, and protein Z is on the right. The complex is formed by moving the figures together, like closing a book.
 
  Figures were selected by the author.  
 
 
    Author's comment    
 
  This is a structure of an in vitro evolved protein-protein complex. Protein Z has been randomized in 13 positions on one surface, creating a library. Variants that bind to various targets are then selected by phage display techniques. In this case a binder was selected to bind to the original protein Z.
Martin Högbom 		 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19759009 L.Holm, P.Moody, and M.Howarth (2009).
Electrophilic affibodies forming covalent bonds to protein targets.
  J Biol Chem, 284, 32906-32913.  
18435759 P.A.Nygren (2008).
Alternative binding proteins: affibody binding proteins developed from a small three-helix bundle scaffold.
  FEBS J, 275, 2668-2676.  
17373906 V.Tolmachev, A.Orlova, F.Y.Nilsson, J.Feldwisch, A.Wennborg, and L.Abrahmsén (2007).
Affibody molecules: potential for in vivo imaging of molecular targets for cancer therapy.
  Expert Opin Biol Ther, 7, 555-568.  
17550252 Y.Ryabov, and D.Fushman (2007).
Structural assembly of multidomain proteins and protein complexes guided by the overall rotational diffusion tensor.
  J Am Chem Soc, 129, 7894-7902.
PDB codes: 2pe9 2pea
17123658 A.Sergeeva, M.G.Kolonin, J.J.Molldrem, R.Pasqualini, and W.Arap (2006).
Display technologies: application for the discovery of drug and gene delivery agents.
  Adv Drug Deliv Rev, 58, 1622-1654.  
16373474 R.J.Hosse, A.Rothe, and B.E.Power (2006).
A new generation of protein display scaffolds for molecular recognition.
  Protein Sci, 15, 14-27.  
16005204 H.K.Binz, and A.Plückthun (2005).
Engineered proteins as specific binding reagents.
  Curr Opin Biotechnol, 16, 459-469.  
16211069 H.K.Binz, P.Amstutz, and A.Plückthun (2005).
Engineering novel binding proteins from nonimmunoglobulin domains.
  Nat Biotechnol, 23, 1257-1268.  
15880677 T.Engfeldt, B.Renberg, H.Brumer, P.A.Nygren, and A.E.Karlström (2005).
Chemical synthesis of triple-labelled three-helix bundle binding proteins for specific fluorescent detection of unlabelled protein.
  Chembiochem, 6, 1043-1050.  
14718654 D.Zheng, J.M.Aramini, and G.T.Montelione (2004).
Validation of helical tilt angles in the solution NMR structure of the Z domain of Staphylococcal protein A by combined analysis of residual dipolar coupling and NOE data.
  Protein Sci, 13, 549-554.
PDB code: 1q2n
14705019 G.Favrin, A.Irbäck, and S.Wallin (2004).
Sequence-based study of two related proteins with different folding behaviors.
  Proteins, 54, 8.  
15268563 N.Gupta, and A.Irbäck (2004).
Coupled folding-binding versus docking: a lattice model study.
  J Chem Phys, 120, 3983-3989.  
15313246 P.Mathonet, and J.Fastrez (2004).
Engineering of non-natural receptors.
  Curr Opin Struct Biol, 14, 505-511.  
12594333 E.Wahlberg, C.Lendel, M.Helgstrand, P.Allard, V.Dincbas-Renqvist, A.Hedqvist, H.Berglund, P.A.Nygren, and T.Härd (2003).
An affibody in complex with a target protein: structure and coupled folding.
  Proc Natl Acad Sci U S A, 100, 3185-3190.
PDB code: 1h0t
12657734 L.Regan (2003).
Molten globules move into action.
  Proc Natl Acad Sci U S A, 100, 3553-3554.  
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.