spacer
spacer

PDBsum entry 1ifh
Go to PDB code: 
protein ligands Protein-protein interface(s) links
Immunoglobulin PDB id
1ifh

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chains
218 a.a. *
220 a.a. *
Ligands
ACE-ASP-VAL-PRO-
ASP-TYR-ALA-SER
Waters ×1
* Residue conservation analysis
PDB id:
1ifh
Name: Immunoglobulin
Title: A detailed analysis of the free and bound conformation of an antibody: x-ray structures of anti-peptide fab 17(slash)9 and three different fab-peptide complexes
Structure: Igg2a-kappa 17/9 fab (light chain). Chain: l. Engineered: yes. Igg2a-kappa 17/9 fab (heavy chain). Chain: h. Engineered: yes. Influenza hemagglutinin ha1 (strain x47) (residues 101- 107). Chain: p.
Source: Mus musculus. House mouse. Organism_taxid: 10090. Strain: a/j.
Biol. unit: Dimer (from PQS)
Resolution:
2.80Å     R-factor:   0.170    
Authors: U.Schulze-Gahmen,I.A.Wilson
Key ref: U.Schulze-Gahmen et al. (1993). Detailed analysis of the free and bound conformations of an antibody. X-ray structures of Fab 17/9 and three different Fab-peptide complexes. J Mol Biol, 234, 1098-1118. PubMed id: 8263915
Date:
06-May-93     Release date:   31-Oct-93    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
No UniProt id for this chain
Struc: 218 a.a.
Protein chain
No UniProt id for this chain
Struc: 220 a.a.
Key:    Secondary structure  CATH domain

 

 
J Mol Biol 234:1098-1118 (1993)
PubMed id: 8263915  
 
 
Detailed analysis of the free and bound conformations of an antibody. X-ray structures of Fab 17/9 and three different Fab-peptide complexes.
U.Schulze-Gahmen, J.M.Rini, I.A.Wilson.
 
  ABSTRACT  
 
A new orthorhombic crystal form of Fab 17/9 has been determined in complex with a 7-mer peptide from influenza virus hemagglutinin (HA1 101-107, acetylated and amidated). The three-dimensional structure was resolved to 2.8 A with an improved refinement and better geometry than two previously determined Fab 17/9-peptide (HA1 100-108) complexes, facilitating a detailed description of the Fab-peptide interactions. The binding pockets and the peptide antigen are structurally similar in all three peptide complexes of Fab 17/9. The peptide adopts an extended conformation (residues 100 to 103) and a type I reverse turn (residues 104 to 107). Additionally, the antigenic determinant described here correlates well with previous epitope mapping studies. The structures of the free and antigen bound Fab illustrate the role of induced fit as a mechanism for antibody-antigen recognition. Fab 17/9 undergoes a large conformational change, mainly in the H3 loop, upon peptide binding. As a result, the shape of the binding pocket changes substantially in the liganded Fab. However, the backbone conformations of the other hypervariable loops (L2, L3, H1 and H2) show no significant difference between free and bound structures. The conformation of the L1 loop is also maintained in all structures, but its position relative to the framework varies in different crystal environments. The availability of three X-ray structures of an Fab-peptide complex in three different space groups makes it possible to clearly distinguish between crystal packing and antigen binding as the cause of structural differences. Two distinct H3-loop conformations, free and bound, are observed with no evidence otherwise for multiple conformations of the hypervariable loops (CDRs) or increased flexibility in either the free or bound forms.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19519742 D.J.Kao, and R.S.Hodges (2009).
Advantages of a synthetic peptide immunogen over a protein immunogen in the development of an anti-pilus vaccine for Pseudomonas aeruginosa.
  Chem Biol Drug Des, 74, 33-42.  
19036813 R.Pantophlet, M.Wang, R.O.Aguilar-Sino, and D.R.Burton (2009).
The human immunodeficiency virus type 1 envelope spike of primary viruses can suppress antibody access to variable regions.
  J Virol, 83, 1649-1659.  
19690368 S.Pletnev, K.S.Morozova, V.V.Verkhusha, and Z.Dauter (2009).
Rotational order-disorder structure of fluorescent protein FP480.
  Acta Crystallogr D Biol Crystallogr, 65, 906-912.
PDB codes: 3h1o 3h1r
19901987 W.Farrugia, A.M.Scott, and P.A.Ramsland (2009).
A possible role for metallic ions in the carbohydrate cluster recognition displayed by a lewis y specific antibody.
  PLoS One, 4, e7777.
PDB code: 3eyv
18566514 A.K.Dhillon, R.L.Stanfield, M.K.Gorny, C.Williams, S.Zolla-Pazner, and I.A.Wilson (2008).
Structure determination of an anti-HIV-1 Fab 447-52D-peptide complex from an epitaxially twinned data set.
  Acta Crystallogr D Biol Crystallogr, 64, 792-802.
PDB code: 3c2a
17292640 A.Erazo, N.Kutchukhidze, M.Leung, A.P.Christ, J.F.Urban, M.A.Curotto de Lafaille, and J.J.Lafaille (2007).
Unique maturation program of the IgE response in vivo.
  Immunity, 26, 191-203.  
17996091 B.D.Silverman (2007).
Using molecular principal axes for structural comparison: determining the tertiary changes of a FAB antibody domain induced by antigenic binding.
  BMC Struct Biol, 7, 77.  
17177888 B.Piekarska, A.Drozd, L.Konieczny, M.Król, W.Jurkowski, I.Roterman, P.Spólnik, B.Stopa, and J.Rybarska (2006).
The indirect generation of long-distance structural changes in antibodies upon their binding to antigen.
  Chem Biol Drug Des, 68, 276-283.  
16195545 A.Honegger, S.Spinelli, C.Cambillau, and A.Plückthun (2005).
A mutation designed to alter crystal packing permits structural analysis of a tight-binding fluorescein-scFv complex.
  Protein Sci, 14, 2537-2549.
PDB codes: 2a9m 2a9n
15485827 J.C.Peter, G.Wallukat, J.Tugler, D.Maurice, J.C.Roegel, J.P.Briand, and J.Hoebeke (2004).
Modulation of the M2 muscarinic acetylcholine receptor activity with monoclonal anti-M2 receptor antibody fragments.
  J Biol Chem, 279, 55697-55706.  
12851924 F.E.Romesberg (2003).
Multidisciplinary experimental approaches to characterizing biomolecular dynamics.
  Chembiochem, 4, 563-571.  
12657787 L.O.Essen, A.Harrenga, C.Ostermeier, and H.Michel (2003).
1.3 A X-ray structure of an antibody Fv fragment used for induced membrane-protein crystallization.
  Acta Crystallogr D Biol Crystallogr, 59, 677-687.
PDB code: 1mqk
12767122 M.Król, I.Roterman, B.Piekarska, L.Konieczny, J.Rybarska, and B.Stopa (2003).
Local and long-range structural effects caused by the removal of the N-terminal polypeptide fragment from immunoglobulin L chain lambda.
  Biopolymers, 69, 189-200.  
12767116 P.J.Cachia, and R.S.Hodges (2003).
Synthetic peptide vaccine and antibody therapeutic development: prevention and treatment of Pseudomonas aeruginosa.
  Biopolymers, 71, 141-168.  
14581222 S.Mohan, N.Sinha, and S.J.Smith-Gill (2003).
Modeling the binding sites of anti-hen egg white lysozyme antibodies HyHEL-8 and HyHEL-26: an insight into the molecular basis of antibody cross-reactivity and specificity.
  Biophys J, 85, 3221-3236.  
12784217 V.Hornak, and C.Simmerling (2003).
Generation of accurate protein loop conformations through low-barrier molecular dynamics.
  Proteins, 51, 577-590.  
11134506 L.Jermutus, A.Honegger, F.Schwesinger, J.Hanes, and A.Plückthun (2001).
Tailoring in vitro evolution for protein affinity or stability.
  Proc Natl Acad Sci U S A, 98, 75-80.  
11101301 A.P.Campbell, W.Y.Wong, R.T.Irvin, and B.D.Sykes (2000).
Interaction of a bacterially expressed peptide from the receptor binding domain of Pseudomonas aeruginosa pili strain PAK with a cross-reactive antibody: conformation of the bound peptide.
  Biochemistry, 39, 14847-14864.  
10500196 J.J.Boniface, Z.Reich, D.S.Lyons, and M.M.Davis (1999).
Thermodynamics of T cell receptor binding to peptide-MHC: evidence for a general mechanism of molecular scanning.
  Proc Natl Acad Sci U S A, 96, 11446-11451.  
10440998 J.L.Pellequer, S.Chen, V.A.Roberts, J.A.Tainer, and E.D.Getzoff (1999).
Unraveling the effect of changes in conformation and compactness at the antibody V(L)-V(H) interface upon antigen binding.
  J Mol Recognit, 12, 267-275.  
10508241 J.L.Torán, L.Kremer, L.Sánchez-Pulido, I.M.de Alborán, G.del Real, M.Llorente, A.Valencia, M.A.de Mon, and C.Martínez-A (1999).
Molecular analysis of HIV-1 gp120 antibody response using isotype IgM and IgG phage display libraries from a long-term non-progressor HIV-1-infected individual.
  Eur J Immunol, 29, 2666-2675.  
10090739 L.Choulier, N.Rauffer-Bruyère, M.Ben Khalifa, F.Martin, T.Vernet, and D.Altschuh (1999).
Kinetic analysis of the effect on Fab binding of identical substitutions in a peptide and its parent protein.
  Biochemistry, 38, 3530-3537.  
10092651 T.Kieber-Emmons, C.Lin, M.H.Foster, and T.R.Kleyman (1999).
Antiidiotypic antibody recognizes an amiloride binding domain within the alpha subunit of the epithelial Na+ channel.
  J Biol Chem, 274, 9648-9655.  
9565600 A.Rodríguez-Romero, O.Almog, M.Tordova, Z.Randhawa, and G.L.Gilliland (1998).
Primary and tertiary structures of the Fab fragment of a monoclonal anti-E-selectin 7A9 antibody that inhibits neutrophil attachment to endothelial cells.
  J Biol Chem, 273, 11770-11775.
PDB code: 1a5f
  10082364 C.L.Casipit, R.Tal, V.Wittman, P.A.Chavaillaz, K.Arbuthnott, J.A.Weidanz, J.A.Jiao, and H.C.Wong (1998).
Improving the binding affinity of an antibody using molecular modeling and site-directed mutagenesis.
  Protein Sci, 7, 1671-1680.  
9261086 C.H.Trinh, S.D.Hemmington, M.E.Verhoeyen, and S.E.Phillips (1997).
Antibody fragment Fv4155 bound to two closely related steroid hormones: the structural basis of fine specificity.
  Structure, 5, 937-948.
PDB codes: 1bfv 1cfv 2bfv
  9300494 J.A.Hubbard, D.P.Raleigh, J.R.Bonnerjea, and C.M.Dobson (1997).
Identification of the epitopes of calcitonin gene-related peptide (CGRP) for two anti-CGRP monoclonal antibodies by 2D NMR.
  Protein Sci, 6, 1945-1952.  
9144168 J.Hanes, and A.Plückthun (1997).
In vitro selection and evolution of functional proteins by using ribosome display.
  Proc Natl Acad Sci U S A, 94, 4937-4942.  
9035111 L.A.Ryabova, D.Desplancq, A.S.Spirin, and A.Plückthun (1997).
Functional antibody production using cell-free translation: effects of protein disulfide isomerase and chaperones.
  Nat Biotechnol, 15, 79-84.  
9012674 M.R.Sawaya, and J.Kraut (1997).
Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: crystallographic evidence.
  Biochemistry, 36, 586-603.
PDB codes: 1dre 1ra1 1ra2 1ra3 1ra8 1ra9 1rb2 1rb3 1rc4 1rd7 1re7 1rf7 1rg7 1rh3 1rx1 1rx2 1rx3 1rx4 1rx5 1rx6 1rx7 1rx8 1rx9
9413990 T.Keitel, A.Kramer, H.Wessner, C.Scholz, J.Schneider-Mergener, and W.Höhne (1997).
Crystallographic analysis of anti-p24 (HIV-1) monoclonal antibody cross-reactivity and polyspecificity.
  Cell, 91, 811-820.
PDB codes: 1bog 1cfn 1cfq 1cfs 1cft 1hi6
7718744 C.Pinilla, J.Appel, S.Blondelle, C.Dooley, B.Dörner, J.Eichler, J.Ostresh, and R.A.Houghten (1995).
A review of the utility of soluble peptide combinatorial libraries.
  Biopolymers, 37, 221-240.  
7836460 R.Kodandapani, B.Veerapandian, T.J.Kunicki, and K.R.Ely (1995).
Crystal structure of the OPG2 Fab. An antireceptor antibody that mimics an RGD cell adhesion site.
  J Biol Chem, 270, 2268-2273.
PDB code: 1opg
7773739 R.L.Stanfield, and I.A.Wilson (1995).
Protein-peptide interactions.
  Curr Opin Struct Biol, 5, 103-113.  
7536111 I.A.Wilson, and R.L.Stanfield (1994).
Antibody-antigen interactions: new structures and new conformational changes.
  Curr Opin Struct Biol, 4, 857-867.  
7765075 R.L.Stanfield, and I.A.Wilson (1994).
Antigen-induced conformational changes in antibodies: a problem for structural prediction and design.
  Trends Biotechnol, 12, 275-279.  
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.

 

spacer
spacer