spacer
spacer

PDBsum entry 1nbv

Go to PDB code: 
protein Protein-protein interface(s) links
Immunoglobulin PDB id
1nbv

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chains
219 a.a.
219 a.a. *
* Residue conservation analysis
PDB id:
1nbv
Name: Immunoglobulin
Title: An autoantibody to single-stranded dna: comparison of the three- dimensional structures of the unliganded fab and a deoxynucleotide- fab complex
Structure: Igg2b-kappa bv04-01 fab (light chain). Chain: l. Engineered: yes. Igg2b-kappa bv04-01 fab (heavy chain). Chain: h. Engineered: yes
Source: Mus musculus. House mouse. Organism_taxid: 10090. Organism_taxid: 10090
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.246    
Authors: J.N.Herron,X.M.He,A.B.Edmundson
Key ref: J.N.Herron et al. (1991). An autoantibody to single-stranded DNA: comparison of the three-dimensional structures of the unliganded Fab and a deoxynucleotide-Fab complex. Proteins, 11, 159-175. PubMed id: 1749770
Date:
16-Mar-93     Release date:   31-Jan-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
A2NHM3  (A2NHM3_MOUSE) -  If kappa light chain (Fragment) from Mus musculus
Seq:
Struc:
219 a.a.
219 a.a.*
Protein chain
Pfam   ArchSchema ?
P01867  (IGG2B_MOUSE) -  Immunoglobulin heavy constant gamma 2B from Mus musculus
Seq:
Struc:
 
Seq:
Struc:
404 a.a.
219 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 11 residue positions (black crosses)

 

 
Proteins 11:159-175 (1991)
PubMed id: 1749770  
 
 
An autoantibody to single-stranded DNA: comparison of the three-dimensional structures of the unliganded Fab and a deoxynucleotide-Fab complex.
J.N.Herron, X.M.He, D.W.Ballard, P.R.Blier, P.E.Pace, A.L.Bothwell, E.W.Voss, A.B.Edmundson.
 
  ABSTRACT  
 
Crystal structures of the Fabs from an autoantibody (BV04-01) with specificity for single-stranded DNA have been determined in the presence and absence of a trinucleotide of deoxythymidylic acid, d(pT)3. Formation of the ligand-protein complex was accompanied by small adjustments in the orientations of the variable (VL and VH) domains. In addition, there were local conformational changes in the first hypervariable loop of the light chain and the third hypervariable loop of the heavy chain, which together with the domain shifts led to an improvement in the complementarity of nucleotide and Fab. The sugar-phosphate chain adopted an extended and "open" conformation, with the base, sugar, and phosphate components available for interactions with the protein. Nucleotide 1 (5'-end) was associated exclusively with the heavy chain, nucleotide 2 was shared by both heavy and light chains, and nucleotide 3 was bound by the light chain. The orientation of phosphate 1 was stabilized by hydrogen bonds with serine H52a and asparagine H53. Phosphate 2 formed an ion pair with arginine H52, but no other charge-charge interactions were observed. Insertion of the side chain of histidine L27d between nucleotides 2 and 3 resulted in a bend in the sugar-phosphate chain. The most dominant contacts with the protein involved the central thymine base, which was immobilized by cooperative stacking and hydrogen bonding interactions. This base was intercalated between a tryptophan ring (no. H100a) from the heavy chain and a tyrosine ring (no. L32) from the light chain. The resulting orientation of thymine was favorable for the simultaneous formation of two hydrogen bonds with the backbone carbonyl oxygen and the side chain hydroxyl group of serine L91 (the thymine atoms were the hydrogen on nitrogen 3 and keto oxygen 4).
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21173256 H.N.Eisen, and A.K.Chakraborty (2010).
Evolving concepts of specificity in immune reactions.
  Proc Natl Acad Sci U S A, 107, 22373-22380.  
20591902 K.R.Abhinandan, and A.C.Martin (2010).
Analysis and prediction of VH/VL packing in antibodies.
  Protein Eng Des Sel, 23, 689-697.  
19274732 K.L.Longenecker, Q.Ruan, E.H.Fry, S.C.Saldana, S.E.Brophy, P.L.Richardson, and S.Y.Tetin (2009).
Crystal structure and thermodynamic analysis of diagnostic mAb 106.3 complexed with BNP 5-13 (C10A).
  Proteins, 76, 536-547.
PDB code: 3e8u
19699528 S.Chang, L.Yang, Y.M.Moon, Y.G.Cho, S.Y.Min, T.J.Kim, Y.J.Kim, W.Patrick, H.Y.Kim, and C.Mohan (2009).
Anti-nuclear antibody reactivity in lupus may be partly hard-wired into the primary B-cell repertoire.
  Mol Immunol, 46, 3420-3426.  
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
19556006 Z.Liang, S.Chang, M.S.Youn, and C.Mohan (2009).
Molecular hallmarks of anti-chromatin antibodies associated with the lupus susceptibility locus, Sle1.
  Mol Immunol, 46, 2671-2681.  
17252586 M.J.Bobeck, and G.D.Glick (2007).
Role of conformational dynamics in sequence-specific autoantibody*ssDNA recognition.
  Biopolymers, 85, 481-489.  
18028946 Z.Ou, C.A.Bottoms, M.T.Henzl, and J.J.Tanner (2007).
Impact of DNA hairpin folding energetics on antibody-ssDNA association.
  J Mol Biol, 374, 1029-1040.
PDB code: 2fr4
16649995 K.Masuda, K.Sakamoto, M.Kojima, T.Aburatani, T.Ueda, and H.Ueda (2006).
The role of interface framework residues in determining antibody V(H)/V(L) interaction strength and antigen-binding affinity.
  FEBS J, 273, 2184-2194.  
16251186 M.J.Clément, A.Fortuné, A.Phalipon, V.Marcel-Peyre, C.Simenel, A.Imberty, M.Delepierre, and L.A.Mulard (2006).
Toward a better understanding of the basis of the molecular mimicry of polysaccharide antigens by peptides: the example of Shigella flexneri 5a.
  J Biol Chem, 281, 2317-2332.  
16551636 Y.R.Kim, J.S.Kim, S.H.Lee, W.R.Lee, J.N.Sohn, Y.C.Chung, H.K.Shim, S.C.Lee, M.H.Kwon, and Y.S.Kim (2006).
Heavy and light chain variable single domains of an anti-DNA binding antibody hydrolyze both double- and single-stranded DNAs without sequence specificity.
  J Biol Chem, 281, 15287-15295.
PDB code: 2gki
15993037 S.Y.Lim, and S.K.Ghosh (2005).
Autoreactive responses to environmental factors: 3. Mouse strain-specific differences in induction and regulation of anti-DNA antibody responses due to phthalate-isomers.
  J Autoimmun, 25, 33-45.  
14699083 E.Meffre, A.Schaefer, H.Wardemann, P.Wilson, E.Davis, and M.C.Nussenzweig (2004).
Surrogate light chain expressing human peripheral B cells produce self-reactive antibodies.
  J Exp Med, 199, 145-150.  
15557264 H.Jin, J.Sepúlveda, and O.R.Burrone (2004).
Specific recognition of a dsDNA sequence motif by an immunoglobulin VH homodimer.
  Protein Sci, 13, 3222-3229.  
15340914 J.P.Schuermann, M.T.Henzl, S.L.Deutscher, and J.J.Tanner (2004).
Structure of an anti-DNA fab complexed with a non-DNA ligand provides insights into cross-reactivity and molecular mimicry.
  Proteins, 57, 269-278.
PDB code: 1p7k
15096189 S.Y.Lim, and S.K.Ghosh (2004).
Autoreactive responses to an environmental factor. 2. Phthalate-induced anti-DNA specificity is downregulated by autoreactive cytotoxic T cells.
  Immunology, 112, 94.  
14757744 Z.Liang, C.Xie, C.Chen, D.Kreska, K.Hsu, L.Li, X.J.Zhou, and C.Mohan (2004).
Pathogenic profiles and molecular signatures of antinuclear autoantibodies rescued from NZM2410 lupus mice.
  J Exp Med, 199, 381-398.  
12851924 F.E.Romesberg (2003).
Multidisciplinary experimental approaches to characterizing biomolecular dynamics.
  Chembiochem, 4, 563-571.  
12610286 J.Foote (2003).
Immunology. Isomeric antibodies.
  Science, 299, 1327-1328.  
14632646 S.Y.Lim, and S.K.Ghosh (2003).
Autoreactive responses to an environmental factor: 1. phthalate induces antibodies exhibiting anti-DNA specificity.
  Immunology, 110, 482-492.  
12447899 A.B.Edmundson, and A.B.Edmundson (2002).
Reminiscences: joyous moments along the road from here to there and back again.
  J Mol Recognit, 15, 227-239.  
12447907 B.L.Hanson, G.J.Bunick, J.M.Harp, and A.B.Edmundson (2002).
Mcg in 2030: new techniques for atomic position determination of immune complexes.
  J Mol Recognit, 15, 297-305.  
11598879 B.Piekarska, L.Konieczny, J.Rybarska, B.Stopa, G.Zemanek, E.Szneler, M.Król, M.Nowak, and I.Roterman (2001).
Heat-induced formation of a specific binding site for self-assembled Congo Red in the V domain of immunoglobulin L chain lambda.
  Biopolymers, 59, 446-456.  
11410373 D.J.Tantillo, and K.N.Houk (2001).
Canonical binding arrays as molecular recognition elements in the immune system: tetrahedral anions and the ester hydrolysis transition state.
  Chem Biol, 8, 535-545.  
11134947 E.O.Saphire, P.W.Parren, C.F.Barbas, D.R.Burton, and I.A.Wilson (2001).
Crystallization and preliminary structure determination of an intact human immunoglobulin, b12: an antibody that broadly neutralizes primary isolates of HIV-1.
  Acta Crystallogr D Biol Crystallogr, 57, 168-171.  
10903952 E.J.Sundberg, and R.A.Mariuzza (2000).
Luxury accommodations: the expanding role of structural plasticity in protein-protein interactions.
  Structure, 8, R137-R142.  
10944338 S.P.Prewitt, A.A.Komissarov, S.L.Deutscher, and J.J.Tanner (2000).
Crystallization and molecular-replacement studies of a recombinant antigen-binding fragment complexed with single-stranded DNA.
  Acta Crystallogr D Biol Crystallogr, 56, 1007-1011.  
10648787 T.Torizawa, N.Yamamoto, T.Suzuki, K.Nobuoka, Y.Komatsu, H.Morioka, O.Nikaido, E.Ohtsuka, K.Kato, and I.Shimada (2000).
DNA binding mode of the Fab fragment of a monoclonal antibody specific for cyclobutane pyrimidine dimer.
  Nucleic Acids Res, 28, 944-951.  
10074464 C.Oefner, A.Binggeli, V.Breu, D.Bur, J.P.Clozel, A.D'Arcy, A.Dorn, W.Fischli, F.Grüninger, R.Güller, G.Hirth, H.Märki, S.Mathews, M.M ller, R.G.Ridley, H.Stadler, E.Vieira, M.Wilhelm, F.Winkler, and W.Wostl (1999).
Renin inhibition by substituted piperidines: a novel paradigm for the inhibition of monomeric aspartic proteinases?
  Chem Biol, 6, 127-131.
PDB codes: 1pr7 1pr8
10488102 H.Kondo, M.Shiroishi, M.Matsushima, K.Tsumoto, and I.Kumagai (1999).
Crystal structure of anti-Hen egg white lysozyme antibody (HyHEL-10) Fv-antigen complex. Local structural changes in the protein antigen and water-mediated interactions of Fv-antigen and light chain-heavy chain interfaces.
  J Biol Chem, 274, 27623-27631.
PDB code: 1c08
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.  
9880525 J.van den Elsen, L.Vandeputte-Rutten, J.Kroon, and P.Gros (1999).
Bactericidal antibody recognition of meningococcal PorA by induced fit. Comparison of liganded and unliganded Fab structures.
  J Biol Chem, 274, 1495-1501.
PDB code: 1mnu
10511458 N.B.Blatt, and G.D.Glick (1999).
Anti-DNA autoantibodies and systemic lupus erythematosus.
  Pharmacol Ther, 83, 125-139.  
10440996 P.A.Ramsland, B.F.Movafagh, M.Reichlin, and A.B.Edmundson (1999).
Interference of rheumatoid factor activity by aspartame, a dipeptide methyl ester.
  J Mol Recognit, 12, 249-257.  
  10593256 S.Kumar, B.Ma, C.J.Tsai, H.Wolfson, and R.Nussinov (1999).
Folding funnels and conformational transitions via hinge-bending motions.
  Cell Biochem Biophys, 31, 141-164.  
10398393 Z.C.Fan, L.Shan, B.Z.Goldsteen, L.W.Guddat, A.Thakur, N.F.Landolfi, M.S.Co, M.Vasquez, C.Queen, P.A.Ramsland, and A.B.Edmundson (1999).
Comparison of the three-dimensional structures of a humanized and a chimeric Fab of an anti-gamma-interferon antibody.
  J Mol Recognit, 12, 19-32.
PDB codes: 1b2w 1b4j
9806374 A.Rahman, D.S.Latchman, and D.A.Isenberg (1998).
The role of in vitro expression systems in the investigation of antibodies to DNA.
  Semin Arthritis Rheum, 28, 130-139.  
  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.  
9463398 M.A.Holmes, T.N.Buss, and J.Foote (1998).
Conformational correction mechanisms aiding antigen recognition by a humanized antibody.
  J Exp Med, 187, 479-485.
PDB code: 1bvk
9738009 S.Vasudevan, T.Tsuruo, and D.R.Rose (1998).
Mode of binding of anti-P-glycoprotein antibody MRK-16 to its antigen. A crystallographic and molecular modeling study.
  J Biol Chem, 273, 25413-25419.
PDB code: 1bln
9341118 A.A.Komissarov, M.T.Marchbank, M.J.Calcutt, T.P.Quinn, and S.L.Deutscher (1997).
Site-specific mutagenesis of a recombinant anti-single-stranded DNA Fab. Role of heavy chain complementarity-determining region 3 residues in antigen interaction.
  J Biol Chem, 272, 26864-26870.  
9186637 B.D.Stollar, J.M.Lecerf, and Y.Hirabayashi (1997).
The role of autoreactivity in B cell selection.
  Ann N Y Acad Sci, 815, 30-39.  
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
9060442 J.Tanha, and J.S.Lee (1997).
Thermodynamic analysis of monoclonal antibody binding to duplex DNA.
  Nucleic Acids Res, 25, 1442-1449.  
  9194175 L.W.Guddat, J.C.Bardwell, T.Zander, and J.L.Martin (1997).
The uncharged surface features surrounding the active site of Escherichia coli DsbA are conserved and are implicated in peptide binding.
  Protein Sci, 6, 1148-1156.  
  9444478 P.A.Bullock (1997).
The initiation of simian virus 40 DNA replication in vitro.
  Crit Rev Biochem Mol Biol, 32, 503-568.  
9380513 Y.Komatsu, T.Tsujino, T.Suzuki, O.Nikaido, and E.Ohtsuka (1997).
Antigen structural requirements for recognition by a cyclobutane thymine dimer-specific monoclonal antibody.
  Nucleic Acids Res, 25, 3889-3894.  
8647821 A.A.Komissarov, M.J.Calcutt, M.T.Marchbank, E.N.Peletskaya, and S.L.Deutsher (1996).
Equilibrium binding studies of recombinant anti-single-stranded DNA Fab. Role of heavy chain complementarity-determining regions.
  J Biol Chem, 271, 12241-12246.  
8601641 P.C.Swanson, R.L.Yung, N.B.Blatt, M.A.Eagan, J.M.Norris, B.C.Richardson, K.J.Johnson, and G.D.Glick (1996).
Ligand recognition by murine anti-DNA autoantibodies. II. Genetic analysis and pathogenicity.
  J Clin Invest, 97, 1748-1760.  
8621386 W.D.Mallender, J.Carrero, and E.W.Voss (1996).
Comparative properties of the single chain antibody and Fv derivatives of mAb 4-4-20. Relationship between interdomain interactions and the high affinity for fluorescein ligand.
  J Biol Chem, 271, 5338-5346.  
  7796805 C.Chen, V.A.Roberts, S.Stevens, M.Brown, M.P.Stenzel-Poore, and M.B.Rittenberg (1995).
Enhancement and destruction of antibody function by somatic mutation: unequal occurrence is controlled by V gene combinatorial associations.
  EMBO J, 14, 2784-2794.  
7621866 M.Herrmann, T.H.Winkler, H.Fehr, and J.R.Kalden (1995).
Preferential recognition of specific DNA motifs by anti-double-stranded DNA autoantibodies.
  Eur J Immunol, 25, 1897-1904.  
7944344 A.G.Gabibov, G.V.Gololobov, O.I.Makarevich, D.V.Schourov, E.A.Chernova, and R.P.Yadav (1994).
DNA-hydrolyzing autoantibodies.
  Appl Biochem Biotechnol, 47, 293.  
7908437 C.Eigenbrot, T.Gonzalez, J.Mayeda, P.Carter, W.Werther, T.Hotaling, J.Fox, and J.Kessler (1994).
X-ray structures of fragments from binding and nonbinding versions of a humanized anti-CD18 antibody: structural indications of the key role of VH residues 59 to 65.
  Proteins, 18, 49-62.
PDB codes: 1fgv 2fgw
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.  
8064241 J.B.Katz, W.Limpanasithikul, and B.Diamond (1994).
Mutational analysis of an autoantibody: differential binding and pathogenicity.
  J Exp Med, 180, 925-932.  
7937957 J.Foote, and C.Milstein (1994).
Conformational isomerism and the diversity of antibodies.
  Proc Natl Acad Sci U S A, 91, 10370-10374.  
7696460 J.N.Herron, A.H.Terry, S.Johnston, X.M.He, L.W.Guddat, E.W.Voss, and A.B.Edmundson (1994).
High resolution structures of the 4-4-20 Fab-fluorescein complex in two solvent systems: effects of solvent on structure and antigen-binding affinity.
  Biophys J, 67, 2167-2183.  
  7849585 P.M.Colman (1994).
Influenza virus neuraminidase: structure, antibodies, and inhibitors.
  Protein Sci, 3, 1687-1696.  
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.  
7775808 T.Kieber-Emmons, M.H.Foster, W.V.Williams, and M.P.Madaio (1994).
Structural properties of a subset of nephritogenic anti-DNA antibodies.
  Immunol Res, 13, 172-185.  
8302837 T.N.Bhat, G.A.Bentley, G.Boulot, M.I.Greene, D.Tello, W.Dall'Acqua, H.Souchon, F.P.Schwarz, R.A.Mariuzza, and R.J.Poljak (1994).
Bound water molecules and conformational stabilization help mediate an antigen-antibody association.
  Proc Natl Acad Sci U S A, 91, 1089-1093.
PDB codes: 1vfa 1vfb
8346191 A.B.Edmundson, D.L.Harris, Z.C.Fan, L.W.Guddat, B.T.Schley, B.L.Hanson, G.Tribbick, and H.M.Geysen (1993).
Principles and pitfalls in designing site-directed peptide ligands.
  Proteins, 16, 246-267.
PDB codes: 1mcb 1mcc 1mcd 1mce 1mcf 1mch 1mci 1mcj 1mck 1mcl 1mcn 1mcq 1mcr 1mcs
8305251 E.W.Voss (1993).
Kinetic measurements of molecular interactions by spectrofluorometry.
  J Mol Recognit, 6, 51-58.  
  7690222 I.Fliss, M.St Laurent, E.Emond, R.Lemieux, R.E.Simard, A.Ettriki, and S.Pandian (1993).
Production and characterization of anti-DNA-RNA monoclonal antibodies and their application in Listeria detection.
  Appl Environ Microbiol, 59, 2698-2705.  
8483943 L.W.Guddat, J.N.Herron, and A.B.Edmundson (1993).
Three-dimensional structure of a human immunoglobulin with a hinge deletion.
  Proc Natl Acad Sci U S A, 90, 4271-4275.
PDB code: 1mco
8460105 O.Vix, B.Rees, J.C.Thierry, and D.Altschuh (1993).
Crystallographic analysis of the interaction between cyclosporin A and the Fab fragment of a monoclonal antibody.
  Proteins, 15, 339-348.  
8069628 R.L.Stanfield, M.Takimoto-Kamimura, J.M.Rini, A.T.Profy, and I.A.Wilson (1993).
Major antigen-induced domain rearrangements in an antibody.
  Structure, 1, 83-93.
PDB codes: 1ggb 1ggc
1427920 A.K.Stewart, C.Huang, A.A.Long, B.D.Stollar, and R.S.Schwartz (1992).
VH-gene representation in autoantibodies reflects the normal human B-cell repertoire.
  Immunol Rev, 128, 101-122.  
1512540 D.M.Tillman, N.T.Jou, R.J.Hill, and T.N.Marion (1992).
Both IgM and IgG anti-DNA antibodies are the products of clonally selective B cell stimulation in (NZB x NZW)F1 mice.
  J Exp Med, 176, 761-779.  
15335962 D.R.Davies, and E.A.Padlan (1992).
Twisting into shape.
  Curr Biol, 2, 254-256.  
1496010 X.M.He, F.Rüker, E.Casale, and D.C.Carter (1992).
Structure of a human monoclonal antibody Fab fragment against gp41 of human immunodeficiency virus type 1.
  Proc Natl Acad Sci U S A, 89, 7154-7158.
PDB code: 1dfb
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.

 

spacer

spacer