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PDBsum entry 1bzq

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protein ligands Protein-protein interface(s) links
Hydrolase/immune system PDB id
1bzq
Jmol
Contents
Protein chains
124 a.a. *
124 a.a. *
Ligands
PO4 ×4
* Residue conservation analysis
PDB id:
1bzq
Name: Hydrolase/immune system
Title: Complex of a dromedary single-domain vhh antibody fragment with rnase a
Structure: Protein (rnase a). Chain: a, b, c, d. Protein (antibody cab-rn05). Chain: k, l, m, n. Fragment: variable domain. Engineered: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organ: pancreas. Other_details: rnase a supplied by sigma. Camelus dromedarius. Arabian camel. Organism_taxid: 9838. Cell: b-lymphocytes.
Biol. unit: Octamer (from PQS)
Resolution:
2.80Å     R-factor:   0.222     R-free:   0.282
Authors: K.Decanniere,A.Desmyter,M.Gahroudhi,M.Lauwereys, S.Muyldermans,L.Wyns
Key ref:
K.Decanniere et al. (1999). A single-domain antibody fragment in complex with RNase A: non-canonical loop structures and nanomolar affinity using two CDR loops. Structure, 7, 361-370. PubMed id: 10196124 DOI: 10.1016/S0969-2126(99)80049-5
Date:
03-Nov-98     Release date:   11-Nov-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P61823  (RNAS1_BOVIN) -  Ribonuclease pancreatic
Seq:
Struc:
150 a.a.
124 a.a.
Protein chains
No UniProt id for this chain
Struc: 124 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D: E.C.3.1.27.5  - Pancreatic ribonuclease.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides ending in C-P or U-P with 2',3'-cyclic phosphate intermediates.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     metabolic process   3 terms 
  Biochemical function     nucleic acid binding     7 terms  

 

 
DOI no: 10.1016/S0969-2126(99)80049-5 Structure 7:361-370 (1999)
PubMed id: 10196124  
 
 
A single-domain antibody fragment in complex with RNase A: non-canonical loop structures and nanomolar affinity using two CDR loops.
K.Decanniere, A.Desmyter, M.Lauwereys, M.A.Ghahroudi, S.Muyldermans, L.Wyns.
 
  ABSTRACT  
 
BACKGROUND: Camelid serum contains a large fraction of functional heavy-chain antibodies - homodimers of heavy chains without light chains. The variable domains of these heavy-chain antibodies (VHH) have a long complementarity determining region 3 (CDR3) loop that compensates for the absence of the antigen-binding loops of the variable light chains (VL). In the case of the VHH fragment cAb-Lys3, part of the 24 amino acid long CDR3 loop protrudes from the antigen-binding surface and inserts into the active-site cleft of its antigen, rendering cAb-Lys3 a competitive enzyme inhibitor. RESULTS: A dromedary VHH with specificity for bovine RNase A, cAb-RN05, has a short CDR3 loop of 12 amino acids and is not a competitive enzyme inhibitor. The structure of the cAb-RN05-RNase A complex has been solved at 2.8 A. The VHH scaffold architecture is close to that of a human VH (variable heavy chain). The structure of the antigen-binding hypervariable 1 loop (H1) of both cAb-RN05 and cAb-Lys3 differ from the known canonical structures; in addition these H1 loops resemble each other. The CDR3 provides an antigen-binding surface and shields the face of the domain that interacts with VL in conventional antibodies. CONCLUSIONS: VHHs adopt the common immunoglobulin fold of variable domains, but the antigen-binding loops deviate from the predicted canonical structure. We define a new canonical structure for the H1 loop of immunoglobulins, with cAb-RN05 and cAb-Lys3 as reference structures. This new loop structure might also occur in human or mouse VH domains. Surprisingly, only two loops are involved in antigen recognition; the CDR2 does not participate. Nevertheless, the antigen binding occurs with nanomolar affinities because of a preferential usage of mainchain atoms for antigen interaction.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Stereoview of the overlap of non-bulged torso CDR3 reference structure (PDB entry code 1flr [32], in blue) and the CDR3 of cAb-RN05 (yellow). Only the backbone atoms are shown for clarity. The hydrogen-bonding pattern of the reference structure is indicated by dotted lines. The position of amino acid residues 92, 97, 99 and 104 are indicated for reference. The figure was generated with SETOR [41].
 
  The above figure is reprinted by permission from Cell Press: Structure (1999, 7, 361-370) copyright 1999.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21244216 F.Rahbarizadeh, D.Ahmadvand, and Z.Sharifzadeh (2011).
Nanobody; an old concept and new vehicle for immunotargeting.
  Immunol Invest, 40, 299-338.  
21151117 Y.Koldobskaya, E.M.Duguid, D.M.Shechner, N.B.Suslov, J.Ye, S.S.Sidhu, D.P.Bartel, S.Koide, A.A.Kossiakoff, and J.A.Piccirilli (2011).
A portable RNA sequence whose recognition by a synthetic antibody facilitates structural determination.
  Nat Struct Mol Biol, 18, 100-106.  
20140750 A.Van den Abbeele, S.De Clercq, A.De Ganck, V.De Corte, B.Van Loo, S.H.Soror, V.Srinivasan, J.Steyaert, J.Vandekerckhove, and J.Gettemans (2010).
A llama-derived gelsolin single-domain antibody blocks gelsolin-G-actin interaction.
  Cell Mol Life Sci, 67, 1519-1535.
PDB codes: 2x1o 2x1p 2x1q
19955323 L.P.Daley, M.A.Kutzler, B.W.Bennett, M.C.Smith, A.L.Glaser, and J.A.Appleton (2010).
Effector functions of camelid heavy-chain antibodies in immunity to West Nile virus.
  Clin Vaccine Immunol, 17, 239-246.  
20945358 M.H.Kubala, O.Kovtun, K.Alexandrov, and B.M.Collins (2010).
Structural and thermodynamic analysis of the GFP:GFP-nanobody complex.
  Protein Sci, 19, 2389-2401.
PDB code: 3ogo
20044483 T.Hattori, M.Umetsu, T.Nakanishi, T.Togashi, N.Yokoo, H.Abe, S.Ohara, T.Adschiri, and I.Kumagai (2010).
High affinity anti-inorganic material antibody generation by integrating graft and evolution technologies: potential of antibodies as biointerface molecules.
  J Biol Chem, 285, 7784-7793.  
19010777 C.Vincke, R.Loris, D.Saerens, S.Martinez-Rodriguez, S.Muyldermans, and K.Conrath (2009).
General Strategy to Humanize a Camelid Single-domain Antibody and Identification of a Universal Humanized Nanobody Scaffold.
  J Biol Chem, 284, 3273-3284.
PDB codes: 3dwt 3eak 3eba
  19241371 K.Conrath, A.S.Pereira, C.E.Martins, C.G.Timóteo, P.Tavares, S.Spinelli, J.Kinne, C.Flaudrops, C.Cambillau, S.Muyldermans, I.Moura, J.J.Moura, M.Tegoni, and A.Desmyter (2009).
Camelid nanobodies raised against an integral membrane enzyme, nitric oxide reductase.
  Protein Sci, 18, 619-628.  
19033278 M.Arbabi-Ghahroudi, R.To, N.Gaudette, T.Hirama, W.Ding, R.MacKenzie, and J.Tanha (2009).
Aggregation-resistant VHs selected by in vitro evolution tend to have disulfide-bonded loops and acidic isoelectric points.
  Protein Eng Des Sel, 22, 59-66.  
19089973 N.Wang, W.F.Smith, B.R.Miller, D.Aivazian, A.A.Lugovskoy, M.E.Reff, S.M.Glaser, L.J.Croner, and S.J.Demarest (2009).
Conserved amino acid networks involved in antibody variable domain interactions.
  Proteins, 76, 99.  
17932913 D.P.Simmons, V.A.Streltsov, O.Dolezal, P.J.Hudson, A.M.Coley, M.Foley, D.F.Proll, and S.D.Nuttall (2008).
Shark IgNAR antibody mimotopes target a murine immunoglobulin through extended CDR3 loop structures.
  Proteins, 71, 119-130.
PDB codes: 2ywy 2ywz
18045863 P.A.Barthelemy, H.Raab, B.A.Appleton, C.J.Bond, P.Wu, C.Wiesmann, and S.S.Sidhu (2008).
Comprehensive Analysis of the Factors Contributing to the Stability and Solubility of Autonomous Human VH Domains.
  J Biol Chem, 283, 3639-3654.
PDB code: 3b9v
18445622 V.Tereshko, S.Uysal, A.Koide, K.Margalef, S.Koide, and A.A.Kossiakoff (2008).
Toward chaperone-assisted crystallography: protein engineering enhancement of crystal packing and X-ray phasing capabilities of a camelid single-domain antibody (VHH) scaffold.
  Protein Sci, 17, 1175-1187.
PDB codes: 2p42 2p43 2p44 2p45 2p46 2p47 2p48
17420456 A.Koide, R.N.Gilbreth, K.Esaki, V.Tereshko, and S.Koide (2007).
High-affinity single-domain binding proteins with a binary-code interface.
  Proc Natl Acad Sci U S A, 104, 6632-6637.
PDB code: 2obg
17888451 A.Koide, V.Tereshko, S.Uysal, K.Margalef, A.A.Kossiakoff, and S.Koide (2007).
Exploring the capacity of minimalist protein interfaces: interface energetics and affinity maturation to picomolar KD of a single-domain antibody with a flat paratope.
  J Mol Biol, 373, 941-953.
PDB codes: 2p49 2p4a
17322532 C.A.Olson, and R.W.Roberts (2007).
Design, expression, and stability of a diverse protein library based on the human fibronectin type III domain.
  Protein Sci, 16, 476-484.  
17256770 V.Lafont, M.Schaefer, R.H.Stote, D.Altschuh, and A.Dejaegere (2007).
Protein-protein recognition and interaction hot spots in an antigen-antibody complex: free energy decomposition identifies "efficient amino acids".
  Proteins, 67, 418-434.  
15659390 E.De Genst, K.Silence, M.A.Ghahroudi, K.Decanniere, R.Loris, J.Kinne, L.Wyns, and S.Muyldermans (2005).
Strong in vivo maturation compensates for structurally restricted H3 loops in antibody repertoires.
  J Biol Chem, 280, 14114-14121.
PDB codes: 1ri8 1rjc
15709914 H.Revets, P.De Baetselier, and S.Muyldermans (2005).
Nanobodies as novel agents for cancer therapy.
  Expert Opin Biol Ther, 5, 111-124.  
16408159 M.Arbabi-Ghahroudi, J.Tanha, and R.MacKenzie (2005).
Prokaryotic expression of antibodies.
  Cancer Metastasis Rev, 24, 501-519.  
15378291 V.Joosten, R.J.Gouka, C.A.van den Hondel, C.T.Verrips, and B.C.Lokman (2005).
Expression and production of llama variable heavy-chain antibody fragments (V(HH)s) by Aspergillus awamori.
  Appl Microbiol Biotechnol, 66, 384-392.  
15130125 E.Veiga, V.de Lorenzo, and L.A.Fernández (2004).
Structural tolerance of bacterial autotransporters for folded passenger protein domains.
  Mol Microbiol, 52, 1069-1080.  
15319492 R.L.Stanfield, H.Dooley, M.F.Flajnik, and I.A.Wilson (2004).
Crystal structure of a shark single-domain antibody V region in complex with lysozyme.
  Science, 305, 1770-1773.
PDB codes: 1sq2 1t6v
12533537 J.Lah, I.Marianovsky, G.Glaser, H.Engelberg-Kulka, J.Kinne, L.Wyns, and R.Loris (2003).
Recognition of the intrinsically flexible addiction antidote MazE by a dromedary single domain antibody fragment. Structure, thermodynamics of binding, stability, and influence on interactions with DNA.
  J Biol Chem, 278, 14101-14111.  
14573361 L.J.Holt, C.Herring, L.S.Jespers, B.P.Woolven, and I.M.Tomlinson (2003).
Domain antibodies: proteins for therapy.
  Trends Biotechnol, 21, 484-490.  
12548621 M.K.Fenwick, and F.A.Escobedo (2003).
Hybrid Monte Carlo with multidimensional replica exchanges: conformational equilibria of the hypervariable regions of a llama VHH antibody domain.
  Biopolymers, 68, 160-177.  
12831531 R.J.Olsen, J.Mazlo, S.A.Koepsell, T.W.McKeithan, and S.H.Hinrichs (2003).
Minimal structural elements of an inhibitory anti-ATF1/CREB single-chain antibody fragment (scFv41.4).
  Hybrid Hybridomics, 22, 65-77.  
12743116 R.Loris, I.Marianovsky, J.Lah, T.Laeremans, H.Engelberg-Kulka, G.Glaser, S.Muyldermans, and L.Wyns (2003).
Crystal structure of the intrinsically flexible addiction antidote MazE.
  J Biol Chem, 278, 28252-28257.
PDB code: 1mvf
11960990 A.Desmyter, S.Spinelli, F.Payan, M.Lauwereys, L.Wyns, S.Muyldermans, and C.Cambillau (2002).
Three camelid VHH domains in complex with porcine pancreatic alpha-amylase. Inhibition and versatility of binding topology.
  J Biol Chem, 277, 23645-23650.
PDB codes: 1kxq 1kxt 1kxv
11141058 J.M.Pérez, J.G.Renisio, J.J.Prompers, C.J.van Platerink, C.Cambillau, H.Darbon, and L.G.Frenken (2001).
Thermal unfolding of a llama antibody fragment: a two-state reversible process.
  Biochemistry, 40, 74-83.  
11295555 S.Muyldermans, C.Cambillau, and L.Wyns (2001).
Recognition of antigens by single-domain antibody fragments: the superfluous luxury of paired domains.
  Trends Biochem Sci, 26, 230-235.  
10931555 A.Skerra (2000).
Engineered protein scaffolds for molecular recognition.
  J Mol Recognit, 13, 167-187.  
11701516 J.Maynard, and G.Georgiou (2000).
Antibody engineering.
  Annu Rev Biomed Eng, 2, 339-376.  
10684599 S.Spinelli, L.G.Frenken, P.Hermans, T.Verrips, K.Brown, M.Tegoni, and C.Cambillau (2000).
Camelid heavy-chain variable domains provide efficient combining sites to haptens.
  Biochemistry, 39, 1217-1222.
PDB code: 1qd0
10698934 V.K.Nguyen, R.Hamers, L.Wyns, and S.Muyldermans (2000).
Camel heavy-chain antibodies: diverse germline V(H)H and specific mechanisms enlarge the antigen-binding repertoire.
  EMBO J, 19, 921-930.  
10508712 P.J.Hudson (1999).
Recombinant antibody constructs in cancer therapy.
  Curr Opin Immunol, 11, 548-557.  
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.