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PDBsum entry 2aai

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protein ligands Protein-protein interface(s) links
Hydrolase PDB id
2aai
Jmol
Contents
Protein chains
267 a.a. *
262 a.a. *
Ligands
GAL-BGC ×2
NDG-NAG-BMA-MAN-
MAN
×2
Waters ×123
* Residue conservation analysis
PDB id:
2aai
Name: Hydrolase
Title: Crystallographic refinement of ricin to 2.5 angstroms
Structure: Ricin (a chain). Chain: a. Engineered: yes. Ricin (b chain). Chain: b. Engineered: yes
Source: Ricinus communis. Castor bean. Organism_taxid: 3988.
Biol. unit: Dimer (from PQS)
Resolution:
2.50Å     R-factor:   0.212    
Authors: E.Rutenber,B.J.Katzin,W.Montfort,J.E.Villafranca,S.R.Ernst, E.J.Collins,D.Mlsna,A.F.Monzingo,M.P.Ready,J.D.Robertus
Key ref: E.Rutenber et al. (1991). Crystallographic refinement of ricin to 2.5 A. Proteins, 10, 240-250. PubMed id: 1881880
Date:
07-Sep-93     Release date:   31-Jan-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P02879  (RICI_RICCO) -  Ricin
Seq:
Struc:
 
Seq:
Struc:
576 a.a.
267 a.a.
Protein chain
Pfam   ArchSchema ?
P02879  (RICI_RICCO) -  Ricin
Seq:
Struc:
 
Seq:
Struc:
576 a.a.
262 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.3.2.2.22  - rRNA N-glycosylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     negative regulation of translation   1 term 
  Biochemical function     rRNA N-glycosylase activity     1 term  

 

 
Proteins 10:240-250 (1991)
PubMed id: 1881880  
 
 
Crystallographic refinement of ricin to 2.5 A.
E.Rutenber, B.J.Katzin, S.Ernst, E.J.Collins, D.Mlsna, M.P.Ready, J.D.Robertus.
 
  ABSTRACT  
 
The plant cytotoxin ricin consists of two disulfide-linked chains, each of about 30,000 daltons. An initial model based on a 2.8 A MIR electron density map has been refined against 2.5 A data using rounds of hand rebuilding coupled with either a restrained least squares algorithm or molecular dynamics (XPLOR). The last model (9) has an R factor of 21.6% and RMS deviations from standard bond lengths and angles of 0.021 A and 4.67 degrees, respectively. Refinement required several peptide segments in the original model to be adjusted translationally along the electron density. A wide range of lesser changes were also made. The RMS deviation of backbone atoms between the original and model 9 was 1.89 A. Molecular dynamics proved to be a very powerful refinement tool. However, tests showed that it could not replace human intervention in making adjustments such as local translations of the peptide chain. The R factor is not a completely satisfactory indicator of refinement progress; difference Fouriers, when observed carefully, may be a better monitor.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21514389 J.P.Yang, X.X.Ma, Y.X.He, W.F.Li, Y.Kang, R.Bao, Y.Chen, and C.Z.Zhou (2011).
Crystal structure of the 30K protein from the silkworm Bombyx mori reveals a new member of the β-trefoil superfamily.
  J Struct Biol, 175, 97.
PDB code: 3pub
21904036 P.M.Legler, R.N.Brey, J.E.Smallshaw, E.S.Vitetta, and C.B.Millard (2011).
Structure of RiVax: a recombinant ricin vaccine.
  Acta Crystallogr D Biol Crystallogr, 67, 826-830.
PDB code: 3srp
20566411 G.Sulzenbacher, V.Roig-Zamboni, W.J.Peumans, P.Rougé, E.J.Van Damme, and Y.Bourne (2010).
Crystal structure of the GalNAc/Gal-specific agglutinin from the phytopathogenic ascomycete Sclerotinia sclerotiorum reveals novel adaptation of a beta-trefoil domain.
  J Mol Biol, 400, 715-723.
PDB codes: 2x2s 2x2t
19066990 J.J.Stewart (2009).
Application of the PM6 method to modeling proteins.
  J Mol Model, 15, 765-805.  
18798567 L.Maveyraud, H.Niwa, V.Guillet, D.I.Svergun, P.V.Konarev, R.A.Palmer, W.J.Peumans, P.Rougé, E.J.Van Damme, C.D.Reynolds, and L.Mourey (2009).
Structural basis for sugar recognition, including the Tn carcinoma antigen, by the lectin SNA-II from Sambucus nigra.
  Proteins, 75, 89.
PDB codes: 3c9z 3ca0 3ca1 3ca3 3ca4 3ca5 3ca6 3cah
19292477 X.P.Li, J.C.Chiou, M.Remacha, J.P.Ballesta, and N.E.Tumer (2009).
A two-step binding model proposed for the electrostatic interactions of ricin a chain with ribosomes.
  Biochemistry, 48, 3853-3863.  
19019145 J.C.Chiou, X.P.Li, M.Remacha, J.P.Ballesta, and N.E.Tumer (2008).
The ribosomal stalk is required for ribosome binding, depurination of the rRNA and cytotoxicity of ricin A chain in Saccharomyces cerevisiae.
  Mol Microbiol, 70, 1441-1452.  
  17277441 N.Kulahin, V.Kiselyov, A.Kochoyan, O.Kristensen, J.S.Kastrup, V.Berezin, E.Bock, and M.Gajhede (2007).
Structure of rat acidic fibroblast growth factor at 1.4 A resolution.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 65-68.
PDB code: 2j3p
17477546 S.Roday, S.Saen-oon, and V.L.Schramm (2007).
Vinyldeoxyadenosine in a sarcin-ricin RNA loop and its binding to ricin toxin a-chain.
  Biochemistry, 46, 6169-6182.  
19693356 V.Rastogi, and O.D.Velev (2007).
Development and evaluation of realistic microbioassays in freely suspended droplets on a chip.
  Biomicrofluidics, 1, 14107.  
17470286 X.Hou, M.Chen, L.Chen, E.J.Meehan, J.Xie, and M.Huang (2007).
X-ray sequence and crystal structure of luffaculin 1, a novel type 1 ribosome-inactivating protein.
  BMC Struct Biol, 7, 29.
PDB code: 2oqa
16772301 A.Bagaria, K.Surendranath, U.A.Ramagopal, S.Ramakumar, and A.A.Karande (2006).
Structure-function analysis and insights into the reduced toxicity of Abrus precatorius agglutinin I in relation to abrin.
  J Biol Chem, 281, 34465-34474.
PDB codes: 2amz 2q3n
16461456 E.S.Vitetta, J.E.Smallshaw, E.Coleman, H.Jafri, C.Foster, R.Munford, and J.Schindler (2006).
A pilot clinical trial of a recombinant ricin vaccine in normal humans.
  Proc Natl Acad Sci U S A, 103, 2268-2273.  
15889996 C.J.Marsden, D.C.Smith, L.M.Roberts, and J.M.Lord (2005).
Ricin: current understanding and prospects for an antiricin vaccine.
  Expert Rev Vaccines, 4, 229-237.  
15935880 N.J.Mantis (2005).
Vaccines against the category B toxins: Staphylococcal enterotoxin B, epsilon toxin and ricin.
  Adv Drug Deliv Rev, 57, 1424-1439.  
14686924 A.Chambery, A.Di Maro, M.M.Monti, F.Stirpe, and A.Parente (2004).
Volkensin from Adenia volkensii Harms (kilyambiti plant), a type 2 ribosome-inactivating protein.
  Eur J Biochem, 271, 108-117.  
15382229 M.J.Bernett, T.Somasundaram, and M.Blaber (2004).
An atomic resolution structure for human fibroblast growth factor 1.
  Proteins, 57, 626-634.
PDB code: 1rg8
12823544 H.Niwa, A.G.Tonevitsky, I.I.Agapov, S.Saward, U.Pfüller, and R.A.Palmer (2003).
Crystal structure at 3 A of mistletoe lectin I, a dimeric type-II ribosome-inactivating protein, complexed with galactose.
  Eur J Biochem, 270, 2739-2749.
PDB code: 1oql
14627732 S.R.Brych, J.Kim, T.M.Logan, and M.Blaber (2003).
Accommodation of a highly symmetric core within a symmetric protein superfold.
  Protein Sci, 12, 2704-2718.
PDB codes: 1jy0 1m16 1nzk 1p63
11854038 R.G.Hu, Q.W.Zhai, W.J.He, L.Mei, and W.Y.Liu (2002).
Bioactivities of ricin retained and its immunoreactivity to anti-ricin polyclonal antibodies alleviated through pegylation.
  Int J Biochem Cell Biol, 34, 396-402.  
12071953 Y.Chen, F.Vandenbussche, P.Rougé, P.Proost, W.J.Peumans, and E.J.Van Damme (2002).
A complex fruit-specific type-2 ribosome-inactivating protein from elderberry (Sambucus nigra) is correctly processed and assembled in transgenic tobacco plants.
  Eur J Biochem, 269, 2897-2906.  
11288182 J.M.Pascal, P.J.Day, A.F.Monzingo, S.R.Ernst, J.D.Robertus, R.Iglesias, Y.Pérez, J.M.Férreras, L.Citores, and T.Girbés (2001).
2.8-A crystal structure of a nontoxic type-II ribosome-inactivating protein, ebulin l.
  Proteins, 43, 319-326.
PDB codes: 1hwm 1hwn 1hwo 1hwp
11722556 L.Xie, B.Z.Wang, R.G.Hu, H.B.Ji, L.Zhang, and W.Y.Liu (2001).
Structural and functional studies of cinnamomin, a new type II ribosome-inactivating protein isolated from the seeds of the camphor tree.
  Eur J Biochem, 268, 5723-5733.  
11551434 M.A.Olson (2001).
Electrostatic effects on the free-energy balance in folding a ribosome-inactivating protein.
  Biophys Chem, 91, 219-229.  
11375527 N.Manoj, A.A.Jeyaprakash, J.V.Pratap, S.S.Komath, R.Kenoth, M.J.Swamy, and M.Vijayan (2001).
Crystallization and preliminary X-ray studies of snake gourd lectin: homology with type II ribosome-inactivating proteins.
  Acta Crystallogr D Biol Crystallogr, 57, 912-914.  
10636890 C.L.Liu, C.C.Tsai, S.C.Lin, L.I.Wang, C.I.Hsu, M.J.Hwang, and J.Y.Lin (2000).
Primary structure and function analysis of the Abrus precatorius agglutinin A chain by site-directed mutagenesis. Pro(199) Of amphiphilic alpha-helix H impairs protein synthesis inhibitory activity.
  J Biol Chem, 275, 1897-1901.  
10785398 E.J.Van Damme, Q.Hao, D.Charels, A.Barre, P.Rougé, F.Van Leuven, and W.J.Peumans (2000).
Characterization and molecular cloning of two different type 2 ribosome-inactivating proteins from the monocotyledonous plant Polygonatum multiflorum.
  Eur J Biochem, 267, 2746-2759.  
11080141 K.Sandvig, and B.van Deurs (2000).
Entry of ricin and Shiga toxin into cells: molecular mechanisms and medical perspectives.
  EMBO J, 19, 5943-5950.  
10944358 M.Li, Y.P.Wang, J.J.Chai, K.Y.Wang, and R.C.Bi (2000).
Molecular-replacement studies of Trichosanthes kirilowii lectin 1: a structure belonging to the family of type 2 ribosome-inactivating proteins.
  Acta Crystallogr D Biol Crystallogr, 56, 1073-1075.  
9876120 M.A.Olson, and L.Cuff (1999).
Free energy determinants of binding the rRNA substrate and small ligands to ricin A-chain.
  Biophys J, 76, 28-39.  
9761837 H.M.Li, Z.H.Zeng, Z.Hu, and D.C.Wang (1998).
Crystallization and preliminary crystallographic analyses of pokeweed antiviral protein from seeds.
  Acta Crystallogr D Biol Crystallogr, 54, 137-139.  
9649321 J.K.Suh, C.J.Hovde, and J.D.Robertus (1998).
Shiga toxin attacks bacterial ribosomes as effectively as eucaryotic ribosomes.
  Biochemistry, 37, 9394-9398.  
9552157 X.Yan, P.Day, T.Hollis, A.F.Monzingo, E.Schelp, J.D.Robertus, G.W.Milne, and S.Wang (1998).
Recognition and interaction of small rings with the ricin A-chain binding site.
  Proteins, 31, 33-41.  
9079659 E.J.Van Damme, A.Barre, P.Rougé, F.Van Leuven, and W.J.Peumans (1997).
Isolation and molecular cloning of a novel type 2 ribosome-inactivating protein with an inactive B chain from elderberry (Sambucus nigra) bark.
  J Biol Chem, 272, 8353-8360.  
9183001 E.J.Van Damme, S.Roy, A.Barre, L.Citores, K.Mostafapous, P.Rougé, F.Van Leuven, T.Girbés, I.J.Goldstein, and W.J.Peumans (1997).
Elderberry (Sambucus nigra) bark contains two structurally different Neu5Ac(alpha2,6)Gal/GalNAc-binding type 2 ribosome-inactivating proteins.
  Eur J Biochem, 245, 648-655.  
9037714 M.A.Olson (1997).
Ricin A-chain structural determinant for binding substrate analogues: a molecular dynamics simulation analysis.
  Proteins, 27, 80-95.  
8631319 E.J.Van Damme, A.Barre, P.Rougé, F.Van Leuven, and W.J.Peumans (1996).
The NeuAc(alpha-2,6)-Gal/GalNAc-binding lectin from elderberry (Sambucus nigra) bark, a type-2 ribosome-inactivating protein with an unusual specificity and structure.
  Eur J Biochem, 235, 128-137.  
8647092 E.J.Van Damme, A.Barre, P.Rougé, F.Van Leuven, and W.J.Peumans (1996).
Characterization and molecular cloning of Sambucus nigra agglutinin V (nigrin b), a GalNAc-specific type-2 ribosome-inactivating protein from the bark of elderberry (Sambucus nigra).
  Eur J Biochem, 237, 505-513.  
8564542 E.M.Marcotte, A.F.Monzingo, S.R.Ernst, R.Brzezinski, and J.D.Robertus (1996).
X-ray structure of an anti-fungal chitosanase from streptomyces N174.
  Nat Struct Biol, 3, 155-162.
PDB code: 1chk
8576142 H.Kaku, Y.Tanaka, K.Tazaki, E.Minami, H.Mizuno, and N.Shibuya (1996).
Sialylated oligosaccharide-specific plant lectin from Japanese elderberry (Sambucus sieboldiana) bark tissue has a homologous structure to type II ribosome-inactivating proteins, ricin and abrin. cDNA cloning and molecular modeling study.
  J Biol Chem, 271, 1480-1485.  
8548448 M.A.Batalia, A.F.Monzingo, S.Ernst, W.Roberts, and J.D.Robertus (1996).
The crystal structure of the antifungal protein zeamatin, a member of the thaumatin-like, PR-5 protein family.
  Nat Struct Biol, 3, 19-23.
PDB code: 1du5
7727515 D.Mohanraj, and S.Ramakrishnan (1995).
Cytotoxic effects of ricin without an interchain disulfide bond: genetic modification and chemical crosslinking studies.
  Biochim Biophys Acta, 1243, 399-406.  
7561975 M.A.Olson, J.P.Scovill, and D.C.Hack (1995).
Simulation analysis of formycin 5'-monophosphate analog substrates in the ricin A-chain active site.
  J Comput Aided Mol Des, 9, 226-236.  
8539247 T.Kohno, T.Senda, H.Narumi, S.Kimura, and Y.Mitsui (1995).
Crystallization and preliminary crystallographic analysis of recombinant abrin-a A-chain with ribosome inactivating activity.
  Proteins, 23, 126-127.  
8521854 W.K.Alderton, D.Thatcher, and C.R.Lowe (1995).
Affinity labeling of recombinant ricin A chain with Procion blue MX-R.
  Eur J Biochem, 233, 880-885.  
8052614 K.N.Morris, and I.G.Wool (1994).
Analysis of the contribution of an amphiphilic alpha-helix to the structure and to the function of ricin A chain.
  Proc Natl Acad Sci U S A, 91, 7530-7533.  
8066085 K.Zhou, Z.Fu, M.Chen, Y.Lin, and K.Pan (1994).
Structure of trichosanthin at 1.88 A resolution.
  Proteins, 19, 4.  
  8453380 D.Mlsna, A.F.Monzingo, B.J.Katzin, S.Ernst, and J.D.Robertus (1993).
Structure of recombinant ricin A chain at 2.3 A.
  Protein Sci, 2, 429-435.
PDB code: 1rtc
8319679 D.Solís, P.Fernández, T.Díaz-Mauriño, J.Jiménez-Barbero, and M.Martín-Lomas (1993).
Hydrogen-bonding pattern of methyl beta-lactoside binding to the Ricinus communis lectins.
  Eur J Biochem, 214, 677-683.  
1594586 K.N.Morris, and I.G.Wool (1992).
Determination by systematic deletion of the amino acids essential for catalysis by ricin A chain.
  Proc Natl Acad Sci U S A, 89, 4869-4873.  
1368443 L.M.Roberts, and J.M.Lord (1992).
Cytotoxic proteins.
  Curr Opin Biotechnol, 3, 422-429.  
1881881 B.J.Katzin, E.J.Collins, and J.D.Robertus (1991).
Structure of ricin A-chain at 2.5 A.
  Proteins, 10, 251-259.  
1881882 E.Rutenber, and J.D.Robertus (1991).
Structure of ricin B-chain at 2.5 A resolution.
  Proteins, 10, 260-269.  
1881883 M.P.Ready, Y.Kim, and J.D.Robertus (1991).
Site-directed mutagenesis of ricin A-chain and implications for the mechanism of action.
  Proteins, 10, 270-278.  
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.