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PDBsum entry 1so8

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protein metals links
Oxidoreductase PDB id
1so8
Jmol
Contents
Protein chain
208 a.a. *
Metals
_CL
_NA ×2
Waters ×118
* Residue conservation analysis
PDB id:
1so8
Name: Oxidoreductase
Title: Abeta-bound human abad structure [also known as 3-hydroxyacy dehydrogenase type ii (type ii hadh), endoplasmic reticulum associated amyloid beta-peptide binding protein (erab)]
Structure: 3-hydroxyacyl-coa dehydrogenase type ii. Chain: a. Synonym: type ii hadh, endoplasmic reticulum-associated amy peptide binding protein (erab), short-chain type dehydrogenase/reductase xh98g2. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: hadh2, erab, xh98g2, schad. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Biol. unit: Octamer (from PDB file)
Resolution:
2.30Å     R-factor:   0.231     R-free:   0.261
Authors: J.W.Lustbader,M.Cirilli,H.Wu
Key ref:
J.W.Lustbader et al. (2004). ABAD directly links Abeta to mitochondrial toxicity in Alzheimer's disease. Science, 304, 448-452. PubMed id: 15087549 DOI: 10.1126/science.1091230
Date:
13-Mar-04     Release date:   11-May-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q99714  (HCD2_HUMAN) -  3-hydroxyacyl-CoA dehydrogenase type-2
Seq:
Struc:
261 a.a.
208 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 2: E.C.1.1.1.178  - 3-hydroxy-2-methylbutyryl-CoA dehydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (2S,3S)-3-hydroxy-2-methylbutanoyl-CoA + NAD+ = 2-methylacetoacetyl-CoA + NADH
(2S,3S)-3-hydroxy-2-methylbutanoyl-CoA
+ NAD(+)
= 2-methylacetoacetyl-CoA
+ NADH
   Enzyme class 3: E.C.1.1.1.35  - 3-hydroxyacyl-CoA dehydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (S)-3-hydroxyacyl-CoA + NAD+ = 3-oxoacyl-CoA + NADH
(S)-3-hydroxyacyl-CoA
+ NAD(+)
= 3-oxoacyl-CoA
+ NADH
   Enzyme class 4: E.C.1.1.1.51  - 3(or 17)-beta-hydroxysteroid dehydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Testosterone + NAD(P)(+) = androst-4-ene-3,17-dione + NAD(P)H
Testosterone
+ NAD(P)(+)
= androst-4-ene-3,17-dione
+ NAD(P)H
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     plasma membrane   6 terms 
  Biological process     metabolic process   7 terms 
  Biochemical function     protein binding     7 terms  

 

 
    reference    
 
 
DOI no: 10.1126/science.1091230 Science 304:448-452 (2004)
PubMed id: 15087549  
 
 
ABAD directly links Abeta to mitochondrial toxicity in Alzheimer's disease.
J.W.Lustbader, M.Cirilli, C.Lin, H.W.Xu, K.Takuma, N.Wang, C.Caspersen, X.Chen, S.Pollak, M.Chaney, F.Trinchese, S.Liu, F.Gunn-Moore, L.F.Lue, D.G.Walker, P.Kuppusamy, Z.L.Zewier, O.Arancio, D.Stern, S.S.Yan, H.Wu.
 
  ABSTRACT  
 
Mitochondrial dysfunction is a hallmark of beta-amyloid (Abeta)-induced neuronal toxicity in Alzheimer's disease (AD). Here, we demonstrate that Abeta-binding alcohol dehydrogenase (ABAD) is a direct molecular link from Abeta to mitochondrial toxicity. Abeta interacts with ABAD in the mitochondria of AD patients and transgenic mice. The crystal structure of Abeta-bound ABAD shows substantial deformation of the active site that prevents nicotinamide adenine dinucleotide (NAD) binding. An ABAD peptide specifically inhibits ABAD-Abeta interaction and suppresses Abeta-induced apoptosis and free-radical generation in neurons. Transgenic mice overexpressing ABAD in an Abeta-rich environment manifest exaggerated neuronal oxidative stress and impaired memory. These data suggest that the ABAD-Abeta interaction may be a therapeutic target in AD.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. ABAD-Aß association in AD patients and transgenic mice. (A) Coimmunoprecipitation of ABAD and Aß in AD patient brains. Results shown are representative of the three patients in each group. (B) Subcellular fractionation was used to prepare fractions of mouse brain enriched for mitochondrial (fraction I), lysosomal (fraction II), or endoplasmic reticulum (fraction III) constituents. Each fraction (20 µg total protein per lane) was immunoblotted with antibodies to Cox IV, cathepsin D, and PDI. Protein loading was identical in each case. Lower panel shows the presence of ABAD in the mitochondrial fraction. (C) Colocalization of ABAD and Aß in cerebral cortex of AD patients (200-fold magnification). (D) Mitochondrial localization of ABAD in cerebral cortex of AD patients (200-fold magnification). VDAC was used as a mitochondrial marker. Mouse anti-VDAC (20 µg/ml), guinea pig anti-ABAD (10 µg/ml), and rabbit anti-Aß (5 µg/ml) IgGs were used in (C) and (D). (E) Colocalization of ABAD and Aß in mitochondria of the brain of a patient with AD with the use of electron microscopy. Double immunogold staining was performed with rabbit anti-Aß IgG and mouse anti-ABAD IgG followed by goat anti-rabbit IgG conjugated to 12-nm gold particles (for Aß1-42) and goat anti-mouse IgG conjugated to 18-nm gold particles (for ABAD). Arrowheads depict gold particles localizing ABAD antigen. The smaller gold particles represent sites of localization of Aß.
Figure 2.
Fig. 2. Crystal structure of Aß-bound human ABAD. (A) A ribbon diagram with labeled secondary structures and the L[D], L[E], and L[F] loops. Helices are shown in green, ß strands are shown in blue, and loops are shown in pink. Disordered regions are shown by dotted lines. (B) Superposition of Aß-bound human ABAD (pink) and rat ABAD in complex with NAD (blue). The L[D] loop of 3 -hydroxysteroid dehydrogenase (3 -HSD) (PDB code 1FJH [PDB] ) is shown in yellow. NAD is shown as a stick model with gray for carbon atoms, red for oxygen atoms, blue for nitrogen atoms, and yellow for phosphate atoms. The proposed Aß-binding loop is indicated. (C) Superposition of the active sites of Aß-bound human ABAD (pink) and rat ABAD (blue), showing distortion of the NAD binding site and the catalytic triad S155, K162, and Y168. Colors are the same as in (B). (D) A section of the crystal packing interactions, showing the large solvent channels. Each ABAD molecule is shown in a different color. The ordered ends of the L[D] loop, residues 94 and 114, are marked as red and blue balls, respectively, and the hypothetical loops are shown in pink as dotted lines.
 
  The above figures are reprinted by permission from the AAAs: Science (2004, 304, 448-452) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21545753 A.Eckert, K.Schmitt, and J.Götz (2011).
Mitochondrial dysfunction - the beginning of the end in Alzheimer's disease? Separate and synergistic modes of tau and amyloid-β toxicity.
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19362755 H.Du, L.Guo, W.Zhang, M.Rydzewska, and S.Yan (2011).
Cyclophilin D deficiency improves mitochondrial function and learning/memory in aging Alzheimer disease mouse model.
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21382475 J.S.Seo, K.W.Lee, T.K.Kim, I.S.Baek, J.Y.Im, and P.L.Han (2011).
Behavioral stress causes mitochondrial dysfunction via ABAD up-regulation and aggravates plaque pathology in the brain of a mouse model of Alzheimer disease.
  Free Radic Biol Med, 50, 1526-1535.  
21459773 M.Manczak, M.J.Calkins, and P.H.Reddy (2011).
Impaired mitochondrial dynamics and abnormal interaction of amyloid beta with mitochondrial protein Drp1 in neurons from patients with Alzheimer's disease: implications for neuronal damage.
  Hum Mol Genet, 20, 2495-2509.  
19233513 Q.Zhang, G.Yang, W.Li, Z.Fan, A.Sun, J.Luo, and Z.J.Ke (2011).
Thiamine deficiency increases β-secretase activity and accumulation of β-amyloid peptides.
  Neurobiol Aging, 32, 42-53.  
21144728 X.M.Xu, and S.G.Møller (2011).
The value of Arabidopsis research in understanding human disease states.
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20683452 Y.Zhang, S.Xing, J.Zhang, J.Li, C.Li, Z.Pei, and J.Zeng (2011).
Reduction of β-amyloid deposits by γ-secretase inhibitor is associated with the attenuation of secondary damage in the ipsilateral thalamus and sensory functional improvement after focal cortical infarction in hypertensive rats.
  J Cereb Blood Flow Metab, 31, 572-579.  
20217279 A.Eckert, K.L.Schulz, V.Rhein, and J.Götz (2010).
Convergence of amyloid-beta and tau pathologies on mitochondria in vivo.
  Mol Neurobiol, 41, 107-114.  
21103401 A.T.Isik (2010).
Late onset Alzheimer's disease in older people.
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S-Nitrosylation of DRP1 does not affect enzymatic activity and is not specific to Alzheimer's disease.
  J Alzheimers Dis, 20, S513-S526.  
19784856 C.Isobe, T.Abe, and Y.Terayama (2010).
Levels of reduced and oxidized coenzyme Q-10 and 8-hydroxy-2'-deoxyguanosine in the CSF of patients with Alzheimer's disease demonstrate that mitochondrial oxidative damage and/or oxidative DNA damage contributes to the neurodegenerative process.
  J Neurol, 257, 399-404.  
20577776 D.H.Cho, T.Nakamura, and S.A.Lipton (2010).
Mitochondrial dynamics in cell death and neurodegeneration.
  Cell Mol Life Sci, 67, 3435-3447.  
19715758 G.E.Gibson, A.Starkov, J.P.Blass, R.R.Ratan, and M.F.Beal (2010).
Cause and consequence: mitochondrial dysfunction initiates and propagates neuronal dysfunction, neuronal death and behavioral abnormalities in age-associated neurodegenerative diseases.
  Biochim Biophys Acta, 1802, 122-134.  
20354705 G.K.Gouras, D.Tampellini, R.H.Takahashi, and E.Capetillo-Zarate (2010).
Intraneuronal beta-amyloid accumulation and synapse pathology in Alzheimer's disease.
  Acta Neuropathol, 119, 523-541.  
20937894 H.Du, L.Guo, S.Yan, A.A.Sosunov, G.M.McKhann, and S.S.Yan (2010).
Early deficits in synaptic mitochondria in an Alzheimer's disease mouse model.
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20186922 H.Vicente Miranda, and T.F.Outeiro (2010).
The sour side of neurodegenerative disorders: the effects of protein glycation.
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20231471 J.M.Wang, C.Singh, L.Liu, R.W.Irwin, S.Chen, E.J.Chung, R.F.Thompson, and R.D.Brinton (2010).
Allopregnanolone reverses neurogenic and cognitive deficits in mouse model of Alzheimer's disease.
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19771514 J.Ye, X.Meng, C.Yan, and C.Wang (2010).
Effect of purple sweet potato anthocyanins on beta-amyloid-mediated PC-12 cells death by inhibition of oxidative stress.
  Neurochem Res, 35, 357-365.  
20175748 K.E.Muirhead, E.Borger, L.Aitken, S.J.Conway, and F.J.Gunn-Moore (2010).
The consequences of mitochondrial amyloid beta-peptide in Alzheimer's disease.
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20065039 K.H.Lauritzen, O.Moldestad, L.Eide, H.Carlsen, G.Nesse, J.F.Storm, I.M.Mansuy, L.H.Bergersen, and A.Klungland (2010).
Mitochondrial DNA toxicity in forebrain neurons causes apoptosis, neurodegeneration, and impaired behavior.
  Mol Cell Biol, 30, 1357-1367.  
  20077426 K.Rauschenberger, K.Schöler, J.O.Sass, S.Sauer, Z.Djuric, C.Rumig, N.I.Wolf, J.G.Okun, S.Kölker, H.Schwarz, C.Fischer, B.Grziwa, H.Runz, A.Nümann, N.Shafqat, K.L.Kavanagh, G.Hämmerling, R.J.Wanders, J.P.Shield, U.Wendel, D.Stern, P.Nawroth, G.F.Hoffmann, C.R.Bartram, B.Arnold, A.Bierhaus, U.Oppermann, H.Steinbeisser, and J.Zschocke (2010).
A non-enzymatic function of 17beta-hydroxysteroid dehydrogenase type 10 is required for mitochondrial integrity and cell survival.
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19619643 L.Devi, and H.K.Anandatheerthavarada (2010).
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21258649 L.J.Martin (2010).
Mitochondrial and Cell Death Mechanisms in Neurodegenerative Diseases.
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21179577 L.M.Saraiva, G.S.Seixas da Silva, A.Galina, W.S.da-Silva, W.L.Klein, S.T.Ferreira, and F.G.De Felice (2010).
Amyloid-β triggers the release of neuronal hexokinase 1 from mitochondria.
  PLoS One, 5, e15230.  
20660724 M.M.Lipinski, B.Zheng, T.Lu, Z.Yan, B.F.Py, A.Ng, R.J.Xavier, C.Li, B.A.Yankner, C.R.Scherzer, and J.Yuan (2010).
Genome-wide analysis reveals mechanisms modulating autophagy in normal brain aging and in Alzheimer's disease.
  Proc Natl Acad Sci U S A, 107, 14164-14169.  
  20463406 M.Manczak, P.Mao, M.J.Calkins, A.Cornea, A.P.Reddy, M.P.Murphy, H.H.Szeto, B.Park, and P.H.Reddy (2010).
Mitochondria-targeted antioxidants protect against amyloid-beta toxicity in Alzheimer's disease neurons.
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  20847424 M.S.Parihar, and G.J.Brewer (2010).
Amyloid-β as a modulator of synaptic plasticity.
  J Alzheimers Dis, 22, 741-763.  
20734416 N.Mairuae, E.C.Hall Ii, P.Cheepsunthorn, S.Y.Lee, and J.R.Connor (2010).
The H63D HFE gene variant promotes activation of the intrinsic apoptotic pathway via mitochondria dysfunction following β-amyloid peptide exposure.
  J Neurosci Res, 88, 3079-3089.  
  20413847 P.H.Reddy, M.Manczak, P.Mao, M.J.Calkins, A.P.Reddy, and U.Shirendeb (2010).
Amyloid-beta and mitochondria in aging and Alzheimer's disease: implications for synaptic damage and cognitive decline.
  J Alzheimers Dis, 20, S499-S512.  
19945483 Q.Ma (2010).
Transcriptional responses to oxidative stress: pathological and toxicological implications.
  Pharmacol Ther, 125, 376-393.  
  20442494 R.H.Swerdlow, J.M.Burns, and S.M.Khan (2010).
The Alzheimer's disease mitochondrial cascade hypothesis.
  J Alzheimers Dis, 20, S265-S279.  
  20661404 R.X.Santos, S.C.Correia, X.Wang, G.Perry, M.A.Smith, P.I.Moreira, and X.Zhu (2010).
Alzheimer's disease: diverse aspects of mitochondrial malfunctioning.
  Int J Clin Exp Pathol, 3, 570-581.  
  20552046 T.A.Bayer, and O.Wirths (2010).
Intracellular accumulation of amyloid-Beta - a predictor for synaptic dysfunction and neuron loss in Alzheimer's disease.
  Front Aging Neurosci, 2, 8.  
  20421693 V.Adam-Vizi, and A.A.Starkov (2010).
Calcium and mitochondrial reactive oxygen species generation: how to read the facts.
  J Alzheimers Dis, 20, S413-S426.  
20808761 V.Rhein, M.Giese, G.Baysang, F.Meier, S.Rao, K.L.Schulz, M.Hamburger, and A.Eckert (2010).
Ginkgo biloba extract ameliorates oxidative phosphorylation performance and rescues abeta-induced failure.
  PLoS One, 5, e12359.  
20461558 W.E.Müller, A.Eckert, C.Kurz, G.P.Eckert, and K.Leuner (2010).
Mitochondrial dysfunction: common final pathway in brain aging and Alzheimer's disease--therapeutic aspects.
  Mol Neurobiol, 41, 159-171.  
18572275 W.S.Liang, T.Dunckley, T.G.Beach, A.Grover, D.Mastroeni, K.Ramsey, R.J.Caselli, W.A.Kukull, D.McKeel, J.C.Morris, C.M.Hulette, D.Schmechel, E.M.Reiman, J.Rogers, and D.A.Stephan (2010).
Neuronal gene expression in non-demented individuals with intermediate Alzheimer's Disease neuropathology.
  Neurobiol Aging, 31, 549-566.  
20186753 Y.A.Lim, V.Rhein, G.Baysang, F.Meier, A.Poljak, M.J.Raftery, M.Guilhaus, L.M.Ittner, A.Eckert, and J.Götz (2010).
Abeta and human amylin share a common toxicity pathway via mitochondrial dysfunction.
  Proteomics, 10, 1621-1633.  
  20651247 Z.Sisková, D.J.Mahad, C.Pudney, G.Campbell, M.Cadogan, A.Asuni, V.O'Connor, and V.H.Perry (2010).
Morphological and functional abnormalities in mitochondria associated with synaptic degeneration in prion disease.
  Am J Pathol, 177, 1411-1421.  
20629991 Z.T.Kincses, J.Toldi, and L.Vécsei (2010).
Kynurenines, neurodegeneration and Alzheimer's disease.
  J Cell Mol Med, 14, 2045-2054.  
20490313 Z.Wu, Y.Zhao, and B.Zhao (2010).
Superoxide anion, uncoupling proteins and Alzheimer's disease.
  J Clin Biochem Nutr, 46, 187-194.  
19458211 A.Fernández, L.Llacuna, J.C.Fernández-Checa, and A.Colell (2009).
Mitochondrial cholesterol loading exacerbates amyloid beta peptide-induced inflammation and neurotoxicity.
  J Neurosci, 29, 6394-6405.  
19690748 A.Rauk (2009).
The chemistry of Alzheimer's disease.
  Chem Soc Rev, 38, 2698-2715.  
19258390 C.F.Cowell, H.Döppler, I.K.Yan, A.Hausser, Y.Umezawa, and P.Storz (2009).
Mitochondrial diacylglycerol initiates protein-kinase D1-mediated ROS signaling.
  J Cell Sci, 122, 919-928.  
19030989 C.Rivière, J.C.Delaunay, F.Immel, C.Cullin, and J.P.Monti (2009).
The polyphenol piceid destabilizes preformed amyloid fibrils and oligomers in vitro: hypothesis on possible molecular mechanisms.
  Neurochem Res, 34, 1120-1128.  
18683046 E.Head (2009).
Oxidative damage and cognitive dysfunction: antioxidant treatments to promote healthy brain aging.
  Neurochem Res, 34, 670-678.  
19417731 F.Fang, and G.T.Liu (2009).
Protective effects of compound FLZ, a novel synthetic analogue of squamosamide, on beta-amyloid-induced rat brain mitochondrial dysfunction in vitro.
  Acta Pharmacol Sin, 30, 522-529.  
18373733 G.Aliev, J.Liu, J.C.Shenk, K.Fischbach, G.J.Pacheco, S.G.Chen, M.E.Obrenovich, W.F.Ward, A.G.Richardson, M.A.Smith, E.Gasimov, G.Perry, and B.N.Ames (2009).
Neuronal mitochondrial amelioration by feeding acetyl-L-carnitine and lipoic acid to aged rats.
  J Cell Mol Med, 13, 320-333.  
19808793 H.Chen, and D.C.Chan (2009).
Mitochondrial dynamics--fusion, fission, movement, and mitophagy--in neurodegenerative diseases.
  Hum Mol Genet, 18, R169-R176.  
  19502709 J.Kooistra, J.Milojevic, G.Melacini, and J.Ortega (2009).
A new function of human HtrA2 as an amyloid-beta oligomerization inhibitor.
  J Alzheimers Dis, 17, 281-294.  
19667196 J.Yao, R.W.Irwin, L.Zhao, J.Nilsen, R.T.Hamilton, and R.D.Brinton (2009).
Mitochondrial bioenergetic deficit precedes Alzheimer's pathology in female mouse model of Alzheimer's disease.
  Proc Natl Acad Sci U S A, 106, 14670-14675.  
19707851 K.A.Jellinger (2009).
Recent advances in our understanding of neurodegeneration.
  J Neural Transm, 116, 1111-1162.  
19901339 K.Takuma, F.Fang, W.Zhang, S.Yan, E.Fukuzaki, H.Du, A.Sosunov, G.McKhann, Y.Funatsu, N.Nakamichi, T.Nagai, H.Mizoguchi, D.Ibi, O.Hori, S.Ogawa, D.M.Stern, K.Yamada, and S.S.Yan (2009).
RAGE-mediated signaling contributes to intraneuronal transport of amyloid-beta and neuronal dysfunction.
  Proc Natl Acad Sci U S A, 106, 20021-20026.  
19828920 K.Takuma, S.Kataoka, Y.Ago, and T.Matsuda (2009).
[Mitochondrial dysfunction and neuronal apoptosis: new molecular approach to prevent Alzheimer's disease]
  Nippon Yakurigaku Zasshi, 134, 180-183.  
19690377 M.Gargouri, C.Manigand, C.Maugé, T.Granier, B.Langlois d'Estaintot, O.Cala, I.Pianet, K.Bathany, J.Chaudière, and B.Gallois (2009).
Structure and epimerase activity of anthocyanidin reductase from Vitis vinifera.
  Acta Crystallogr D Biol Crystallogr, 65, 989.
PDB codes: 2rh8 3hfs
19073272 M.R.Hass, C.Sato, R.Kopan, and G.Zhao (2009).
Presenilin: RIP and beyond.
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Apoptosis and in vitro Alzheimer disease neuronal models.
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Amyloid beta, mitochondrial structural and functional dynamics in Alzheimer's disease.
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Possible role of amyloid-beta, adenine nucleotide translocase and cyclophilin-D interaction in mitochondrial dysfunction of Alzheimer's disease.
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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.