Molecular conformation of erabutoxin b; Atomic coordinates at 2.5 Å resolution

Kimball, M. R.; Sato, Atsushi; Richardson, Jane S.; Rosen, Lawrence S.; Low, Barbara W.

doi:10.1016/0006-291x(79)91500-6

Cited by 86 publications

(46 citation statements)

References 4 publications

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“…The threedimensional structure of erabutoxin b was reported previously from analyses at lower resolution (Low, Preston, Sato, Rosen, Searl, Rudko & Richardson, 1976;Kimball, Sato, Richardson, Rosen & Low, 1979) as were the results of an earlier stage of the crystallographic refinement at 1.4 A resolution (Bourne, Sato, Corfield, Rosen, Birken & Low, 1985;Low & Corfield, 1986). The earlier refinement provided starting parameters for the work reported here, corrected errors in the amino-acid sequence of erabutoxin b, and established the identity of erabutoxin b and neurotoxin b, toxins from the venom of L. semifasciata from different regions of the Pacific.…”

Section: Introductionsupporting

confidence: 58%

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Refinement at 1.4 Å resolution of a model of erabutoxin b: treatment of ordered solvent and discrete disorder

Smith¹,

Corfield²,

Hendrickson³

et al. 1988

Acta Cryst Sect A

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The latter stages in the refinement of the protein erabutoxin b are described. The crystal structure of the 62-residue protein has been refined to a conventional R factor of 0.144 by stereochemically restrained least-squares methods using diffraction data to a limit of 1.4/~ spacings. Emphasis was placed on determining as accurately as possible the solvent * Author to whom correspondence should be addressed at Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.0108-7673 / 88/030357-12503.00 structure and the structures of heterogeneous groups in the protein. The final model includes two conformers for each of seven side chains and for an octapeptide segment. A total of 111 sites for water molecules have been located as well as one sulfate ion with a total of 68 site occupancies. 65 of the solvent sites overlap either with protein atoms belonging to groups in two alternative conformations or with other solvent sites. Dual protein conformers and overlapping solvent sites were both included in the least-squares refinement. Individual thermal and occupancy parameters were refined for solvent molecules. An analysis of these parameters has provided useful structural information. IntroductionErabutoxin b is a postsynaptic neurotoxic protein of 62 amino-acid residues found in venom of the Pacific sea snake Laticauda semifasciata. The threedimensional structure of erabutoxin b was reported previously from analyses at lower resolution (Low, Preston, Sato, Rosen, Searl, Rudko & Richardson, 1976;Kimball, Sato, Richardson, Rosen & Low, 1979) as were the results of an earlier stage of the crystallographic refinement at 1.4 A resolution (Bourne, Sato, Corfield, Rosen, Birken & Low, 1985;Low & Corfield, 1986). The earlier refinement provided starting parameters for the work reported here, corrected errors in the amino-acid sequence of erabutoxin b, and established the identity of erabutoxin b and neurotoxin b, toxins from the venom of L. semifasciata from different regions of the Pacific. The crystal structure of neurotoxin b was reported by Tsernoglou & Petsko (1976). We describe here a further refinement of the erabutoxin b model using diffraction data to 1-4 A spacings.One of the goals of this project was to determine the structure of the ordered solvent in erabutoxin b crystals. Both thermal and occupancy parameters were refined for solvent molecules in the model, and the physical significance of these highly correlated parameters was considered in interpreting the results. As part of an effort to streamline the time-consuming process of addition of solvent to a protein model, all significant density in IF o[-I F~[ electron density maps was systematically surveyed. In many cases the difference density was more reasonably interpreted as structural heterogeneity rather than as new solvent molecules. The term structural heterogeneity refers to discrete crystallographic disorder (Smith, Hendrickson, Honzatko & Sheriff, 1986). This is ubiquitous in protein crystals owing to limited lattic...

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Section: Introductionsupporting

confidence: 58%

“…The diffraction data employed in the initial stages of this study were those used earlier (Low et al, 1976;Kimball et al, 1979) and in the phases 0 through IV of refinement that are described in the preliminary report (Bourne et al, 1985). This data set did not include estimated standard deviations for structure amplitudes.…”

Section: Diffraction Datamentioning

confidence: 99%

Refinement at 1.4 Å resolution of a model of erabutoxin b: treatment of ordered solvent and discrete disorder

Smith¹,

Corfield²,

Hendrickson³

et al. 1988

Acta Cryst Sect A

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“…Amino acid residues incorporated in the epitope recognized by Mcr2-3. The spatial structure is based on X-ray data of erabutoxin b [23,24] according to Kimball et al [22]. The three underlined residues at position 27, 29 and 47 are common to both the epitope and the AcChR-binding site.…”

Section: Resultsmentioning

confidence: 99%

A monoclonal antibody which recognized the functional site of snake neurotoxins and which neutralizes all short‐chain variants

et al. 1986

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We isolated a neurotoxin-specific monoclonal antibody (Mab) which is capable of recognizing and neutralizing all short-chain toxin variants that have been tested, including those with widely divergent sequences. The epitope incorporates the three invariant residues Lys-27, Trp-29 and Lys-47 which form part of the site by which the toxins bind to the nicotinic acetylcholine receptor. To our knowledge, this is the first Mab which possesses the universal capacity of neutralizing all natural variants of a toxic protein. Monoclonal antibody Toxin Acetylcholine receptor

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“…The function of the rare cys-cys sequence, as in other proteins containing this sequence (18,19,33,47,91), is to form disulfide bridges with other cysteine residues, linking three peptide segments in close proximity . The structure of the common peptide bond does not allow a disulfide bridge between adjacent cysteine residues.…”

mentioning

confidence: 99%

A model for the structure of chromatin in mammalian sperm.

Balhorn¹

1982

The Journal of Cell Biology

505

269

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DNA in mammalian, and most vertebrate sperm, is packaged by protamines into a highly condensed, biochemically inert form of chromatin. A model is proposed for the structure of this DNA-protamine complex which describes the site and mode of protamine binding to DNA and postulates, for the first time, specific inter- and intraprotamine interactions essential for the organization of this highly specialized chromatin. In this model, the central polyarginine segment of protamine binds in the minor groove of DNA, crosslinking and neutralizing the phosphodiester backbone of DNA while the COOH- and NH2-terminal ends of protamine participate in the formation of inter- and intraprotamine hydrogen, hydrophobic, and disulfide bonds. Each protamine segment is of sufficient length to fill one turn of DNA, and adjacent protamines are locked in place around DNA by multiple disulfide bridges. Such an arrangement generates a neutral, insoluble chromatin complex, uses all protamine sulfhydryl groups for cross linking, conserves volume, and effectively renders the chromatin invulnerable to most external influences.

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Molecular conformation of erabutoxin b; Atomic coordinates at 2.5 Å resolution

Cited by 86 publications

References 4 publications

Refinement at 1.4 Å resolution of a model of erabutoxin b: treatment of ordered solvent and discrete disorder

Refinement at 1.4 Å resolution of a model of erabutoxin b: treatment of ordered solvent and discrete disorder

A monoclonal antibody which recognized the functional site of snake neurotoxins and which neutralizes all short‐chain variants

A model for the structure of chromatin in mammalian sperm.

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