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pdb database files  (Molecular Dynamics Inc)

 
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    Molecular Dynamics Inc pdb database files
    Pdb Database Files, supplied by Molecular Dynamics Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    The MIN1 N terminus is a predicted C2 domain. (A) ClustalW alignment of the MIN1 C2 domain with similar C2 domain sequences identified using blastp. Asterisks denote positions at which all of the sequences have identical residues. Dots denote conservation of residues in ≥50% of the sequences. MIN1 residues D19, D77, K37, K42, and T38 are indicated by large asterisks. The GenBank accession number of each aligned protein follows the sequence: Tribolium castaneum (red flour beetle) predicted protein, Gallus gallus (chicken) predicted protein, Caenorhabditis elegans hypothetical protein T12A2.15a, Leishmania infantum hypothetical protein LinJ31.0710, Trypanosoma cruzi hypothetical protein, Arabidopsis thaliana C2/GRAM domain protein At1G03370, Oryza sativa C2/GRAM domain protein (rice 08g0492400), and Oryza sativa C2/GRAM protein (rice 02g0199800). (B) ClustalW alignment of the MIN1 C2 domain with Brookhaven Protein DataBank sequences 1wfj (Arabidopsis C2 domain-containing protein from a putative elicitor-responsive gene) and 1rlw (50) (C2 domain from Homo sapiens <t>phospholipase</t> <t>A2)</t> (60). Structurally determined (PDB sequences) and predicted (MIN1) β-sheet residues are italicized. Asterisks above the sequence indicate conserved residues D19, K37, T38, K42, and D77. (C) Ribbon diagram of the three-dimensional fold of the MIN1 C2 domain, predicted by the LOOPP algorithm (45, 81), based on the structure of the C2 domain in an Arabidopsis putative elicitor-responsive protein (PDB file 1wfj) (50). The diagram, produced using PyMOL (http://www.pymol.org) (10), illustrates the eight β-strands (1 through 8) of the C2 domain sandwich, the residues corresponding to the conserved loop aspartates in Ca2+-dependent domains (D19, N24, Q71, G73, and D77), and conserved residue T38, discussed in the text.
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    The MIN1 N terminus is a predicted C2 domain. (A) ClustalW alignment of the MIN1 C2 domain with similar C2 domain sequences identified using blastp. Asterisks denote positions at which all of the sequences have identical residues. Dots denote conservation of residues in ≥50% of the sequences. MIN1 residues D19, D77, K37, K42, and T38 are indicated by large asterisks. The GenBank accession number of each aligned protein follows the sequence: Tribolium castaneum (red flour beetle) predicted protein, Gallus gallus (chicken) predicted protein, Caenorhabditis elegans hypothetical protein T12A2.15a, Leishmania infantum hypothetical protein LinJ31.0710, Trypanosoma cruzi hypothetical protein, Arabidopsis thaliana C2/GRAM domain protein At1G03370, Oryza sativa C2/GRAM domain protein (rice 08g0492400), and Oryza sativa C2/GRAM protein (rice 02g0199800). (B) ClustalW alignment of the MIN1 C2 domain with Brookhaven Protein DataBank sequences 1wfj (Arabidopsis C2 domain-containing protein from a putative elicitor-responsive gene) and 1rlw (50) (C2 domain from Homo sapiens <t>phospholipase</t> <t>A2)</t> (60). Structurally determined (PDB sequences) and predicted (MIN1) β-sheet residues are italicized. Asterisks above the sequence indicate conserved residues D19, K37, T38, K42, and D77. (C) Ribbon diagram of the three-dimensional fold of the MIN1 C2 domain, predicted by the LOOPP algorithm (45, 81), based on the structure of the C2 domain in an Arabidopsis putative elicitor-responsive protein (PDB file 1wfj) (50). The diagram, produced using PyMOL (http://www.pymol.org) (10), illustrates the eight β-strands (1 through 8) of the C2 domain sandwich, the residues corresponding to the conserved loop aspartates in Ca2+-dependent domains (D19, N24, Q71, G73, and D77), and conserved residue T38, discussed in the text.
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    The MIN1 N terminus is a predicted C2 domain. (A) ClustalW alignment of the MIN1 C2 domain with similar C2 domain sequences identified using blastp. Asterisks denote positions at which all of the sequences have identical residues. Dots denote conservation of residues in ≥50% of the sequences. MIN1 residues D19, D77, K37, K42, and T38 are indicated by large asterisks. The GenBank accession number of each aligned protein follows the sequence: Tribolium castaneum (red flour beetle) predicted protein, Gallus gallus (chicken) predicted protein, Caenorhabditis elegans hypothetical protein T12A2.15a, Leishmania infantum hypothetical protein LinJ31.0710, Trypanosoma cruzi hypothetical protein, Arabidopsis thaliana C2/GRAM domain protein At1G03370, Oryza sativa C2/GRAM domain protein (rice 08g0492400), and Oryza sativa C2/GRAM protein (rice 02g0199800). (B) ClustalW alignment of the MIN1 C2 domain with Brookhaven Protein DataBank sequences 1wfj (Arabidopsis C2 domain-containing protein from a putative elicitor-responsive gene) and 1rlw (50) (C2 domain from Homo sapiens phospholipase A2) (60). Structurally determined (PDB sequences) and predicted (MIN1) β-sheet residues are italicized. Asterisks above the sequence indicate conserved residues D19, K37, T38, K42, and D77. (C) Ribbon diagram of the three-dimensional fold of the MIN1 C2 domain, predicted by the LOOPP algorithm (45, 81), based on the structure of the C2 domain in an Arabidopsis putative elicitor-responsive protein (PDB file 1wfj) (50). The diagram, produced using PyMOL (http://www.pymol.org) (10), illustrates the eight β-strands (1 through 8) of the C2 domain sandwich, the residues corresponding to the conserved loop aspartates in Ca2+-dependent domains (D19, N24, Q71, G73, and D77), and conserved residue T38, discussed in the text.

    Journal:

    Article Title: C2 Domain Protein MIN1 Promotes Eyespot Organization in Chlamydomonas reinhardtii ▿ †

    doi: 10.1128/EC.00118-08

    Figure Lengend Snippet: The MIN1 N terminus is a predicted C2 domain. (A) ClustalW alignment of the MIN1 C2 domain with similar C2 domain sequences identified using blastp. Asterisks denote positions at which all of the sequences have identical residues. Dots denote conservation of residues in ≥50% of the sequences. MIN1 residues D19, D77, K37, K42, and T38 are indicated by large asterisks. The GenBank accession number of each aligned protein follows the sequence: Tribolium castaneum (red flour beetle) predicted protein, Gallus gallus (chicken) predicted protein, Caenorhabditis elegans hypothetical protein T12A2.15a, Leishmania infantum hypothetical protein LinJ31.0710, Trypanosoma cruzi hypothetical protein, Arabidopsis thaliana C2/GRAM domain protein At1G03370, Oryza sativa C2/GRAM domain protein (rice 08g0492400), and Oryza sativa C2/GRAM protein (rice 02g0199800). (B) ClustalW alignment of the MIN1 C2 domain with Brookhaven Protein DataBank sequences 1wfj (Arabidopsis C2 domain-containing protein from a putative elicitor-responsive gene) and 1rlw (50) (C2 domain from Homo sapiens phospholipase A2) (60). Structurally determined (PDB sequences) and predicted (MIN1) β-sheet residues are italicized. Asterisks above the sequence indicate conserved residues D19, K37, T38, K42, and D77. (C) Ribbon diagram of the three-dimensional fold of the MIN1 C2 domain, predicted by the LOOPP algorithm (45, 81), based on the structure of the C2 domain in an Arabidopsis putative elicitor-responsive protein (PDB file 1wfj) (50). The diagram, produced using PyMOL (http://www.pymol.org) (10), illustrates the eight β-strands (1 through 8) of the C2 domain sandwich, the residues corresponding to the conserved loop aspartates in Ca2+-dependent domains (D19, N24, Q71, G73, and D77), and conserved residue T38, discussed in the text.

    Article Snippet: The 3D-PSSM ( 28 ) and LOOPP ( 45 , 81 ) threading algorithms predicted that the three-dimensional structure of the MIN1 C2 domain is most similar to those of the topology II C2 domains in human phospholipase A2 (Brookhaven Protein Database [PDB] file 1rlw [ 60 ]; 15% identity with the MIN1 C2 domain) and an Arabidopsis putative elicitor-responsive protein (PDB file 1wfj [ 50 ]; 18% identity).

    Techniques: Sequencing, Produced, Residue