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DeLano Scientific structural analysis program pymol
Identification of P152Lp53 mutation in a patient sample and prevalence of somatic P152Lp53 missense mutations in human cancers. a, immunohistochemistry for mutant p53 by PAb240 antibody (indicated by →) on an oral cancer sample; b, sequence chromatogram showing C > T substitution at 152 position; c, location of Pro-152 (shown in pink) in 3D structure of the p53 core domain bound <t>to</t> <t>DNA</t> visualized by <t>PyMOL</t> (molecular visualization software); d, multiple sequence alignment of human TP53 protein sequence across various organisms. The Pro-152 residue is indicated by a black arrow. e, prevalence of missense mutations in a stretch of 150–155 amino acids of p53 analyzed from COSMIC database version 86; f, bar plot representation of number and frequency of various missense mutations present at TP53 (Pro-152) loci out of 111 samples of available data at COSMIC. The percentage frequency of various amino acid substitutions are shown above the bars. g, bar plot representation of number and frequency distribution of P152Lp53 mutation occurrence over various cancer tissue types out of 111 samples of P152L mutations. CNS, central nervous system, others: adrenal gland, breast, hematopoietic and lymphoid tissue, liver, lung, pancreas, skin, soft tissue, and stomach tissue.
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1) Product Images from "The cancer-associated, gain-of-function TP53 variant P152Lp53 activates multiple signaling pathways implicated in tumorigenesis"

Article Title: The cancer-associated, gain-of-function TP53 variant P152Lp53 activates multiple signaling pathways implicated in tumorigenesis

Journal: The Journal of Biological Chemistry

doi: 10.1074/jbc.RA118.007265

Identification of P152Lp53 mutation in a patient sample and prevalence of somatic P152Lp53 missense mutations in human cancers. a, immunohistochemistry for mutant p53 by PAb240 antibody (indicated by →) on an oral cancer sample; b, sequence chromatogram showing C > T substitution at 152 position; c, location of Pro-152 (shown in pink) in 3D structure of the p53 core domain bound to DNA visualized by PyMOL (molecular visualization software); d, multiple sequence alignment of human TP53 protein sequence across various organisms. The Pro-152 residue is indicated by a black arrow. e, prevalence of missense mutations in a stretch of 150–155 amino acids of p53 analyzed from COSMIC database version 86; f, bar plot representation of number and frequency of various missense mutations present at TP53 (Pro-152) loci out of 111 samples of available data at COSMIC. The percentage frequency of various amino acid substitutions are shown above the bars. g, bar plot representation of number and frequency distribution of P152Lp53 mutation occurrence over various cancer tissue types out of 111 samples of P152L mutations. CNS, central nervous system, others: adrenal gland, breast, hematopoietic and lymphoid tissue, liver, lung, pancreas, skin, soft tissue, and stomach tissue.
Figure Legend Snippet: Identification of P152Lp53 mutation in a patient sample and prevalence of somatic P152Lp53 missense mutations in human cancers. a, immunohistochemistry for mutant p53 by PAb240 antibody (indicated by →) on an oral cancer sample; b, sequence chromatogram showing C > T substitution at 152 position; c, location of Pro-152 (shown in pink) in 3D structure of the p53 core domain bound to DNA visualized by PyMOL (molecular visualization software); d, multiple sequence alignment of human TP53 protein sequence across various organisms. The Pro-152 residue is indicated by a black arrow. e, prevalence of missense mutations in a stretch of 150–155 amino acids of p53 analyzed from COSMIC database version 86; f, bar plot representation of number and frequency of various missense mutations present at TP53 (Pro-152) loci out of 111 samples of available data at COSMIC. The percentage frequency of various amino acid substitutions are shown above the bars. g, bar plot representation of number and frequency distribution of P152Lp53 mutation occurrence over various cancer tissue types out of 111 samples of P152L mutations. CNS, central nervous system, others: adrenal gland, breast, hematopoietic and lymphoid tissue, liver, lung, pancreas, skin, soft tissue, and stomach tissue.

Techniques Used: Mutagenesis, Immunohistochemistry, Sequencing, Software, Residue

Related Articles

Mutagenesis:

Article Title: Activation of Multiple Signalling Pathways by P152Lp53 Mutant Reveals New Gain-of-function Implicating Tumorigenesis
Article Snippet: To model the location of proline at position 152 of p53, coordinates of the human p53 DNA-binding domain bound to DNA with accession code 1TUP, tumor suppressor p53 complexed with DNA were taken from RCSB ( https://www.rcsb.org ), and analysed with structural analysis program PyMol (DeLano Scientific, Palo Alto, CA)

Article Title: The cancer-associated, gain-of-function TP53 variant P152Lp53 activates multiple signaling pathways implicated in tumorigenesis
Article Snippet: To model the location of proline at position 152 of p53, coordinates of the human p53 DNA-binding domain bound to DNA with accession code 1TUP, tumor suppressor p53 complexed with DNA were taken from RCSB, and analyzed with the structural analysis program PyMOL (DeLano Scientific, Palo Alto, CA).

Article Title: The cancer-associated, gain-of-function TP53 variant P152Lp53 activates multiple signaling pathways implicated in tumorigenesis
Article Snippet: substitution at 152nd amino acid position in p53: To model the location of proline at position 152 of p53, coordinates of the human p53 DNA-binding domain bound to DNA with accession code 1TUP, tumor suppressor p53 complexed with DNA were taken from RCSB (https://www.rcsb.org), and analysed with structural analysis program PyMol (DeLano Scientific, Palo Alto, CA)

Immunohistochemistry:

Article Title: Activation of Multiple Signalling Pathways by P152Lp53 Mutant Reveals New Gain-of-function Implicating Tumorigenesis
Article Snippet: To model the location of proline at position 152 of p53, coordinates of the human p53 DNA-binding domain bound to DNA with accession code 1TUP, tumor suppressor p53 complexed with DNA were taken from RCSB ( https://www.rcsb.org ), and analysed with structural analysis program PyMol (DeLano Scientific, Palo Alto, CA)

Article Title: The cancer-associated, gain-of-function TP53 variant P152Lp53 activates multiple signaling pathways implicated in tumorigenesis
Article Snippet: To model the location of proline at position 152 of p53, coordinates of the human p53 DNA-binding domain bound to DNA with accession code 1TUP, tumor suppressor p53 complexed with DNA were taken from RCSB, and analyzed with the structural analysis program PyMOL (DeLano Scientific, Palo Alto, CA).

Article Title: The cancer-associated, gain-of-function TP53 variant P152Lp53 activates multiple signaling pathways implicated in tumorigenesis
Article Snippet: substitution at 152nd amino acid position in p53: To model the location of proline at position 152 of p53, coordinates of the human p53 DNA-binding domain bound to DNA with accession code 1TUP, tumor suppressor p53 complexed with DNA were taken from RCSB (https://www.rcsb.org), and analysed with structural analysis program PyMol (DeLano Scientific, Palo Alto, CA)

Sequencing:

Article Title: Activation of Multiple Signalling Pathways by P152Lp53 Mutant Reveals New Gain-of-function Implicating Tumorigenesis
Article Snippet: To model the location of proline at position 152 of p53, coordinates of the human p53 DNA-binding domain bound to DNA with accession code 1TUP, tumor suppressor p53 complexed with DNA were taken from RCSB ( https://www.rcsb.org ), and analysed with structural analysis program PyMol (DeLano Scientific, Palo Alto, CA)

Article Title: The cancer-associated, gain-of-function TP53 variant P152Lp53 activates multiple signaling pathways implicated in tumorigenesis
Article Snippet: To model the location of proline at position 152 of p53, coordinates of the human p53 DNA-binding domain bound to DNA with accession code 1TUP, tumor suppressor p53 complexed with DNA were taken from RCSB, and analyzed with the structural analysis program PyMOL (DeLano Scientific, Palo Alto, CA).

Article Title: The cancer-associated, gain-of-function TP53 variant P152Lp53 activates multiple signaling pathways implicated in tumorigenesis
Article Snippet: substitution at 152nd amino acid position in p53: To model the location of proline at position 152 of p53, coordinates of the human p53 DNA-binding domain bound to DNA with accession code 1TUP, tumor suppressor p53 complexed with DNA were taken from RCSB (https://www.rcsb.org), and analysed with structural analysis program PyMol (DeLano Scientific, Palo Alto, CA)

Software:

Article Title: Activation of Multiple Signalling Pathways by P152Lp53 Mutant Reveals New Gain-of-function Implicating Tumorigenesis
Article Snippet: To model the location of proline at position 152 of p53, coordinates of the human p53 DNA-binding domain bound to DNA with accession code 1TUP, tumor suppressor p53 complexed with DNA were taken from RCSB ( https://www.rcsb.org ), and analysed with structural analysis program PyMol (DeLano Scientific, Palo Alto, CA)

Article Title: The cancer-associated, gain-of-function TP53 variant P152Lp53 activates multiple signaling pathways implicated in tumorigenesis
Article Snippet: To model the location of proline at position 152 of p53, coordinates of the human p53 DNA-binding domain bound to DNA with accession code 1TUP, tumor suppressor p53 complexed with DNA were taken from RCSB, and analyzed with the structural analysis program PyMOL (DeLano Scientific, Palo Alto, CA).

Article Title: The cancer-associated, gain-of-function TP53 variant P152Lp53 activates multiple signaling pathways implicated in tumorigenesis
Article Snippet: substitution at 152nd amino acid position in p53: To model the location of proline at position 152 of p53, coordinates of the human p53 DNA-binding domain bound to DNA with accession code 1TUP, tumor suppressor p53 complexed with DNA were taken from RCSB (https://www.rcsb.org), and analysed with structural analysis program PyMol (DeLano Scientific, Palo Alto, CA)

Residue:

Article Title: Activation of Multiple Signalling Pathways by P152Lp53 Mutant Reveals New Gain-of-function Implicating Tumorigenesis
Article Snippet: To model the location of proline at position 152 of p53, coordinates of the human p53 DNA-binding domain bound to DNA with accession code 1TUP, tumor suppressor p53 complexed with DNA were taken from RCSB ( https://www.rcsb.org ), and analysed with structural analysis program PyMol (DeLano Scientific, Palo Alto, CA)

Article Title: The cancer-associated, gain-of-function TP53 variant P152Lp53 activates multiple signaling pathways implicated in tumorigenesis
Article Snippet: To model the location of proline at position 152 of p53, coordinates of the human p53 DNA-binding domain bound to DNA with accession code 1TUP, tumor suppressor p53 complexed with DNA were taken from RCSB, and analyzed with the structural analysis program PyMOL (DeLano Scientific, Palo Alto, CA).

Article Title: The cancer-associated, gain-of-function TP53 variant P152Lp53 activates multiple signaling pathways implicated in tumorigenesis
Article Snippet: substitution at 152nd amino acid position in p53: To model the location of proline at position 152 of p53, coordinates of the human p53 DNA-binding domain bound to DNA with accession code 1TUP, tumor suppressor p53 complexed with DNA were taken from RCSB (https://www.rcsb.org), and analysed with structural analysis program PyMol (DeLano Scientific, Palo Alto, CA)



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a Crystal structure of a parallel signal transducer and activator of transcription 3 ( STAT3 ) dimer bound to DNA in orthogonal views. The surface structure is colored according to atom type, with oxygen in red, nitrogen in blue, sulfur in dark yellow, and carbon in either bright yellow or green depending on the protomer. The double-helix structure of DNA is colored in cyan. The crystallographic data were taken from the Protein Data Bank (PDB) file 1BG1 for the STAT3 parallel dimer . b Ribbon diagram of an anti-parallel STAT3 dimer. The α‑helical coiled-coil domains are colored in yellow, the DNA-binding domains in cyan, the linker domains in green , and the SH2 domains in red. Structural data were from the PDB file 6TLC for STAT3 . Figures b and c were created with the program <t>PyMOL</t> <t>(DeLano</t> Scientific). c Schematic model of the interleukin (IL)-6-induced JAK/STAT3 signaling pathway. Binding of IL‑6 or a related cytokine to the heterodimeric cell surface receptor triggers a series of tyrosine-phosphorylation steps catalyzed by non-covalently bound Janus kinase ( JAK ), including JAK auto-phosphorylation and receptor phosphorylation. The phosphorylated receptor tail recruits STAT3 molecules, which are then phosphorylated at a single tyrosine ( 1 ). Through spontaneous dissociation and re-association, the activated STAT3 proteins constantly oscillate between a parallel and an antiparallel dimer conformation ( 2 ). After binding to importins ( 3 ), phospho-STAT3 dimers are imported into the nucleus via nuclear pore complexes ( 4 ). In the nucleus, STAT3 proteins modulate gene expression ( 5 ) and rearrange in an antiparallel dimer conformation ( 6 ) to be dephosphorylated ( 7 )
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a Crystal structure of a parallel signal transducer and activator of transcription 3 ( STAT3 ) dimer bound to DNA in orthogonal views. The surface structure is colored according to atom type, with oxygen in red, nitrogen in blue, sulfur in dark yellow, and carbon in either bright yellow or green depending on the protomer. The double-helix structure of DNA is colored in cyan. The crystallographic data were taken from the Protein Data Bank (PDB) file 1BG1 for the STAT3 parallel dimer . b Ribbon diagram of an anti-parallel STAT3 dimer. The α‑helical coiled-coil domains are colored in yellow, the DNA-binding domains in cyan, the linker domains in green , and the SH2 domains in red. Structural data were from the PDB file 6TLC for STAT3 . Figures b and c were created with the program <t>PyMOL</t> <t>(DeLano</t> Scientific). c Schematic model of the interleukin (IL)-6-induced JAK/STAT3 signaling pathway. Binding of IL‑6 or a related cytokine to the heterodimeric cell surface receptor triggers a series of tyrosine-phosphorylation steps catalyzed by non-covalently bound Janus kinase ( JAK ), including JAK auto-phosphorylation and receptor phosphorylation. The phosphorylated receptor tail recruits STAT3 molecules, which are then phosphorylated at a single tyrosine ( 1 ). Through spontaneous dissociation and re-association, the activated STAT3 proteins constantly oscillate between a parallel and an antiparallel dimer conformation ( 2 ). After binding to importins ( 3 ), phospho-STAT3 dimers are imported into the nucleus via nuclear pore complexes ( 4 ). In the nucleus, STAT3 proteins modulate gene expression ( 5 ) and rearrange in an antiparallel dimer conformation ( 6 ) to be dephosphorylated ( 7 )
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Image Search Results


a Crystal structure of a parallel signal transducer and activator of transcription 3 ( STAT3 ) dimer bound to DNA in orthogonal views. The surface structure is colored according to atom type, with oxygen in red, nitrogen in blue, sulfur in dark yellow, and carbon in either bright yellow or green depending on the protomer. The double-helix structure of DNA is colored in cyan. The crystallographic data were taken from the Protein Data Bank (PDB) file 1BG1 for the STAT3 parallel dimer . b Ribbon diagram of an anti-parallel STAT3 dimer. The α‑helical coiled-coil domains are colored in yellow, the DNA-binding domains in cyan, the linker domains in green , and the SH2 domains in red. Structural data were from the PDB file 6TLC for STAT3 . Figures b and c were created with the program PyMOL (DeLano Scientific). c Schematic model of the interleukin (IL)-6-induced JAK/STAT3 signaling pathway. Binding of IL‑6 or a related cytokine to the heterodimeric cell surface receptor triggers a series of tyrosine-phosphorylation steps catalyzed by non-covalently bound Janus kinase ( JAK ), including JAK auto-phosphorylation and receptor phosphorylation. The phosphorylated receptor tail recruits STAT3 molecules, which are then phosphorylated at a single tyrosine ( 1 ). Through spontaneous dissociation and re-association, the activated STAT3 proteins constantly oscillate between a parallel and an antiparallel dimer conformation ( 2 ). After binding to importins ( 3 ), phospho-STAT3 dimers are imported into the nucleus via nuclear pore complexes ( 4 ). In the nucleus, STAT3 proteins modulate gene expression ( 5 ) and rearrange in an antiparallel dimer conformation ( 6 ) to be dephosphorylated ( 7 )

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Figure Lengend Snippet: a Crystal structure of a parallel signal transducer and activator of transcription 3 ( STAT3 ) dimer bound to DNA in orthogonal views. The surface structure is colored according to atom type, with oxygen in red, nitrogen in blue, sulfur in dark yellow, and carbon in either bright yellow or green depending on the protomer. The double-helix structure of DNA is colored in cyan. The crystallographic data were taken from the Protein Data Bank (PDB) file 1BG1 for the STAT3 parallel dimer . b Ribbon diagram of an anti-parallel STAT3 dimer. The α‑helical coiled-coil domains are colored in yellow, the DNA-binding domains in cyan, the linker domains in green , and the SH2 domains in red. Structural data were from the PDB file 6TLC for STAT3 . Figures b and c were created with the program PyMOL (DeLano Scientific). c Schematic model of the interleukin (IL)-6-induced JAK/STAT3 signaling pathway. Binding of IL‑6 or a related cytokine to the heterodimeric cell surface receptor triggers a series of tyrosine-phosphorylation steps catalyzed by non-covalently bound Janus kinase ( JAK ), including JAK auto-phosphorylation and receptor phosphorylation. The phosphorylated receptor tail recruits STAT3 molecules, which are then phosphorylated at a single tyrosine ( 1 ). Through spontaneous dissociation and re-association, the activated STAT3 proteins constantly oscillate between a parallel and an antiparallel dimer conformation ( 2 ). After binding to importins ( 3 ), phospho-STAT3 dimers are imported into the nucleus via nuclear pore complexes ( 4 ). In the nucleus, STAT3 proteins modulate gene expression ( 5 ) and rearrange in an antiparallel dimer conformation ( 6 ) to be dephosphorylated ( 7 )

Article Snippet: Figures b and c were created with the program PyMOL (DeLano Scientific). c Schematic model of the interleukin (IL)-6-induced JAK/STAT3 signaling pathway.

Techniques: Binding Assay, Cell Surface Receptor Assay, Phospho-proteomics, Gene Expression