Protein:PDCD4 |
Protein Summary |
 Gene summary |
| Gene name: PDCD4 | ASpdb.0 ID: 27250 | Gene | Gene symbol | PDCD4 | Gene ID | 27250 |
| Gene name | programmed cell death 4 |
| Synonyms | H731 |
| Cytomap | 10q25.2 |
| Type of gene | protein-coding |
| Description | programmed cell death protein 4neoplastic transformation inhibitor proteinnuclear antigen H731programmed cell death 4 (neoplastic transformation inhibitor)protein 197/15a |
| Modification date | 20240305 |
| UniProtAcc | Q53EL6 |
| Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Gene | PDCD4 | GO:0005829 | cytosol | 12054647 |
| Gene | PDCD4 | GO:0030509 | BMP signaling pathway | 18548003 |
| Gene | PDCD4 | GO:0045892 | negative regulation of DNA-templated transcription | 16357133 |
| Gene | PDCD4 | GO:1905064 | negative regulation of vascular associated smooth muscle cell differentiation | 18548003 |
AS Summary |
| Information of the canonical protein with experimentally identified structure from PDB (2023). |
| UniProt Acc | File name | PDB ID | Method | Resolution | Chain | Start | End |
| Q53EL6-1 | Q53EL6-1_3eij_A.pdb | 3EIJ | X-ray | 2.8 | A | 157 | 450 |
| ASpdb's canonical and alternatively spliced isoform information. |
| accession_id | gene_name | canonical_id | alternative_id | canonical_length | alternative_length | canonical_start | canonical_end | type | originalSEQ | variationSEQ | alternative_start | alternative_end |
| Q53EL6 | PDCD4 | Q53EL6-1 | Q53EL6-2 | 469 | 458 | 1 | 15 | Substitution | MDVENEQILNVNPAD | MTKY | 1 | 4 |
| Multiple sequence alignment of our canonical and alternatively spliced PDCD4 |
| Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of PDCD4 |
| UniProt-id | ENSG | ENST | ENSP |
| Q53EL6-1 | ENSG00000150593.18 | ENST00000280154.12 | ENSP00000280154.7 |
| Q53EL6-2 | ENSG00000150593.18 | ENST00000393104.6 | ENSP00000376816.2 |
| UniProt-id | NM ID | NP ID |
| Q53EL6-1 | NM_014456.4 | NP_055271.2 |
| Q53EL6-2 | NM_145341.3 | NP_663314.1 |
| Amino acid sequences of our canonical and alternatively spliced PDCD4 |
| accession_id | Protein sequence |
| Q53EL6-1 | MDVENEQILNVNPADPDNLSDSLFSGDEENAGTEEIKNEINGNWISASSINEARINAKAKRRLRKNSSRDSGRGDSVSDSGSDALRSGLT VPTSPKGRLLDRRSRSGKGRGLPKKGGAGGKGVWGTPGQVYDVEEVDVKDPNYDDDQENCVYETVVLPLDERAFEKTLTPIIQEYFEHGD TNEVAEMLRDLNLGEMKSGVPVLAVSLALEGKASHREMTSKLLSDLCGTVMSTTDVEKSFDKLLKDLPELALDTPRAPQLVGQFIARAVG DGILCNTYIDSYKGTVDCVQARAALDKATVLLSMSKGGKRKDSVWGSGGGQQSVNHLVKEIDMLLKEYLLSGDISEAEHCLKELEVPHFH HELVYEAIIMVLESTGESTFKMILDLLKSLWKSSTITVDQMKRGYERIYNEIPDINLDVPHSYSVLERFVEECFQAGIISKQLRDLCPSR |
| Q53EL6-2 | MTKYPDNLSDSLFSGDEENAGTEEIKNEINGNWISASSINEARINAKAKRRLRKNSSRDSGRGDSVSDSGSDALRSGLTVPTSPKGRLLD RRSRSGKGRGLPKKGGAGGKGVWGTPGQVYDVEEVDVKDPNYDDDQENCVYETVVLPLDERAFEKTLTPIIQEYFEHGDTNEVAEMLRDL NLGEMKSGVPVLAVSLALEGKASHREMTSKLLSDLCGTVMSTTDVEKSFDKLLKDLPELALDTPRAPQLVGQFIARAVGDGILCNTYIDS YKGTVDCVQARAALDKATVLLSMSKGGKRKDSVWGSGGGQQSVNHLVKEIDMLLKEYLLSGDISEAEHCLKELEVPHFHHELVYEAIIMV LESTGESTFKMILDLLKSLWKSSTITVDQMKRGYERIYNEIPDINLDVPHSYSVLERFVEECFQAGIISKQLRDLCPSRGRKRFVSEGDG |
Protein Functional Features |
| Main function of this protein. (from UniProt) |
| PDCD4 (go to UniProt):Q53EL6 |
| Retention analysis result of protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at * Minus value of BPloci means that the break pointn is located before the CDS. |
| - Retained protein feature among the 13 regional features. |
| Accession_id | Subsection | Start | End | Funcitonal feature | Splicing information |
| Q53EL6 | Region | 1 | 38 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Substitution;Start=1;End=15 |
| Q53EL6 | Compositional bias | 11 | 27 | Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Substitution;Start=1;End=15 |
Gene Isoform Structures and Expression Levels for PDCD4 |
| Gene structures of our canonical and alternative spliced genes of PDCD4 * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
| Expression levels of gene isoforms across GTEx. |
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| Expression levels of gene isoforms across TCGA. |
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Protein Structures |
| PDB and CIF files of the predicted protein structures * Here we show the 3D structure of the proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format. |
| 3D view using mol* of Q53EL6-1 |
| 3D view using mol* of Q53EL6-2 |
pLDDT Score Distribution |
| pLDDT score distribution of the predicted protein structures from AlphaFold2 * AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. |
| pLDDT distribution across the protein length of Q53EL6-1 |
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| pLDDT distribution across the protein length of Q53EL6-2 |
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Ramachandran Plot of Protein Structures |
| Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this protein peptide. |
| Ramachandran plot of Q53EL6-1 |
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| Ramachandran plot of Q53EL6-2 |
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Potential Active Site Information |
| The potential binding sites of these proteins were identified using SiteMap, a module of the Schrodinger suite. |
| UniProt-id | Site score | Size | D score | Volume | Exposure | Enclosure | Contact | Phobic | Philic | Balance | Don/Acc | Residues |
| Q53EL6-1 | 0.998 | 109 | 1.042 | 316.589 | 0.684 | 0.65 | 0.818 | 0.707 | 0.883 | 0.8 | 1.394 | 175,176,177,179,212,213,214,215,216,217,218,221,31 3,315,316,317,318,319,320,321,322,330,333,334,337, 346,347,350,353,354,355 |
| Q53EL6-2 | 0.996 | 148 | 0.998 | 336.483 | 0.533 | 0.692 | 0.944 | 0.575 | 1.095 | 0.525 | 1.077 | 33,34,35,36,39,40,43,44,47,48,49,50,51,52,145,146, 148,160,163,166,167,172,175,176,179,180 |
Protein Structure and Feature Comparision |
| Protein Structure Comparision Using Template Modeling Scores (TM-score). |
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| Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Canonical validated structure (PDB)(green) |
| 3D view using mol* of Q53EL6-1_Q53EL6-1_3eij_A.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical validated structure (PDB)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of Q53EL6-1_3eij_A_Q53EL6-2.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of Q53EL6-1_Q53EL6-2.pdb |
| Protein Feature Comparison of the protein sequendary structures among the protiens. |
| ./stats/secondary_structure/figure/Q53EL6-1_vs_Q53EL6-2.png |
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| Protein Feature Comparison of the relative accessible surface area (ASA) among the protiens. |
| ./stats/relative_asa/Q53EL6-1_vs_Q53EL6-2.png |
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Protein-Protein Interaction |
| Interactors from UniProt. |
| Accession_id | Subsection | Start | End | Funcitonal feature | Splicing information |
| Interactors from STRING. |
| Gene name | Interactors |
Related Drugs to PDCD4 |
| Drugs targeting this gene/protein. (DrugBank) |
| UniProt accession | Gene name | DrugBank ID | Drug name | Drug group | Actions |
Related Diseases to PDCD4 |
| Previous studies relating to the alternative splicing of PDCD4 and disease information from the MeSH term (PubMed) |
| Gene | PMID | Title | Abstract | MeSH ID | MeSH term |
| PDCD4 | 24292556 | Splicing factor SRSF3 represses the translation of programmed cell death 4 mRNA by associating with the 5'-UTR region. | Serine/arginine-rich splicing factor 3 (SRSF3), a member of the serine/arginine (SR)-rich family of proteins, regulates both alternative splicing of pre-mRNA and export of mature mRNA from the nucleus. Although its role in nuclear mRNA processing is well understood, the mechanism by which it alters the fate of cytoplasmic mRNA molecules remains elusive. Here, we provide evidence that SRSF3 not only regulates the alternative splicing pattern of programmed cell death 4 (PDCD4) mRNA, but also modulates its translational efficiency in the cytoplasm by lowering translation levels. We observed a marked increase in PDCD4 mRNA in translating polysome fractions upon silencing of SRSF3, and, conversely, ectopic overexpression of SRSF3 shifted PDCD4 mRNA into non-translating ribosomal fractions. In live cells, SRSF3 colocalized with PDCD4 mRNA in P-bodies (PBs), where translationally silenced mRNAs are deposited, and this localization was abrogated upon SRSF3 silencing. Furthermore, using two different reporter systems, we showed that SRSF3 interacts directly with PDCD4 mRNA and mediates translational repression by binding to the 5'-untranslated region (5'-UTR). In summary, our data suggest that the oncogenic potential of SRSF3 might be realized, in part, through the translational repression of PDCD4 mRNA. | D009369 | Neoplasms |
Clinically important variants in PDCD4 |
| (ClinVar, 04/20/2024) |
| accession_id | uniprot_id | gene_name | Type | Variant | Clinical_significance |
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