Protein:DDX3X |
Protein Summary |
 Gene summary |
| Gene name: DDX3X | ASpdb.0 ID: 1654 | Gene | Gene symbol | DDX3X | Gene ID | 1654 |
| Gene name | DEAD-box helicase 3 X-linked |
| Synonyms | CAP-Rf|DBX|DDX14|DDX3|HLP2|MRX102|MRXSSB |
| Cytomap | Xp11.4 |
| Type of gene | protein-coding |
| Description | ATP-dependent RNA helicase DDX3XDEAD (Asp-Glu-Ala-Asp) box helicase 3, X-linkedDEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linkedDEAD box protein 3, X-chromosomalDEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3DEAD/H box-3helicase-like protein 2 |
| Modification date | 20240407 |
| UniProtAcc | O00571 |
| Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Gene | DDX3X | GO:0003677 | DNA binding | 21589879 |
| Gene | DDX3X | GO:0003678 | DNA helicase activity | 21589879 |
| Gene | DDX3X | GO:0003723 | RNA binding | 21589879 |
| Gene | DDX3X | GO:0003724 | RNA helicase activity | 21589879|31575075 |
| Gene | DDX3X | GO:0003729 | mRNA binding | 29062139 |
| Gene | DDX3X | GO:0003924 | GTPase activity | 10074132 |
| Gene | DDX3X | GO:0005634 | nucleus | 10074132|10329544|29899501|30131165|31575075 |
| Gene | DDX3X | GO:0005654 | nucleoplasm | - |
| Gene | DDX3X | GO:0005737 | cytoplasm | 18636090 |
| Gene | DDX3X | GO:0005737 | cytoplasm | 10329544|24965446|27736973|28733330|30131165|30341167|31575075 |
| Gene | DDX3X | GO:0005813 | centrosome | 28842590 |
| Gene | DDX3X | GO:0005829 | cytosol | - |
| Gene | DDX3X | GO:0005852 | eukaryotic translation initiation factor 3 complex | 18628297 |
| Gene | DDX3X | GO:0005886 | plasma membrane | 29899501 |
| Gene | DDX3X | GO:0008134 | transcription factor binding | 16818630 |
| Gene | DDX3X | GO:0008143 | poly(A) binding | 18596238 |
| Gene | DDX3X | GO:0008190 | eukaryotic initiation factor 4E binding | 17667941 |
| Gene | DDX3X | GO:0009615 | response to virus | 18636090 |
| Gene | DDX3X | GO:0010494 | cytoplasmic stress granule | 18596238|21883093 |
| Gene | DDX3X | GO:0010501 | RNA secondary structure unwinding | 22872150 |
| Gene | DDX3X | GO:0010628 | positive regulation of gene expression | 10074132 |
| Gene | DDX3X | GO:0016887 | ATP hydrolysis activity | 10074132|21589879 |
| Gene | DDX3X | GO:0017111 | ribonucleoside triphosphate phosphatase activity | 10074132 |
| Gene | DDX3X | GO:0022627 | cytosolic small ribosomal subunit | 18596238 |
| Gene | DDX3X | GO:0030308 | negative regulation of cell growth | 16818630 |
| Gene | DDX3X | GO:0031252 | cell leading edge | 28733330 |
| Gene | DDX3X | GO:0031333 | negative regulation of protein-containing complex assembly | 17667941 |
| Gene | DDX3X | GO:0031369 | translation initiation factor binding | 22323517|22872150 |
| Gene | DDX3X | GO:0031954 | positive regulation of protein autophosphorylation | 30341167 |
| Gene | DDX3X | GO:0032481 | positive regulation of type I interferon production | 23478265 |
| Gene | DDX3X | GO:0032727 | positive regulation of interferon-alpha production | 30341167 |
| Gene | DDX3X | GO:0032728 | positive regulation of interferon-beta production | 27980081|31575075 |
| Gene | DDX3X | GO:0033592 | RNA strand annealing activity | 27546789 |
| Gene | DDX3X | GO:0034063 | stress granule assembly | 21883093 |
| Gene | DDX3X | GO:0034157 | positive regulation of toll-like receptor 7 signaling pathway | 30341167 |
| Gene | DDX3X | GO:0034161 | positive regulation of toll-like receptor 8 signaling pathway | 30341167 |
| Gene | DDX3X | GO:0035556 | intracellular signal transduction | 18636090 |
| Gene | DDX3X | GO:0035591 | signaling adaptor activity | 23478265 |
| Gene | DDX3X | GO:0035613 | RNA stem-loop binding | 22872150 |
| Gene | DDX3X | GO:0043015 | gamma-tubulin binding | 28842590 |
| Gene | DDX3X | GO:0043024 | ribosomal small subunit binding | 22323517 |
| Gene | DDX3X | GO:0043273 | CTPase activity | 10074132 |
| Gene | DDX3X | GO:0043539 | protein serine/threonine kinase activator activity | 23413191 |
| Gene | DDX3X | GO:0045727 | positive regulation of translation | 18596238|22872150 |
| Gene | DDX3X | GO:0045944 | positive regulation of transcription by RNA polymerase II | 16818630|18636090|28128295 |
| Gene | DDX3X | GO:0048027 | mRNA 5'-UTR binding | 22872150 |
| Gene | DDX3X | GO:0071243 | cellular response to arsenic-containing substance | 21883093 |
| Gene | DDX3X | GO:0071470 | cellular response to osmotic stress | 21883093 |
| Gene | DDX3X | GO:0071902 | positive regulation of protein serine/threonine kinase activity | 23413191 |
| Gene | DDX3X | GO:0098586 | cellular response to virus | 31575075 |
| Gene | DDX3X | GO:1902523 | positive regulation of protein K63-linked ubiquitination | 27980081 |
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 |
| O00571-1 | O00571-1_5e7j_A.pdb | 5E7J | X-ray | 2.23 | A | 133 | 584 |
| 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 |
| O00571 | DDX3X | O00571-1 | O00571-2 | 662 | 646 | 35 | 51 | Substitution | KGRYIPPHLRNREATKG | S | 35 | 35 |
| Multiple sequence alignment of our canonical and alternatively spliced DDX3X |
| Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of DDX3X |
| UniProt-id | ENSG | ENST | ENSP |
| O00571-1 | ENSG00000215301.11 | ENST00000478993.5 | ENSP00000478443.1 |
| O00571-1 | ENSG00000215301.11 | ENST00000629496.3 | ENSP00000487224.1 |
| O00571-1 | ENSG00000215301.11 | ENST00000629785.2 | ENSP00000486516.1 |
| O00571-1 | ENSG00000215301.11 | ENST00000630255.2 | ENSP00000486720.1 |
| O00571-1 | ENSG00000215301.11 | ENST00000644876.2 | ENSP00000494040.1 |
| O00571-2 | ENSG00000215301.11 | ENST00000457138.7 | ENSP00000392494.2 |
| UniProt-id | NM ID | NP ID |
| O00571-1 | NM_001356.4 | NP_001347.3 |
| O00571-2 | NM_001193417.2 | NP_001180346.1 |
| Amino acid sequences of our canonical and alternatively spliced DDX3X |
| accession_id | Protein sequence |
| O00571-1 | MSHVAVENALGLDQQFAGLDLNSSDNQSGGSTASKGRYIPPHLRNREATKGFYDKDSSGWSSSKDKDAYSSFGSRSDSRGKSSFFSDRGS GSRGRFDDRGRSDYDGIGSRGDRSGFGKFERGGNSRWCDKSDEDDWSKPLPPSERLEQELFSGGNTGINFEKYDDIPVEATGNNCPPHIE SFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKENGRYGRRKQYPISL VLAPTRELAVQIYEEARKFSYRSRVRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKYLVLDEADRMLDMGFEPQ IRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGSTSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVET KKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGL ATSFFNERNINITKDLLDLLVEAKQEVPSWLENMAYEHHYKGSSRGRSKSSRFSGGFGARDYRQSSGASSSSFSSSRASSSRSGGGGHGS |
| O00571-2 | MSHVAVENALGLDQQFAGLDLNSSDNQSGGSTASSFYDKDSSGWSSSKDKDAYSSFGSRSDSRGKSSFFSDRGSGSRGRFDDRGRSDYDG IGSRGDRSGFGKFERGGNSRWCDKSDEDDWSKPLPPSERLEQELFSGGNTGINFEKYDDIPVEATGNNCPPHIESFSDVEMGEIIMGNIE LTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEA RKFSYRSRVRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKYLVLDEADRMLDMGFEPQIRRIVEQDTMPPKGVR HTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGSTSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGY ACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDL LDLLVEAKQEVPSWLENMAYEHHYKGSSRGRSKSSRFSGGFGARDYRQSSGASSSSFSSSRASSSRSGGGGHGSSRGFGGGGYGGFYNSD |
Protein Functional Features |
| Main function of this protein. (from UniProt) |
| DDX3X (go to UniProt):O00571 |
| 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 |
| O00571 | Region | 2 | 139 | Note=Required for TBK1 and IKBKE-dependent IFNB1 activation;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:18636090;Dbxref=PMID:18636090 | Type=Substitution;Start=35;End=51 |
| O00571 | Region | 19 | 144 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Substitution;Start=35;End=51 |
| O00571 | Region | 38 | 44 | Note=Interaction with EIF4E;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17667941;Dbxref=PMID:17667941 | Type=Substitution;Start=35;End=51 |
Gene Isoform Structures and Expression Levels for DDX3X |
| Gene structures of our canonical and alternative spliced genes of DDX3X * 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 O00571-1 |
| 3D view using mol* of O00571-2 |
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 O00571-1 |
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| pLDDT distribution across the protein length of O00571-2 |
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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 O00571-1 |
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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 |
| O00571-1 | 1.034 | 328 | 1.01 | 829.031 | 0.505 | 0.749 | 0.996 | 0.367 | 1.164 | 0.315 | 0.892 | 159,162,163,165,166,167,169,171,224,225,226,227,22 8,350,353,354,383,384,385,386,388,389,390,402,404, 405,406,407,408,409,410,411,412,413,414,415,522,52 3,526,527,529,530,532,533,534,535,536,554,555,558, 559,562,563,564,597,598,599,600,601,602,604 |
| O00571-2 | 1.033 | 291 | 0.959 | 798.847 | 0.563 | 0.748 | 0.949 | 0.354 | 1.317 | 0.269 | 0.411 | 133,134,135,136,137,138,139,140,141,142,144,147,16 6,181,182,183,184,185,186,188,189,191,210,211,212, 213,214,215,216,260,261,262,264,265,268,269,272,33 1,332,335,425,426,427,461,465,468,469,472,488,489, 490,492,493,494,495,515,516,517,518,519,521,522,52 3 |
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 O00571-1_O00571-1_5e7j_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 O00571-1_5e7j_A_O00571-2.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of O00571-1_O00571-2.pdb |
| Protein Feature Comparison of the protein sequendary structures among the protiens. |
| ./stats/secondary_structure/figure/O00571-1_vs_O00571-2.png |
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| Protein Feature Comparison of the relative accessible surface area (ASA) among the protiens. |
| ./stats/relative_asa/O00571-1_vs_O00571-2.png |
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Protein-Protein Interaction |
| Interactors from UniProt. |
| Accession_id | Subsection | Start | End | Funcitonal feature | Splicing information |
| O00571 | Region | 38 | 44 | Note=Interaction with EIF4E;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17667941;Dbxref=PMID:17667941 | Type=Substitution;Start=35;End=51 |
| Interactors from STRING. |
| Gene name | Interactors |
Related Drugs to DDX3X |
| Drugs targeting this gene/protein. (DrugBank) |
| UniProt accession | Gene name | DrugBank ID | Drug name | Drug group | Actions |
Related Diseases to DDX3X |
| Previous studies relating to the alternative splicing of DDX3X and disease information from the MeSH term (PubMed) |
| Gene | PMID | Title | Abstract | MeSH ID | MeSH term |
| DDX3X | 24711643 | Identifying biological pathways that underlie primordial short stature using network analysis. | Mutations in CUL7, OBSL1 and CCDC8, leading to disordered ubiquitination, cause one of the commonest primordial growth disorders, 3-M syndrome. This condition is associated with i) abnormal p53 function, ii) GH and/or IGF1 resistance, which may relate to failure to recycle signalling molecules, and iii) cellular IGF2 deficiency. However the exact molecular mechanisms that may link these abnormalities generating growth restriction remain undefined. In this study, we have used immunoprecipitation/mass spectrometry and transcriptomic studies to generate a 3-M 'interactome', to define key cellular pathways and biological functions associated with growth failure seen in 3-M. We identified 189 proteins which interacted with CUL7, OBSL1 and CCDC8, from which a network including 176 of these proteins was generated. To strengthen the association to 3-M syndrome, these proteins were compared with an inferred network generated from the genes that were differentially expressed in 3-M fibroblasts compared with controls. This resulted in a final 3-M network of 131 proteins, with the most significant biological pathway within the network being mRNA splicing/processing. We have shown using an exogenous insulin receptor (INSR) minigene system that alternative splicing of exon 11 is significantly changed in HEK293 cells with altered expression of CUL7, OBSL1 and CCDC8 and in 3-M fibroblasts. The net result is a reduction in the expression of the mitogenic INSR isoform in 3-M syndrome. From these preliminary data, we hypothesise that disordered ubiquitination could result in aberrant mRNA splicing in 3-M; however, further investigation is required to determine whether this contributes to growth failure. | D004392 | Dwarfism |
| DDX3X | 24711643 | Identifying biological pathways that underlie primordial short stature using network analysis. | Mutations in CUL7, OBSL1 and CCDC8, leading to disordered ubiquitination, cause one of the commonest primordial growth disorders, 3-M syndrome. This condition is associated with i) abnormal p53 function, ii) GH and/or IGF1 resistance, which may relate to failure to recycle signalling molecules, and iii) cellular IGF2 deficiency. However the exact molecular mechanisms that may link these abnormalities generating growth restriction remain undefined. In this study, we have used immunoprecipitation/mass spectrometry and transcriptomic studies to generate a 3-M 'interactome', to define key cellular pathways and biological functions associated with growth failure seen in 3-M. We identified 189 proteins which interacted with CUL7, OBSL1 and CCDC8, from which a network including 176 of these proteins was generated. To strengthen the association to 3-M syndrome, these proteins were compared with an inferred network generated from the genes that were differentially expressed in 3-M fibroblasts compared with controls. This resulted in a final 3-M network of 131 proteins, with the most significant biological pathway within the network being mRNA splicing/processing. We have shown using an exogenous insulin receptor (INSR) minigene system that alternative splicing of exon 11 is significantly changed in HEK293 cells with altered expression of CUL7, OBSL1 and CCDC8 and in 3-M fibroblasts. The net result is a reduction in the expression of the mitogenic INSR isoform in 3-M syndrome. From these preliminary data, we hypothesise that disordered ubiquitination could result in aberrant mRNA splicing in 3-M; however, further investigation is required to determine whether this contributes to growth failure. | D006130 | Growth Disorders |
| DDX3X | 24711643 | Identifying biological pathways that underlie primordial short stature using network analysis. | Mutations in CUL7, OBSL1 and CCDC8, leading to disordered ubiquitination, cause one of the commonest primordial growth disorders, 3-M syndrome. This condition is associated with i) abnormal p53 function, ii) GH and/or IGF1 resistance, which may relate to failure to recycle signalling molecules, and iii) cellular IGF2 deficiency. However the exact molecular mechanisms that may link these abnormalities generating growth restriction remain undefined. In this study, we have used immunoprecipitation/mass spectrometry and transcriptomic studies to generate a 3-M 'interactome', to define key cellular pathways and biological functions associated with growth failure seen in 3-M. We identified 189 proteins which interacted with CUL7, OBSL1 and CCDC8, from which a network including 176 of these proteins was generated. To strengthen the association to 3-M syndrome, these proteins were compared with an inferred network generated from the genes that were differentially expressed in 3-M fibroblasts compared with controls. This resulted in a final 3-M network of 131 proteins, with the most significant biological pathway within the network being mRNA splicing/processing. We have shown using an exogenous insulin receptor (INSR) minigene system that alternative splicing of exon 11 is significantly changed in HEK293 cells with altered expression of CUL7, OBSL1 and CCDC8 and in 3-M fibroblasts. The net result is a reduction in the expression of the mitogenic INSR isoform in 3-M syndrome. From these preliminary data, we hypothesise that disordered ubiquitination could result in aberrant mRNA splicing in 3-M; however, further investigation is required to determine whether this contributes to growth failure. | D009123 | Muscle Hypotonia |
Clinically important variants in DDX3X |
| (ClinVar, 04/20/2024) |
| accession_id | uniprot_id | gene_name | Type | Variant | Clinical_significance |
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