Protein:NEDD4 |
Protein Summary |
 Gene summary |
| Gene name: NEDD4 | ASpdb.0 ID: 4734 | Gene | Gene symbol | NEDD4 | Gene ID | 4734 |
| Gene name | NEDD4 E3 ubiquitin protein ligase |
| Synonyms | NEDD4-1|RPF1 |
| Cytomap | 15q21.3 |
| Type of gene | protein-coding |
| Description | E3 ubiquitin-protein ligase NEDD4HECT-type E3 ubiquitin transferase NEDD4cell proliferation-inducing gene 53 proteinneural precursor cell expressed, developmentally down-regulated 4, E3 ubiquitin protein ligasereceptor-potentiating factor 1 |
| Modification date | 20240407 |
| UniProtAcc | P46934 |
| Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Gene | NEDD4 | GO:0000785 | chromatin | 17996703 |
| Gene | NEDD4 | GO:0005634 | nucleus | 11342538 |
| Gene | NEDD4 | GO:0005737 | cytoplasm | 11342538|12796489 |
| Gene | NEDD4 | GO:0005794 | Golgi apparatus | 16118794 |
| Gene | NEDD4 | GO:0005886 | plasma membrane | 16118794 |
| Gene | NEDD4 | GO:0005938 | cell cortex | 9990509 |
| Gene | NEDD4 | GO:0006511 | ubiquitin-dependent protein catabolic process | 11342538|20086093|26263374 |
| Gene | NEDD4 | GO:0007041 | lysosomal transport | 18544533 |
| Gene | NEDD4 | GO:0010766 | negative regulation of sodium ion transport | 10642508 |
| Gene | NEDD4 | GO:0016567 | protein ubiquitination | 26280536 |
| Gene | NEDD4 | GO:0016567 | protein ubiquitination | 17116753|17996703|18305167|25631046 |
| Gene | NEDD4 | GO:0019871 | sodium channel inhibitor activity | 10642508 |
| Gene | NEDD4 | GO:0031623 | receptor internalization | 18544533 |
| Gene | NEDD4 | GO:0031698 | beta-2 adrenergic receptor binding | 18544533 |
| Gene | NEDD4 | GO:0032801 | receptor catabolic process | 18544533 |
| Gene | NEDD4 | GO:0032991 | protein-containing complex | 17116753 |
| Gene | NEDD4 | GO:0034765 | regulation of monoatomic ion transmembrane transport | 17289006 |
| Gene | NEDD4 | GO:0042391 | regulation of membrane potential | 17289006 |
| Gene | NEDD4 | GO:0042921 | glucocorticoid receptor signaling pathway | 8649367 |
| Gene | NEDD4 | GO:0043130 | ubiquitin binding | 9990509 |
| Gene | NEDD4 | GO:0045087 | innate immune response | 23951545 |
| Gene | NEDD4 | GO:0045732 | positive regulation of protein catabolic process | 14973438 |
| Gene | NEDD4 | GO:0046824 | positive regulation of nucleocytoplasmic transport | 17218261 |
| Gene | NEDD4 | GO:0048471 | perinuclear region of cytoplasm | 9990509 |
| Gene | NEDD4 | GO:0050847 | progesterone receptor signaling pathway | 8649367 |
| Gene | NEDD4 | GO:0061630 | ubiquitin protein ligase activity | 11342538|17116753|17996703|20086093|26006083|34880843 |
| Gene | NEDD4 | GO:1901016 | regulation of potassium ion transmembrane transporter activity | 17289006 |
| Gene | NEDD4 | GO:2000650 | negative regulation of sodium ion transmembrane transporter activity | 10642508 |
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 |
| P46934-1 | P46934-1_4bbn_A.pdb | 4BBN | X-ray | 2.51 | A | 938 | 1315 |
| 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 |
| P46934 | NEDD4 | P46934-1 | P46934-4 | 1319 | 900 | 1 | 419 | Deletion | none | none | 0 | 0 |
| P46934 | NEDD4 | P46934-1 | P46934-4 | 1319 | 900 | 420 | 516 | Substitution | SACLPSSQNVDCQININGELERPHSQMNKNHGILRRSISLGGAYPNISCLSSLKHNCSKGGPSQLLIKFASGNEGKVDNLSRDSNRDCTNELSNSCK | MATCAVEVFGLLEDEENSRIVRVRVIAGIGLAKKDILGASDPYVRVTLYDPMNGVLTSVQTKTIKKSLNPKWNEEILFRVHPQQHRLLFEVFDENRL | 1 | 97 |
| Multiple sequence alignment of our canonical and alternatively spliced NEDD4 |
| Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of NEDD4 |
| UniProt-id | ENSG | ENST | ENSP |
| P46934-1 | ENSG00000069869.17 | ENST00000508342.5 | ENSP00000424827.1 |
| P46934-4 | ENSG00000069869.17 | ENST00000435532.8 | ENSP00000410613.3 |
| UniProt-id | NM ID | NP ID |
| P46934-1 | NM_001284338.1 | NP_001271267.1 |
| P46934-4 | NM_006154.3 | NP_006145.2 |
| Amino acid sequences of our canonical and alternatively spliced NEDD4 |
| accession_id | Protein sequence |
| P46934-1 | MAQSLRLHFAARRSNTYPLSETSGDDLDSHVHMCFKRPTRISTSNVVQMKLTPRQTALAPLIKENVQSQERSSVPSSENVNKKSSCLQIS LQPTRYSGYLQSSNVLADSDDASFTCILKDGIYSSAVVDNELNAVNDGHLVSSPAICSGSLSNFSTSDNGSYSSNGSDFGSCASITSGGS YTNSVISDSSSYTFPPSDDTFLGGNLPSDSTSNRSVPNRNTTPCEIFSRSTSTDPFVQDDLEHGLEIMKLPVSRNTKIPLKRYSSLVIFP RSPSTTRPTSPTSLCTLLSKGSYQTSHQFIISPSEIAHNEDGTSAKGFLSTAVNGLRLSKTICTPGEVRDIRPLHRKGSLQKKIVLSNNT PRQTVCEKSSEGYSCVSVHFTQRKAATLDCETTNGDCKPEMSEIKLNSDSEYIKLMHRTSACLPSSQNVDCQININGELERPHSQMNKNH GILRRSISLGGAYPNISCLSSLKHNCSKGGPSQLLIKFASGNEGKVDNLSRDSNRDCTNELSNSCKTRDDFLGQVDVPLYPLPTENPRLE RPYTFKDFVLHPRSHKSRVKGYLRLKMTYLPKTSGSEDDNAEQAEELEPGWVVLDQPDAACHLQQQQEPSPLPPGWEERQDILGRTYYVN HESRRTQWKRPTPQDNLTDAENGNIQLQAQRAFTTRRQISEETESVDNRESSENWEIIREDEATMYSNQAFPSPPPSSNLDVPTHLAEEL NARLTIFGNSAVSQPASSSNHSSRRGSLQAYTFEEQPTLPVLLPTSSGLPPGWEEKQDERGRSYYVDHNSRTTTWTKPTVQATVETSQLT SSQSSAGPQSQASTSDSGQQVTQPSEIEQGFLPKGWEVRHAPNGRPFFIDHNTKTTTWEDPRLKIPAHLRGKTSLDTSNDLGPLPPGWEE RTHTDGRIFYINHNIKRTQWEDPRLENVAITGPAVPYSRDYKRKYEFFRRKLKKQNDIPNKFEMKLRRATVLEDSYRRIMGVKRADFLKA RLWIEFDGEKGLDYGGVAREWFFLISKEMFNPYYGLFEYSATDNYTLQINPNSGLCNEDHLSYFKFIGRVAGMAVYHGKLLDGFFIRPFY KMMLHKPITLHDMESVDSEYYNSLRWILENDPTELDLRFIIDEELFGQTHQHELKNGGSEIVVTNKNKKEYIYLVIQWRFVNRIQKQMAA FKEGFFELIPQDLIKIFDENELELLMCGLGDVDVNDWREHTKYKNGYSANHQVIQWFWKAVLMMDSEKRIRLLQFVTGTSRVPMNGFAEL |
| P46934-4 | MATCAVEVFGLLEDEENSRIVRVRVIAGIGLAKKDILGASDPYVRVTLYDPMNGVLTSVQTKTIKKSLNPKWNEEILFRVHPQQHRLLFE VFDENRLTRDDFLGQVDVPLYPLPTENPRLERPYTFKDFVLHPRSHKSRVKGYLRLKMTYLPKTSGSEDDNAEQAEELEPGWVVLDQPDA ACHLQQQQEPSPLPPGWEERQDILGRTYYVNHESRRTQWKRPTPQDNLTDAENGNIQLQAQRAFTTRRQISEETESVDNRESSENWEIIR EDEATMYSNQAFPSPPPSSNLDVPTHLAEELNARLTIFGNSAVSQPASSSNHSSRRGSLQAYTFEEQPTLPVLLPTSSGLPPGWEEKQDE RGRSYYVDHNSRTTTWTKPTVQATVETSQLTSSQSSAGPQSQASTSDSGQQVTQPSEIEQGFLPKGWEVRHAPNGRPFFIDHNTKTTTWE DPRLKIPAHLRGKTSLDTSNDLGPLPPGWEERTHTDGRIFYINHNIKRTQWEDPRLENVAITGPAVPYSRDYKRKYEFFRRKLKKQNDIP NKFEMKLRRATVLEDSYRRIMGVKRADFLKARLWIEFDGEKGLDYGGVAREWFFLISKEMFNPYYGLFEYSATDNYTLQINPNSGLCNED HLSYFKFIGRVAGMAVYHGKLLDGFFIRPFYKMMLHKPITLHDMESVDSEYYNSLRWILENDPTELDLRFIIDEELFGQTHQHELKNGGS EIVVTNKNKKEYIYLVIQWRFVNRIQKQMAAFKEGFFELIPQDLIKIFDENELELLMCGLGDVDVNDWREHTKYKNGYSANHQVIQWFWK AVLMMDSEKRIRLLQFVTGTSRVPMNGFAELYGSNGPQSFTVEQWGTPEKLPRAHTCFNRLDLPPYESFEELWDKLQMAIENTQGFDGVD |
Protein Functional Features |
| Main function of this protein. (from UniProt) |
| NEDD4 (go to UniProt):P46934 |
| 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 |
| P46934 | Region | 204 | 229 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=1;End=419 |
Gene Isoform Structures and Expression Levels for NEDD4 |
| Gene structures of our canonical and alternative spliced genes of NEDD4 * 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 P46934-1 |
| 3D view using mol* of P46934-4 |
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 P46934-1 |
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| pLDDT distribution across the protein length of P46934-4 |
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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 P46934-1 |
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| Ramachandran plot of P46934-4 |
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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 |
| P46934-1 | 1.054 | 259 | 1.1 | 600.936 | 0.46 | 0.718 | 0.95 | 1.148 | 0.83 | 1.383 | 0.718 | 1,2,5,7,87,88,89,90,91,92,93,94,378,482,483,484,48 5,486,487,488,529,532,535,545,564,565,566,567,568, 569,570 |
| P46934-4 | 1.041 | 352 | 1.078 | 1047.865 | 0.6 | 0.718 | 0.929 | 0.753 | 0.898 | 0.838 | 1.001 | 505,506,507,508,509,510,511,513,514,515,516,518,51 9,522,523,526,530,598,601,602,603,610,613,614,616, 617,618,646,649,650,651,653,654,655,656,657,658,66 1,675,676,677,679,771,774,775,776,779,780,781,782, 783,784,785,786,787,789,800,806,809,810,813,814,81 5,816,817,818,820,824,828,829,830,832,833,834,835, 837,838,841,842,843,844,866,867,869 |
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 P46934-1_P46934-1_4bbn_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 P46934-1_4bbn_A_P46934-4.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of P46934-1_P46934-4.pdb |
| Protein Feature Comparison of the protein sequendary structures among the protiens. |
| ./stats/secondary_structure/figure/P46934-1_vs_P46934-4.png |
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| Protein Feature Comparison of the relative accessible surface area (ASA) among the protiens. |
| ./stats/relative_asa/P46934-1_vs_P46934-4.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 NEDD4 |
| Drugs targeting this gene/protein. (DrugBank) |
| UniProt accession | Gene name | DrugBank ID | Drug name | Drug group | Actions |
Related Diseases to NEDD4 |
| Previous studies relating to the alternative splicing of NEDD4 and disease information from the MeSH term (PubMed) |
| Gene | PMID | Title | Abstract | MeSH ID | MeSH term |
Clinically important variants in NEDD4 |
| (ClinVar, 04/20/2024) |
| accession_id | uniprot_id | gene_name | Type | Variant | Clinical_significance |
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