This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

6jvy

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Crystal structure of RBM38 in complex with single-stranded DNA

Structural highlights

6jvy is a 2 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.003Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RBM38_HUMAN RNA-binding protein that specifically bind the 3'-UTR of CDKN1A transcripts, leading to maintain the stability of CDKN1A transcripts, thereby acting as a mediator of the p53/TP53 family to regulate CDKN1A. CDKN1A is a cyclin-dependent kinase inhibitor transcriptionally regulated by the p53/TP53 family to induce cell cycle arrest. Isoform 1, but not isoform 2, has the ability to induce cell cycle arrest in G1 and maintain the stability of CDKN1A transcripts induced by p53/TP53. Also acts as a mRNA splicing factor. Specifically regulates the expression of FGFR2-IIIb, an epithelial cell-specific isoform of FGFR2. Plays a role in myogenic differentiation.^[1] ^[2]

Publication Abstract from PubMed

RNA-binding protein RBM38 was reported to bind the mRNA of several p53-related genes through its RRM domain and to upregulate or downregulate protein translation by increasing mRNA stability or recruitment of other effector proteins. The recognition mechanism, however, for RNA-binding of RBM38 remains unclear. Here we report the crystal structure of the RRM domain of human RBM38 in complex with a single-stranded RNA. Our structural and biological results revealed that RBM38 recognizes G(U/C/A)GUG sequence single-stranded RNA in a sequence-specific and structure-specific manner. Two phenylalanine stacked with bases of RNA were crucial for RNA binding, and a series of hydrogen bonds between the base atoms of RNA and main-chain or side-chain atoms of RBM38 determine the sequence-specific recognition. Our results revealed the RNA-recognition mechanism of human RBM38 and provided structural information for understanding the RNA-binding property of RBM38.

Structural basis for mRNA recognition by human RBM38.,Qian K, Li M, Wang J, Zhang M, Wang M Biochem J. 2019 Dec 20. pii: 221657. doi: 10.1042/BCJ20190652. PMID:31860021^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Shu L, Yan W, Chen X. RNPC1, an RNA-binding protein and a target of the p53 family, is required for maintaining the stability of the basal and stress-induced p21 transcript. Genes Dev. 2006 Nov 1;20(21):2961-72. Epub 2006 Oct 18. PMID:17050675 doi:http://dx.doi.org/10.1101/gad.1463306
↑ Warzecha CC, Sato TK, Nabet B, Hogenesch JB, Carstens RP. ESRP1 and ESRP2 are epithelial cell-type-specific regulators of FGFR2 splicing. Mol Cell. 2009 Mar 13;33(5):591-601. doi: 10.1016/j.molcel.2009.01.025. PMID:19285943 doi:http://dx.doi.org/10.1016/j.molcel.2009.01.025
↑ Qian K, Li M, Wang J, Zhang M, Wang M. Structural basis for mRNA recognition by human RBM38. Biochem J. 2019 Dec 20. pii: 221657. doi: 10.1042/BCJ20190652. PMID:31860021 doi:http://dx.doi.org/10.1042/BCJ20190652

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6jvy"

@@ Line 3: / Line 3: @@
 <StructureSection load='6jvy' size='340' side='right'caption='[[6jvy]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6jvy]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JVY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JVY FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6jvy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JVY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JVY FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.003&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6jvx|6jvx]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6jvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jvy OCA], [http://pdbe.org/6jvy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jvy RCSB], [http://www.ebi.ac.uk/pdbsum/6jvy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jvy ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6jvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jvy OCA], [https://pdbe.org/6jvy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jvy RCSB], [https://www.ebi.ac.uk/pdbsum/6jvy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jvy ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RBM38_HUMAN RBM38_HUMAN]] RNA-binding protein that specifically bind the 3'-UTR of CDKN1A transcripts, leading to maintain the stability of CDKN1A transcripts, thereby acting as a mediator of the p53/TP53 family to regulate CDKN1A. CDKN1A is a cyclin-dependent kinase inhibitor transcriptionally regulated by the p53/TP53 family to induce cell cycle arrest. Isoform 1, but not isoform 2, has the ability to induce cell cycle arrest in G1 and maintain the stability of CDKN1A transcripts induced by p53/TP53. Also acts as a mRNA splicing factor. Specifically regulates the expression of FGFR2-IIIb, an epithelial cell-specific isoform of FGFR2. Plays a role in myogenic differentiation.<ref>PMID:17050675</ref> <ref>PMID:19285943</ref>
+[https://www.uniprot.org/uniprot/RBM38_HUMAN RBM38_HUMAN] RNA-binding protein that specifically bind the 3'-UTR of CDKN1A transcripts, leading to maintain the stability of CDKN1A transcripts, thereby acting as a mediator of the p53/TP53 family to regulate CDKN1A. CDKN1A is a cyclin-dependent kinase inhibitor transcriptionally regulated by the p53/TP53 family to induce cell cycle arrest. Isoform 1, but not isoform 2, has the ability to induce cell cycle arrest in G1 and maintain the stability of CDKN1A transcripts induced by p53/TP53. Also acts as a mRNA splicing factor. Specifically regulates the expression of FGFR2-IIIb, an epithelial cell-specific isoform of FGFR2. Plays a role in myogenic differentiation.<ref>PMID:17050675</ref> <ref>PMID:19285943</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 23: @@
 __TOC__
 </StructureSection>
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Li, M]]
+[[Category: Li M]]
-[[Category: Qian, K]]
+[[Category: Qian K]]
-[[Category: Wang, J]]
+[[Category: Wang J]]
-[[Category: Wang, M]]
+[[Category: Wang M]]
-[[Category: Zhang, M]]
+[[Category: Zhang M]]
-[[Category: Rbm38]]
-[[Category: Rna binding]]
-[[Category: Rna binding protein]]
-[[Category: Rna binding protein-dna complex]]
-[[Category: Translational regulation]]

6jvy

From Proteopedia

Current revision

Crystal structure of RBM38 in complex with single-stranded DNA

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox