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.

6iqf

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

crystal structure of Arabidopsis thaliana Profilin 3

Structural highlights

6iqf is a 1 chain structure with sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.457Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PRF3_ARATH Binds to actin monomers and regulates the organization of the actin cytoskeleton (PubMed:23052593, PubMed:29861135). Can increase the critical concentration (Cc) of actin assembly in vitro (PubMed:23052593). Acts as downstream effector of the hydrogen sulfide signaling to regulate the assembly and depolymerization of F-actin (PubMed:25652660). At high concentrations, profilin prevents the polymerization of actin, whereas it enhances it at low concentrations (Probable). Binding to the poly-proline motif of formin induces oligomerization of PRF3 (PubMed:29861135). PRF3 oligomers inhibit formin-mediated actin assembly to modulate plant immunity triggered by pathogen-associated molecular patterns (PAMPs) (PubMed:29861135).^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

Profilins are abundant cytosolic proteins that are universally expressed in eukaryotes and regulate actin filament elongation by binding to both monomeric actin (G-actin) and formin proteins. The atypical profilin Arabidopsis AtPRF3 has been reported to cooperate with canonical profilin isoforms in suppressing formin-mediated actin polymerization during plant innate immunity responses. AtPRF3 has a 37-amino-acid-long N terminal extension (NTE), and its suppressive effect on actin assembly is derived from enhanced interaction with the poly-proline (Poly-P) of the formin AtFH1. However, the molecular mechanism remains unclear. Here, we solved the crystal structures of AtPRF3Delta22 and AtPRF3Delta37, as well as AtPRF2 apo form and in complex with AtFH1 Poly-P at 1.5-3.6 A resolutions. By combining these structures with molecular modeling, we found that AtPRF3Delta22 NTE has high plasticity, with a primary "closed" conformation that can adopt an open conformation that enables Poly-P binding. Furthermore, using molecular dynamics simulation and free-energy calculations of protein-protein binding, along with experimental validation, we show that the AtPRF3Delta22 binds to Poly-P in an adaptive manner, thereby enabling different binding modes that maintain the interaction through disordered sequences. Together, our structural and simulation results suggest that the dynamic conformational changes of the AtPRF3 NTE upon Poly-P binding modulate their interactions to fine-tune formin-mediated actin assembly.

Structural and computational examination of the Arabidopsis profilin-Poly-P complex reveals mechanistic details in profilin-regulated actin assembly.,Qiao Z, Sun H, Ng JTY, Ma Q, Koh SH, Mu Y, Miao Y, Gao YG J Biol Chem. 2019 Oct 25. pii: RA119.011307. doi: 10.1074/jbc.RA119.011307. PMID:31653702^[5]

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

References

↑ Fan T, Zhai H, Shi W, Wang J, Jia H, Xiang Y, An L. Overexpression of profilin 3 affects cell elongation and F-actin organization in Arabidopsis thaliana. Plant Cell Rep. 2013 Jan;32(1):149-60. PMID:23052593 doi:10.1007/s00299-012-1349-2
↑ Jia H, Hu Y, Fan T, Li J. Hydrogen sulfide modulates actin-dependent auxin transport via regulating ABPs results in changing of root development in Arabidopsis. Sci Rep. 2015 Feb 5;5:8251. PMID:25652660 doi:10.1038/srep08251
↑ Sun H, Qiao Z, Chua KP, Tursic A, Liu X, Gao YG, Mu Y, Hou X, Miao Y. Profilin Negatively Regulates Formin-Mediated Actin Assembly to Modulate PAMP-Triggered Plant Immunity. Curr Biol. 2018 Jun 18;28(12):1882-1895.e7. PMID:29861135 doi:10.1016/j.cub.2018.04.045
↑ Sun H, Qiao Z, Chua KP, Tursic A, Liu X, Gao YG, Mu Y, Hou X, Miao Y. Profilin Negatively Regulates Formin-Mediated Actin Assembly to Modulate PAMP-Triggered Plant Immunity. Curr Biol. 2018 Jun 18;28(12):1882-1895.e7. PMID:29861135 doi:10.1016/j.cub.2018.04.045
↑ Qiao Z, Sun H, Ng JTY, Ma Q, Koh SH, Mu Y, Miao Y, Gao YG. Structural and computational examination of the Arabidopsis profilin-Poly-P complex reveals mechanistic details in profilin-regulated actin assembly. J Biol Chem. 2019 Oct 25. pii: RA119.011307. doi: 10.1074/jbc.RA119.011307. PMID:31653702 doi:http://dx.doi.org/10.1074/jbc.RA119.011307

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

Categories: Arabidopsis thaliana | Large Structures | Gao Y | Qiao Z

@@ Line 3: / Line 3: @@
 <StructureSection load='6iqf' size='340' side='right'caption='[[6iqf]], [[Resolution|resolution]] 1.46&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6iqf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IQF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IQF FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6iqf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IQF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IQF FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PRF3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</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]] 1.457&#8491;</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=6iqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6iqf OCA], [http://pdbe.org/6iqf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6iqf RCSB], [http://www.ebi.ac.uk/pdbsum/6iqf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6iqf 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=6iqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6iqf OCA], [https://pdbe.org/6iqf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6iqf RCSB], [https://www.ebi.ac.uk/pdbsum/6iqf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6iqf ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PROF5_ARATH PROF5_ARATH]] Binds to actin and affects the structure of the cytoskeleton. At high concentrations, profilin prevents the polymerization of actin, whereas it enhances it at low concentrations. By binding to PIP2, it inhibits the formation of IP3 and DG (By similarity).
+[https://www.uniprot.org/uniprot/PRF3_ARATH PRF3_ARATH] Binds to actin monomers and regulates the organization of the actin cytoskeleton (PubMed:23052593, PubMed:29861135). Can increase the critical concentration (Cc) of actin assembly in vitro (PubMed:23052593). Acts as downstream effector of the hydrogen sulfide signaling to regulate the assembly and depolymerization of F-actin (PubMed:25652660). At high concentrations, profilin prevents the polymerization of actin, whereas it enhances it at low concentrations (Probable). Binding to the poly-proline motif of formin induces oligomerization of PRF3 (PubMed:29861135). PRF3 oligomers inhibit formin-mediated actin assembly to modulate plant immunity triggered by pathogen-associated molecular patterns (PAMPs) (PubMed:29861135).<ref>PMID:23052593</ref> <ref>PMID:25652660</ref> <ref>PMID:29861135</ref> <ref>PMID:29861135</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 25: / Line 25: @@
 __TOC__
 </StructureSection>
-[[Category: Arath]]
+[[Category: Arabidopsis thaliana]]
 [[Category: Large Structures]]
-[[Category: Gao, Y]]
+[[Category: Gao Y]]
-[[Category: Qiao, Z]]
+[[Category: Qiao Z]]
-[[Category: Actin binding]]
-[[Category: Plant protein]]
-[[Category: Regulate actin network]]

6iqf

From Proteopedia

Current revision

crystal structure of Arabidopsis thaliana Profilin 3

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox