8pn2: Difference between revisions

Revision as of 05:28, 17 April 2024

CryoEM structure of Nal1 protein, allele IR64, from Oryza sativa indica cultivar

Structural highlights

8pn2 is a 6 chain structure with sequence from Oryza sativa Indica Group. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 2.63Å
Ligands:	ATP, MG
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NAL1_ORYSJ Involved in the regulation of lateral leaf growth (PubMed:18562767, PubMed:22179305, PubMed:23985993). May be involved in the regulation of basipetal polar auxin transport (PAT) and vascular patterning in leaves (PubMed:18562767). Controls photosynthesis rate by regulating carboxylation efficiency and consequently photosynthesis rate (PubMed:23985993). Controls panicle and spikelet numbers, and grain yield (PubMed:23985993, PubMed:24297875, PubMed:24795339).^[1] ^[2] ^[3] ^[4] ^[5]

References

↑ Qi J, Qian Q, Bu Q, Li S, Chen Q, Sun J, Liang W, Zhou Y, Chu C, Li X, Ren F, Palme K, Zhao B, Chen J, Chen M, Li C. Mutation of the rice Narrow leaf1 gene, which encodes a novel protein, affects vein patterning and polar auxin transport. Plant Physiol. 2008 Aug;147(4):1947-59. PMID:18562767 doi:10.1104/pp.108.118778
↑ Chen M, Luo J, Shao G, Wei X, Tang S, Sheng Z, Song J, Hu P. Fine mapping of a major QTL for flag leaf width in rice, qFLW4, which might be caused by alternative splicing of NAL1. Plant Cell Rep. 2012 May;31(5):863-72. PMID:22179305 doi:10.1007/s00299-011-1207-7
↑ Takai T, Adachi S, Taguchi-Shiobara F, Sanoh-Arai Y, Iwasawa N, Yoshinaga S, Hirose S, Taniguchi Y, Yamanouchi U, Wu J, Matsumoto T, Sugimoto K, Kondo K, Ikka T, Ando T, Kono I, Ito S, Shomura A, Ookawa T, Hirasawa T, Yano M, Kondo M, Yamamoto T. A natural variant of NAL1, selected in high-yield rice breeding programs, pleiotropically increases photosynthesis rate. Sci Rep. 2013;3:2149. PMID:23985993 doi:10.1038/srep02149
↑ Fujita D, Trijatmiko KR, Tagle AG, Sapasap MV, Koide Y, Sasaki K, Tsakirpaloglou N, Gannaban RB, Nishimura T, Yanagihara S, Fukuta Y, Koshiba T, Slamet-Loedin IH, Ishimaru T, Kobayashi N. NAL1 allele from a rice landrace greatly increases yield in modern indica cultivars. Proc Natl Acad Sci U S A. 2013 Dec 17;110(51):20431-6. PMID:24297875 doi:10.1073/pnas.1310790110
↑ Zhang GH, Li SY, Wang L, Ye WJ, Zeng DL, Rao YC, Peng YL, Hu J, Yang YL, Xu J, Ren DY, Gao ZY, Zhu L, Dong GJ, Hu XM, Yan MX, Guo LB, Li CY, Qian Q. LSCHL4 from Japonica Cultivar, which is allelic to NAL1, increases yield of indica super rice 93-11. Mol Plant. 2014 Aug;7(8):1350-1364. PMID:24795339 doi:10.1093/mp/ssu055

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OCA

[1] Qi J, Qian Q, Bu Q, Li S, Chen Q, Sun J, Liang W, Zhou Y, Chu C, Li X, Ren F, Palme K, Zhao B, Chen J, Chen M, Li C. Mutation of the rice Narrow leaf1 gene, which encodes a novel protein, affects vein patterning and polar auxin transport. Plant Physiol. 2008 Aug;147(4):1947-59. PMID:18562767 doi:10.1104/pp.108.118778

[2] Chen M, Luo J, Shao G, Wei X, Tang S, Sheng Z, Song J, Hu P. Fine mapping of a major QTL for flag leaf width in rice, qFLW4, which might be caused by alternative splicing of NAL1. Plant Cell Rep. 2012 May;31(5):863-72. PMID:22179305 doi:10.1007/s00299-011-1207-7

[3] Takai T, Adachi S, Taguchi-Shiobara F, Sanoh-Arai Y, Iwasawa N, Yoshinaga S, Hirose S, Taniguchi Y, Yamanouchi U, Wu J, Matsumoto T, Sugimoto K, Kondo K, Ikka T, Ando T, Kono I, Ito S, Shomura A, Ookawa T, Hirasawa T, Yano M, Kondo M, Yamamoto T. A natural variant of NAL1, selected in high-yield rice breeding programs, pleiotropically increases photosynthesis rate. Sci Rep. 2013;3:2149. PMID:23985993 doi:10.1038/srep02149

[4] Fujita D, Trijatmiko KR, Tagle AG, Sapasap MV, Koide Y, Sasaki K, Tsakirpaloglou N, Gannaban RB, Nishimura T, Yanagihara S, Fukuta Y, Koshiba T, Slamet-Loedin IH, Ishimaru T, Kobayashi N. NAL1 allele from a rice landrace greatly increases yield in modern indica cultivars. Proc Natl Acad Sci U S A. 2013 Dec 17;110(51):20431-6. PMID:24297875 doi:10.1073/pnas.1310790110

[5] Zhang GH, Li SY, Wang L, Ye WJ, Zeng DL, Rao YC, Peng YL, Hu J, Yang YL, Xu J, Ren DY, Gao ZY, Zhu L, Dong GJ, Hu XM, Yan MX, Guo LB, Li CY, Qian Q. LSCHL4 from Japonica Cultivar, which is allelic to NAL1, increases yield of indica super rice 93-11. Mol Plant. 2014 Aug;7(8):1350-1364. PMID:24795339 doi:10.1093/mp/ssu055

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 8pn2 is ON HOLD  until Paper Publication
+==CryoEM structure of Nal1 protein, allele IR64, from Oryza sativa indica cultivar==
+<StructureSection load='8pn2' size='340' side='right'caption='[[8pn2]], [[Resolution|resolution]] 2.63&Aring;' scene=''>
-Authors: Huang, L.Y., Rety, S., Xi, X.G.
+== Structural highlights ==
+<table><tr><td colspan='2'>[[8pn2]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryza_sativa_Indica_Group Oryza sativa Indica Group]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8PN2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8PN2 FirstGlance]. <br>
-Description: CryoEM structure of Nal1 protein, allele IR64, from Oryza sativa indica cultivar
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 2.63&#8491;</td></tr>
-[[Category: Unreleased Structures]]
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-[[Category: Xi, X.G]]
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8pn2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8pn2 OCA], [https://pdbe.org/8pn2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8pn2 RCSB], [https://www.ebi.ac.uk/pdbsum/8pn2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8pn2 ProSAT]</span></td></tr>
-[[Category: Rety, S]]
+</table>
-[[Category: Huang, L.Y]]
+== Function ==
+[https://www.uniprot.org/uniprot/NAL1_ORYSJ NAL1_ORYSJ] Involved in the regulation of lateral leaf growth (PubMed:18562767, PubMed:22179305, PubMed:23985993). May be involved in the regulation of basipetal polar auxin transport (PAT) and vascular patterning in leaves (PubMed:18562767). Controls photosynthesis rate by regulating carboxylation efficiency and consequently photosynthesis rate (PubMed:23985993). Controls panicle and spikelet numbers, and grain yield (PubMed:23985993, PubMed:24297875, PubMed:24795339).<ref>PMID:18562767</ref> <ref>PMID:22179305</ref> <ref>PMID:23985993</ref> <ref>PMID:24297875</ref> <ref>PMID:24795339</ref>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Oryza sativa Indica Group]]
+[[Category: Huang LY]]
+[[Category: Rety S]]
+[[Category: Xi XG]]

8pn2: Difference between revisions

Revision as of 05:28, 17 April 2024

CryoEM structure of Nal1 protein, allele IR64, from Oryza sativa indica cultivar

Structural highlights

Function

References

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