5mmj

From Proteopedia

(Difference between revisions)

Revision as of 16:36, 18 January 2017

Structure of the small subunit of the chloroplast ribosome

Structural highlights

5mmj is a 26 chain structure with sequence from Spinacia oleracea. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
NonStd Res:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[RR19_SPIOL] This protein binds directly to 16S ribosomal RNA.^[1] [RR5_SPIOL] Binds directly to 16S ribosomal RNA. Involved in spectinomycin and neamine resistance and streptomycin independence.[:] [RR14_SPIOL] Binds 16S rRNA, required for the assembly of 30S particles (By similarity).[:] [RR4_SPIOL] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit (By similarity).[HAMAP-Rule:MF_01306] With S5 and S12 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_01306] [PRSP1_SPIOL] A ribosome-binding factor that may be involved in an unknown stress response. Modeling onto the 70S spinach chloroplast ribosome and its position in the E.coli 70S ribosome suggests it binds in the decoding region of the 30S ribosomal subunit, precluding the binding of tRNA to the ribosome. Its position is incompatible with translation. Upon expression in E.coli binds to 30S and 70S ribosomes, decreases binding of tRNA(fMet). Stabilizes 70S ribosomes against dissociation. May be recycled by the combined action of ribosome-recycling factor (RRF) and EF-G.^[2] [RRP3_SPIOL] One of the plastid-specific ribosomal proteins. [RR7_SPIOL] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit (By similarity).[HAMAP-Rule:MF_00480] [RR12_SPIOL] With S4 and S5 plays an important role in translational accuracy. Located at the interface of the 30S and 50S subunits (By similarity).[HAMAP-Rule:MF_00403_B] [RRP2_SPIOL] May have a role in the recruitment of stored chloroplast mRNAs for active protein synthesis.^[3] [RR8_SPIOL] One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit (By similarity).[HAMAP-Rule:MF_01302]

Publication Abstract from PubMed

Chloroplasts are cellular organelles of plants and algae that are responsible for energy conversion and carbon fixation by the photosynthetic reaction. As a consequence of their endosymbiotic origin, they still contain their own genome and the machinery for protein biosynthesis. Here, we present the atomic structure of the chloroplast 70S ribosome prepared from spinach leaves and resolved by cryo-EM at 3.4 A resolution. The complete structure reveals the features of the 4.5S rRNA, which probably evolved by the fragmentation of the 23S rRNA, and all five plastid-specific ribosomal proteins. These proteins, required for proper assembly and function of the chloroplast translation machinery, bind and stabilize rRNA including regions that only exist in the chloroplast ribosome. Furthermore, the structure reveals plastid-specific extensions of ribosomal proteins that extensively remodel the mRNA entry and exit site on the small subunit as well as the polypeptide tunnel exit and the putative binding site of the signal recognition particle on the large subunit. The translation factor pY, involved in light- and temperature-dependent control of protein synthesis, is bound to the mRNA channel of the small subunit and interacts with 16S rRNA nucleotides at the A-site and P-site, where it protects the decoding centre and inhibits translation by preventing tRNA binding. The small subunit is locked by pY in a non-rotated state, in which the intersubunit bridges to the large subunit are stabilized.

The complete structure of the chloroplast 70S ribosome in complex with translation factor pY.,Bieri P, Leibundgut M, Saurer M, Boehringer D, Ban N EMBO J. 2016 Dec 22. pii: e201695959. doi: 10.15252/embj.201695959. PMID:28007896^[4]

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

References

↑ Yamaguchi K, von Knoblauch K, Subramanian AR. The plastid ribosomal proteins. Identification of all the proteins in the 30 S subunit of an organelle ribosome (chloroplast). J Biol Chem. 2000 Sep 15;275(37):28455-65. PMID:10874039 doi:http://dx.doi.org/10.1074/jbc.M004350200
↑ Sharma MR, Donhofer A, Barat C, Marquez V, Datta PP, Fucini P, Wilson DN, Agrawal RK. PSRP1 is not a ribosomal protein, but a ribosome-binding factor that is recycled by the ribosome-recycling factor (RRF) and elongation factor G (EF-G). J Biol Chem. 2010 Feb 5;285(6):4006-14. doi: 10.1074/jbc.M109.062299. Epub 2009, Dec 4. PMID:19965869 doi:http://dx.doi.org/10.1074/jbc.M109.062299
↑ Yamaguchi K, Subramanian AR. Proteomic identification of all plastid-specific ribosomal proteins in higher plant chloroplast 30S ribosomal subunit. Eur J Biochem. 2003 Jan;270(2):190-205. PMID:12605670
↑ Bieri P, Leibundgut M, Saurer M, Boehringer D, Ban N. The complete structure of the chloroplast 70S ribosome in complex with translation factor pY. EMBO J. 2016 Dec 22. pii: e201695959. doi: 10.15252/embj.201695959. PMID:28007896 doi:http://dx.doi.org/10.15252/embj.201695959

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/5mmj"

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 5mmj is ON HOLD
+==Structure of the small subunit of the chloroplast ribosome==
+<StructureSection load='5mmj' size='340' side='right' caption='[[5mmj]], [[Resolution|resolution]] 3.65&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5mmj]] is a 26 chain structure with sequence from [http://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MMJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MMJ FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</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=5mmj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mmj OCA], [http://pdbe.org/5mmj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mmj RCSB], [http://www.ebi.ac.uk/pdbsum/5mmj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mmj ProSAT]</span></td></tr>
+</table>
+== Function ==
+[[http://www.uniprot.org/uniprot/RR19_SPIOL RR19_SPIOL]] This protein binds directly to 16S ribosomal RNA.<ref>PMID:10874039</ref>  [[http://www.uniprot.org/uniprot/RR5_SPIOL RR5_SPIOL]] Binds directly to 16S ribosomal RNA. Involved in spectinomycin and neamine resistance and streptomycin independence.[:] [[http://www.uniprot.org/uniprot/RR14_SPIOL RR14_SPIOL]] Binds 16S rRNA, required for the assembly of 30S particles (By similarity).[:] [[http://www.uniprot.org/uniprot/RR4_SPIOL RR4_SPIOL]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit (By similarity).[HAMAP-Rule:MF_01306]  With S5 and S12 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_01306] [[http://www.uniprot.org/uniprot/PRSP1_SPIOL PRSP1_SPIOL]] A ribosome-binding factor that may be involved in an unknown stress response. Modeling onto the 70S spinach chloroplast ribosome and its position in the E.coli 70S ribosome suggests it binds in the decoding region of the 30S ribosomal subunit, precluding the binding of tRNA to the ribosome. Its position is incompatible with translation. Upon expression in E.coli binds to 30S and 70S ribosomes, decreases binding of tRNA(fMet). Stabilizes 70S ribosomes against dissociation. May be recycled by the combined action of ribosome-recycling factor (RRF) and EF-G.<ref>PMID:19965869</ref>  [[http://www.uniprot.org/uniprot/RRP3_SPIOL RRP3_SPIOL]] One of the plastid-specific ribosomal proteins. [[http://www.uniprot.org/uniprot/RR7_SPIOL RR7_SPIOL]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit (By similarity).[HAMAP-Rule:MF_00480] [[http://www.uniprot.org/uniprot/RR12_SPIOL RR12_SPIOL]] With S4 and S5 plays an important role in translational accuracy. Located at the interface of the 30S and 50S subunits (By similarity).[HAMAP-Rule:MF_00403_B] [[http://www.uniprot.org/uniprot/RRP2_SPIOL RRP2_SPIOL]] May have a role in the recruitment of stored chloroplast mRNAs for active protein synthesis.<ref>PMID:12605670</ref>  [[http://www.uniprot.org/uniprot/RR8_SPIOL RR8_SPIOL]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit (By similarity).[HAMAP-Rule:MF_01302]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Chloroplasts are cellular organelles of plants and algae that are responsible for energy conversion and carbon fixation by the photosynthetic reaction. As a consequence of their endosymbiotic origin, they still contain their own genome and the machinery for protein biosynthesis. Here, we present the atomic structure of the chloroplast 70S ribosome prepared from spinach leaves and resolved by cryo-EM at 3.4 A resolution. The complete structure reveals the features of the 4.5S rRNA, which probably evolved by the fragmentation of the 23S rRNA, and all five plastid-specific ribosomal proteins. These proteins, required for proper assembly and function of the chloroplast translation machinery, bind and stabilize rRNA including regions that only exist in the chloroplast ribosome. Furthermore, the structure reveals plastid-specific extensions of ribosomal proteins that extensively remodel the mRNA entry and exit site on the small subunit as well as the polypeptide tunnel exit and the putative binding site of the signal recognition particle on the large subunit. The translation factor pY, involved in light- and temperature-dependent control of protein synthesis, is bound to the mRNA channel of the small subunit and interacts with 16S rRNA nucleotides at the A-site and P-site, where it protects the decoding centre and inhibits translation by preventing tRNA binding. The small subunit is locked by pY in a non-rotated state, in which the intersubunit bridges to the large subunit are stabilized.
-Authors:
+The complete structure of the chloroplast 70S ribosome in complex with translation factor pY.,Bieri P, Leibundgut M, Saurer M, Boehringer D, Ban N EMBO J. 2016 Dec 22. pii: e201695959. doi: 10.15252/embj.201695959. PMID:28007896<ref>PMID:28007896</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 5mmj" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Spinacia oleracea]]
+[[Category: Ban, N]]
+[[Category: Bieri, P]]
+[[Category: Boehringer, D]]
+[[Category: Leibundgut, M]]
+[[Category: Saurer, M]]
+[[Category: Chloroplast]]
+[[Category: Cryo-em]]
+[[Category: Ribosome]]
+[[Category: Translation]]

5mmj

From Proteopedia

Revision as of 16:36, 18 January 2017

Structure of the small subunit of the chloroplast ribosome

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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