5mlc: Difference between revisions

Latest revision as of 10:19, 17 October 2024

Cryo-EM structure of the spinach chloroplast ribosome reveals the location of plastid-specific ribosomal proteins and extensionsCryo-EM structure of the spinach chloroplast ribosome reveals the location of plastid-specific ribosomal proteins and extensions

5mlc, resolution 3.60Å

Structural highlights

5mlc is a 10 chain structure with sequence from Spinacia oleracea. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 3.6Å
Experimental data:	Check
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RK2_SPIOL

Publication Abstract from PubMed

Ribosomes are the protein synthesizing machines of the cell. Recent advances in cryo-EM have led to the determination of structures from a variety of species, including bacterial 70S and eukaryotic 80S ribosomes as well as mitoribosomes from eukaryotic mitochondria, however, to date high resolution structures of plastid 70S ribosomes have been lacking. Here we present a cryo-EM structure of the spinach chloroplast 70S ribosome, with an average resolution of 5.4 A for the small 30S subunit and 3.6 A for the large 50S ribosomal subunit. The structure reveals the location of the plastid-specific ribosomal proteins (RPs) PSRP1, PSRP4, PSRP5 and PSRP6 as well as the numerous plastid-specific extensions of the RPs. We discover many features by which the plastid-specific extensions stabilize the ribosome via establishing additional interactions with surrounding ribosomal RNA and RPs. Moreover, we identify a large conglomerate of plastid-specific protein mass adjacent to the tunnel exit site that could facilitate interaction of the chloroplast ribosome with the thylakoid membrane and the protein-targeting machinery. Comparing the Escherichia coli 70S ribosome with that of the spinach chloroplast ribosome provides detailed insight into the co-evolution of RP and rRNA.

Cryo-EM structure of the spinach chloroplast ribosome reveals the location of plastid-specific ribosomal proteins and extensions.,Graf M, Arenz S, Huter P, Donhofer A, Novacek J, Wilson DN Nucleic Acids Res. 2016 Dec 15. pii: gkw1272. PMID:27986857^[1]

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

References

↑ Graf M, Arenz S, Huter P, Donhofer A, Novacek J, Wilson DN. Cryo-EM structure of the spinach chloroplast ribosome reveals the location of plastid-specific ribosomal proteins and extensions. Nucleic Acids Res. 2016 Dec 15. pii: gkw1272. PMID:27986857 doi:http://dx.doi.org/10.1093/nar/gkw1272

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OCA

[1] Graf M, Arenz S, Huter P, Donhofer A, Novacek J, Wilson DN. Cryo-EM structure of the spinach chloroplast ribosome reveals the location of plastid-specific ribosomal proteins and extensions. Nucleic Acids Res. 2016 Dec 15. pii: gkw1272. PMID:27986857 doi:http://dx.doi.org/10.1093/nar/gkw1272

[1]

@@ Line 1: / Line 1: @@
 ==Cryo-EM structure of the spinach chloroplast ribosome reveals the location of plastid-specific ribosomal proteins and extensions==
-<SX load='5mlc' size='340' side='right' viewer='molstar' caption='[[5mlc]], [[Resolution|resolution]] 3.90&Aring;' scene=''>
+<SX load='5mlc' size='340' side='right' viewer='molstar' caption='[[5mlc]], [[Resolution|resolution]] 3.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5mlc]] is a 32 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=5MLC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MLC FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5mlc]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MLC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5MLC FirstGlance]. <br>
-</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=5mlc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mlc OCA], [http://pdbe.org/5mlc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mlc RCSB], [http://www.ebi.ac.uk/pdbsum/5mlc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mlc ProSAT]</span></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.6&#8491;</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=5mlc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mlc OCA], [https://pdbe.org/5mlc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5mlc RCSB], [https://www.ebi.ac.uk/pdbsum/5mlc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5mlc ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RK14_SPIOL RK14_SPIOL]] Binds to 23S rRNA (By similarity). [[http://www.uniprot.org/uniprot/RK24_SPIOL RK24_SPIOL]] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit (By similarity). Located at the polypeptide exit tunnel on the outside of the subunit. [[http://www.uniprot.org/uniprot/RK5_SPIOL RK5_SPIOL]] Binds 5S rRNA, forms part of the central protuberance of the 50S subunit (By similarity). [[http://www.uniprot.org/uniprot/RK20_SPIOL RK20_SPIOL]] Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit (By similarity).[HAMAP-Rule:MF_00382] [[http://www.uniprot.org/uniprot/RK21_SPIOL RK21_SPIOL]] This protein binds to 23S ribosomal RNA in the presence of protein L20 (By similarity). [[http://www.uniprot.org/uniprot/RRFC_SPIOL RRFC_SPIOL]] Responsible for the release of ribosomes from messenger RNA at the termination of chloroplastic protein biosynthesis. [[http://www.uniprot.org/uniprot/RK19_SPIOL RK19_SPIOL]] Located at the 30S-50S ribosomal subunit interface and binds directly to 23S ribosomal RNA (By similarity).[:] [[http://www.uniprot.org/uniprot/RK4_SPIOL RK4_SPIOL]] Probably binds the 23S rRNA (By similarity).  This protein (expressed without the transit peptide) is able to provoke transcription termination from the spinach chloroplast rDNA operon and the E.coli S10 operon in vitro. [[http://www.uniprot.org/uniprot/RK34_SPIOL RK34_SPIOL]] This protein binds directly to 23S ribosomal RNA (By similarity). [[http://www.uniprot.org/uniprot/RK23_SPIOL RK23_SPIOL]] Binds to 23S rRNA (By similarity). Located at the polypeptide exit tunnel on the outside of the subunit. [[http://www.uniprot.org/uniprot/RK22_SPIOL RK22_SPIOL]] This protein binds specifically to 23S rRNA (By similarity).  The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome (By similarity).  Binds an erythromycin derivative added to the 50S subunit.
+[https://www.uniprot.org/uniprot/RK2_SPIOL RK2_SPIOL]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 20: / Line 21: @@
 ==See Also==
 *[[Ribosome 3D structures|Ribosome 3D structures]]
+*[[Ribosome recycling factor|Ribosome recycling factor]]
 == References ==
 <references/>
@@ Line 26: / Line 28: @@
 [[Category: Large Structures]]
 [[Category: Spinacia oleracea]]
-[[Category: Arenz, S]]
+[[Category: Arenz S]]
-[[Category: Doenhoefer, A]]
+[[Category: Doenhoefer A]]
-[[Category: Graf, M]]
+[[Category: Graf M]]
-[[Category: Huter, P]]
+[[Category: Huter P]]
-[[Category: Novacek, J]]
+[[Category: Novacek J]]
-[[Category: Wilson, D N]]
+[[Category: Wilson DN]]
-[[Category: Chloroplast]]
-[[Category: Ribosomal protein]]
-[[Category: Ribosome]]
-[[Category: Translation]]

5mlc: Difference between revisions

Latest revision as of 10:19, 17 October 2024

Cryo-EM structure of the spinach chloroplast ribosome reveals the location of plastid-specific ribosomal proteins and extensionsCryo-EM structure of the spinach chloroplast ribosome reveals the location of plastid-specific ribosomal proteins and extensions

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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5mlc: Difference between revisions

Latest revision as of 10:19, 17 October 2024

Cryo-EM structure of the spinach chloroplast ribosome reveals the location of plastid-specific ribosomal proteins and extensionsCryo-EM structure of the spinach chloroplast ribosome reveals the location of plastid-specific ribosomal proteins and extensions

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Navigation menu

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