5x8r

From Proteopedia

(Difference between revisions)

Revision as of 20:09, 6 March 2020

Structure of the 30S small subunit of chloroplast ribosome from spinach

5x8r, resolution 3.70Å

Structural highlights

5x8r 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.
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[RR13_SPIOL] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA.[HAMAP-Rule:MF_01315] [RRP3_SPIOL] One of the plastid-specific ribosomal proteins. [RR9_SPIOL] Binds directly to 16S ribosomal RNA.^[1] [:] [RR1_SPIOL] Component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus (PubMed:10874039, PubMed:28007896). Actively engaged in the initiation complex formation via a strong mRNA-binding activity. Possesses a poly(A)-binding activity which might play a role as a control element in chloroplast mRNA translation (PubMed:1527032).^[2] ^[3] ^[4] [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] [RRP2_SPIOL] May have a role in the recruitment of stored chloroplast mRNAs for active protein synthesis.^[5] [RR19_SPIOL] This protein binds directly to 16S ribosomal RNA.^[6] [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] [RR5_SPIOL] Binds directly to 16S ribosomal RNA. Involved in spectinomycin and neamine resistance and streptomycin independence.[:] [RR6_SPIOL] Binds together with S18 to 16S ribosomal RNA (By similarity).[UniProtKB:O78447] [RR14_SPIOL] Binds 16S rRNA, required for the assembly of 30S particles (By similarity).[:] [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] [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.^[7] [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]

Publication Abstract from PubMed

Chloroplastic translation is mediated by a bacterial-type 70S chloroplast ribosome. During the evolution, chloroplast ribosomes have acquired five plastid-specific ribosomal proteins or PSRPs (cS22, cS23, bTHXc, cL37 and cL38) which have been suggested to play important regulatory roles in translation. However, their exact locations on the chloroplast ribosome remain elusive due to lack of a high-resolution structure, hindering our progress to understand their possible roles. Here we present a cryo-EM structure of the 70S chloroplast ribosome from spinach resolved to 3.4 A and focus our discussion mainly on the architecture of the 30S small subunit (SSU) which is resolved to 3.7 A. cS22 localizes at the SSU foot where it seems to compensate for the deletions in 16S rRNA. The mRNA exit site is highly remodeled due to the presence of cS23 suggesting an alternative mode of translation initiation. bTHXc is positioned at the SSU head and appears to stabilize the intersubunit bridge B1b during thermal fluctuations. The translation factor plastid pY binds to the SSU on the intersubunit side and interacts with the conserved nucleotide bases involved in decoding. Most of the intersubunit bridges are conserved compared to the bacteria, except for a new bridge involving uL2c and bS6c.

Unique localization of the plastid-specific ribosomal proteins in the chloroplast ribosome small subunit provides mechanistic insights into the chloroplastic translation.,Ahmed T, Shi J, Bhushan S Nucleic Acids Res. 2017 Aug 21;45(14):8581-8595. doi: 10.1093/nar/gkx499. PMID:28582576^[8]

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
↑ Franzetti B, Carol P, Mache R. Characterization and RNA-binding properties of a chloroplast S1-like ribosomal protein. J Biol Chem. 1992 Sep 25;267(27):19075-81. PMID:1527032
↑ 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
↑ 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
↑ 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
↑ 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
↑ Ahmed T, Shi J, Bhushan S. Unique localization of the plastid-specific ribosomal proteins in the chloroplast ribosome small subunit provides mechanistic insights into the chloroplastic translation. Nucleic Acids Res. 2017 Aug 21;45(14):8581-8595. doi: 10.1093/nar/gkx499. PMID:28582576 doi:http://dx.doi.org/10.1093/nar/gkx499

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/5x8r"

@@ Line 1: / Line 1: @@
 ==Structure of the 30S small subunit of chloroplast ribosome from spinach==
-<StructureSection load='5x8r' size='340' side='right'caption='[[5x8r]], [[Resolution|resolution]] 3.70&Aring;' scene=''>
+<SX load='5x8r' size='340' side='right' viewer='molstar' caption='[[5x8r]], [[Resolution|resolution]] 3.70&Aring;' scene=''>
 == Structural highlights ==
 <table><tr><td colspan='2'>[[5x8r]] 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=5X8R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X8R FirstGlance]. <br>
@@ Line 7: / Line 7: @@
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RR13_SPIOL RR13_SPIOL]] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA.[HAMAP-Rule:MF_01315] [[http://www.uniprot.org/uniprot/RRP3_SPIOL RRP3_SPIOL]] One of the plastid-specific ribosomal proteins. [[http://www.uniprot.org/uniprot/RR9_SPIOL RR9_SPIOL]] Binds directly to 16S ribosomal RNA.<ref>PMID:10874039</ref> [:] [[http://www.uniprot.org/uniprot/RR1_SPIOL RR1_SPIOL]] Component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus (PubMed:10874039, PubMed:28007896). Actively engaged in the initiation complex formation via a strong mRNA-binding activity. Possesses a poly(A)-binding activity which might play a role as a control element in chloroplast mRNA translation (PubMed:1527032).<ref>PMID:1527032</ref> <ref>PMID:10874039</ref> <ref>PMID:28007896</ref>  [[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/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/RR19_SPIOL RR19_SPIOL]] This protein binds directly to 16S ribosomal RNA.<ref>PMID:10874039</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] [[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/RR6_SPIOL RR6_SPIOL]] Binds together with S18 to 16S ribosomal RNA (By similarity).[UniProtKB:O78447] [[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/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/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/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/RR13_SPIOL RR13_SPIOL]] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA.[HAMAP-Rule:MF_01315] [[http://www.uniprot.org/uniprot/RRP3_SPIOL RRP3_SPIOL]] One of the plastid-specific ribosomal proteins. [[http://www.uniprot.org/uniprot/RR9_SPIOL RR9_SPIOL]] Binds directly to 16S ribosomal RNA.<ref>PMID:10874039</ref> [:] [[http://www.uniprot.org/uniprot/RR1_SPIOL RR1_SPIOL]] Component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus (PubMed:10874039, PubMed:28007896). Actively engaged in the initiation complex formation via a strong mRNA-binding activity. Possesses a poly(A)-binding activity which might play a role as a control element in chloroplast mRNA translation (PubMed:1527032).<ref>PMID:1527032</ref> <ref>PMID:10874039</ref> <ref>PMID:28007896</ref>  [[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/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/RR19_SPIOL RR19_SPIOL]] This protein binds directly to 16S ribosomal RNA.<ref>PMID:10874039</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] [[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/RR6_SPIOL RR6_SPIOL]] Binds together with S18 to 16S ribosomal RNA (By similarity).[UniProtKB:O78447] [[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/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/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/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]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 23: @@
 <references/>
 __TOC__
-</StructureSection>
+</SX>
 [[Category: Large Structures]]
 [[Category: Spinacia oleracea]]

5x8r

From Proteopedia

Revision as of 20:09, 6 March 2020

Structure of the 30S small subunit of chloroplast ribosome from spinach

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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