4l6m
From Proteopedia
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| - | + | {{Large structure}} | |
| + | {{STRUCTURE_4l6m| PDB=4l6m | SCENE= }} | ||
| + | ===Crystal Structure of Blasticidin S Bound to Thermus Thermophilus 70S Ribosome. This file contains the 30S subunit, tRNA and mRNA molecules from the second 70S ribosome.=== | ||
| + | {{ABSTRACT_PUBMED_23824292}} | ||
| - | + | ==Function== | |
| + | [[http://www.uniprot.org/uniprot/RS11_THET2 RS11_THET2]] Located on the upper part of the platform of the 30S subunit, where it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome (By similarity). [[http://www.uniprot.org/uniprot/RSHX_THET2 RSHX_THET2]] Binds at the top of the head of the 30S subunit. It stabilizes a number of different RNA elements and thus is important for subunit structure (By similarity). [[http://www.uniprot.org/uniprot/RS7_THET2 RS7_THET2]] 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. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA (By similarity). [[http://www.uniprot.org/uniprot/RS2_THET2 RS2_THET2]] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS17_THET2 RS17_THET2]] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA (By similarity). [[http://www.uniprot.org/uniprot/RS18_THET2 RS18_THET2]] Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS13_THET2 RS13_THET2]] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites (By similarity). [[http://www.uniprot.org/uniprot/RS16_THET2 RS16_THET2]] Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains (By similarity). [[http://www.uniprot.org/uniprot/RS6_THET2 RS6_THET2]] Located on the outer edge of the platform on the body of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS3_THET2 RS3_THET2]] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation (By similarity). [[http://www.uniprot.org/uniprot/RS9_THET2 RS9_THET2]] Part of the top of the head of the 30S subunit. The C-terminal region penetrates the head emerging in the P-site where it contacts tRNA (By similarity). [[http://www.uniprot.org/uniprot/RS12_THET2 RS12_THET2]] With S4 and S5 plays an important role in translational accuracy (By similarity). Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS14Z_THET2 RS14Z_THET2]] Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site (By similarity). [[http://www.uniprot.org/uniprot/RS15_THET2 RS15_THET2]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA (By similarity). Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome (By similarity). [[http://www.uniprot.org/uniprot/RS20_THET2 RS20_THET2]] Binds directly to 16S ribosomal RNA (By similarity). [[http://www.uniprot.org/uniprot/RS8_THET2 RS8_THET2]] 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). [[http://www.uniprot.org/uniprot/RS4_THET2 RS4_THET2]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the body and platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS10_THET2 RS10_THET2]] Involved in the binding of tRNA to the ribosomes (By similarity). [[http://www.uniprot.org/uniprot/RS19_THET2 RS19_THET2]] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA (By similarity). [[http://www.uniprot.org/uniprot/RS5_THET2 RS5_THET2]] With S4 and S12 plays an important role in translational accuracy (By similarity). Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body (By similarity). | ||
| - | + | ==About this Structure== | |
| + | [[4l6m]] is a 24 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4L6M OCA]. | ||
| - | + | ==Reference== | |
| + | <ref group="xtra">PMID:023824292</ref><references group="xtra"/><references/> | ||
| + | [[Category: Escherichia coli]] | ||
| + | [[Category: Thermus thermophilus]] | ||
| + | [[Category: Korostelev, A A.]] | ||
| + | [[Category: Svidritskiy, E.]] | ||
| + | [[Category: Blasticidin s]] | ||
| + | [[Category: Peptidyl transfer]] | ||
| + | [[Category: Ribosomal crystal structure]] | ||
| + | [[Category: Ribosome]] | ||
| + | [[Category: Translation inhibitor]] | ||
| + | [[Category: Translation termination]] | ||
Revision as of 05:26, 1 August 2013
Contents |
Crystal Structure of Blasticidin S Bound to Thermus Thermophilus 70S Ribosome. This file contains the 30S subunit, tRNA and mRNA molecules from the second 70S ribosome.
Template:ABSTRACT PUBMED 23824292
Function
[RS11_THET2] Located on the upper part of the platform of the 30S subunit, where it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome (By similarity). [RSHX_THET2] Binds at the top of the head of the 30S subunit. It stabilizes a number of different RNA elements and thus is important for subunit structure (By similarity). [RS7_THET2] 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. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA (By similarity). [RS2_THET2] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit (By similarity). [RS17_THET2] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA (By similarity). [RS18_THET2] Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit (By similarity). [RS13_THET2] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites (By similarity). [RS16_THET2] Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains (By similarity). [RS6_THET2] Located on the outer edge of the platform on the body of the 30S subunit (By similarity). [RS3_THET2] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation (By similarity). [RS9_THET2] Part of the top of the head of the 30S subunit. The C-terminal region penetrates the head emerging in the P-site where it contacts tRNA (By similarity). [RS12_THET2] With S4 and S5 plays an important role in translational accuracy (By similarity). Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit (By similarity). [RS14Z_THET2] Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site (By similarity). [RS15_THET2] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA (By similarity). Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome (By similarity). [RS20_THET2] Binds directly to 16S ribosomal RNA (By similarity). [RS8_THET2] 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). [RS4_THET2] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the body and platform of the 30S subunit (By similarity). [RS10_THET2] Involved in the binding of tRNA to the ribosomes (By similarity). [RS19_THET2] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA (By similarity). [RS5_THET2] With S4 and S12 plays an important role in translational accuracy (By similarity). Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body (By similarity).
About this Structure
4l6m is a 24 chain structure with sequence from Escherichia coli and Thermus thermophilus. Full crystallographic information is available from OCA.
Reference
- Svidritskiy E, Ling C, Ermolenko DN, Korostelev AA. Blasticidin S inhibits translation by trapping deformed tRNA on the ribosome. Proc Natl Acad Sci U S A. 2013 Jul 23;110(30):12283-8. doi:, 10.1073/pnas.1304922110. Epub 2013 Jul 3. PMID:23824292 doi:10.1073/pnas.1304922110
