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234,440 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Keywords HAS EXACT PHRASE "RIBOSOMAL PROTEIN/RNA"

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Search Summary

This query matches 19 Structures.

Refinements

Structure Determination Methodology

experimental (19)

Scientific Name of Source Organism

	Bacillus subtilis (5)
	Escherichia coli K-12 (3)
	Oceanobacillus iheyensis (3)
	Oceanobacillus iheyensis HTE831 (2)
	Thermus thermophilus (2)
	Thermus thermophilus HB8 (2)
	synthetic construct (2)
	Bacillus anthracis str. Sterne (1)
	Bacillus subtilis subsp. subtilis str. 168 (1)
	Caldanaerobacter subterraneus subsp. tengcongensis (1)

More...

Taxonomy

	Bacteria (16)
	Eukaryota (2)
	other sequences (2)
	Archaea (1)

Experimental Method

	X-RAY DIFFRACTION (10)
	ELECTRON MICROSCOPY (9)

Polymer Entity Type

	Protein (19)
	RNA (19)

Refinement Resolution (Å)

	1.5 - 2.0 (1)
	2.0 - 2.5 (1)
	2.5 - 3.0 (2)
	3.0 - 3.5 (2)
	3.5 - 4.0 (1)
	4.0 - 4.5 (1)
	> 4.5 (11)

Release Date

	2005 - 2009 (5)
	2010 - 2014 (11)
	2015 - 2019 (3)

Enzyme Classification Name

Transferases (1)

Symmetry Type

	Asymmetric (18)
	Cyclic (1)

SCOP Classification

	All alpha proteins (1)
	Alpha and beta proteins (a+b) (1)
	Low resolution protein structures (1)

AllSelected

1 to 19 of 19 Structures

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2R1G \| pdb_00002r1g	Download File View File

Coordinates of the thermus thermophilus 30S components neighboring RbfA as obtained by fitting into the CRYO-EM map of A 30S-RBFA complex

Datta, P.P., Wilson, D.N., Kawazoe, M., Swami, N.K., Kaminishi, T., Sharma, M.R., Booth, T.M., Takemoto, C., Fucini, P., Yokoyama, S., Agrawal, R.K.

(2007) Mol Cell 28: 434-445

Released	2008-03-18
Method	ELECTRON MICROSCOPY 12.5 Å
Organisms	Thermus thermophilus HB27 synthetic construct
Macromolecule	Unique protein chains: 3 Unique nucleic acid chains: 7

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2X7N \| pdb_00002x7n	Download File View File

Mechanism of eIF6s anti-association activity

Gartmann, M., Blau, M., Armache, J.-P., Mielke, T., Topf, M., Beckmann, R.

(2010) J Biological Chem 285: 14848

Released	2010-03-31
Method	ELECTRON MICROSCOPY 11.8 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	60S RIBOSOMAL PROTEIN L23 (protein) 60S RIBOSOMAL PROTEIN L24-A (protein) EUKARYOTIC TRANSLATION INITIATION FACTOR 6 (protein) SARCIN-RICIN LOOP (nucleic acid)

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3EP2 \| pdb_00003ep2	Download File View File

Model of Phe-tRNA(Phe) in the ribosomal pre-accommodated state revealed by cryo-EM

Frank, J., Li, W., Agirrezabala, X.

(2008) EMBO J 27: 3322-3331

Released	2008-12-16
Method	ELECTRON MICROSCOPY 9 Å
Organisms	Escherichia coli K-12
Macromolecule	Unique protein chains: 3 Unique nucleic acid chains: 6

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3EQ3 \| pdb_00003eq3	Download File View File

Model of tRNA(Trp)-EF-Tu in the ribosomal pre-accommodated state revealed by cryo-EM

Frank, J., Li, W., Agirrezabala, X.

(2008) EMBO J 27: 3322-3331

Released	2008-12-16
Method	ELECTRON MICROSCOPY 9 Å
Organisms	Escherichia coli K-12
Macromolecule	Unique protein chains: 3 Unique nucleic acid chains: 6

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3EQ4 \| pdb_00003eq4	Download File View File

Model of tRNA(Leu)-EF-Tu in the ribosomal pre-accommodated state revealed by cryo-EM

Frank, J., Li, W., Agirrezabala, X.

(2008) EMBO J 27: 3322-3331

Released	2008-12-16
Method	ELECTRON MICROSCOPY 12 Å
Organisms	Escherichia coli K-12
Macromolecule	Unique protein chains: 3 Unique nucleic acid chains: 6

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3IYQ \| pdb_00003iyq	Download File View File

tmRNA-SmpB: a journey to the center of the bacterial ribosome

Weis, F., Bron, P., Giudice, E., Rolland, J.P., Thomas, D., Felden, B., Gillet, R.

(2010) EMBO J 29: 3810-3818

Released	2010-10-20
Method	ELECTRON MICROSCOPY 13 Å
Organisms	Thermus thermophilus HB8
Macromolecule	SsrA-binding protein (protein) tmRNA (nucleic acid)

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3IYR \| pdb_00003iyr	Download File View File

tmRNA-SmpB: a journey to the center of the bacterial ribosome

Weis, F., Bron, P., Giudice, E., Rolland, J.P., Thomas, D., Felden, B., Gillet, R.

(2010) EMBO J 29: 3810-3818

Released	2010-10-20
Method	ELECTRON MICROSCOPY 13 Å
Organisms	Thermus thermophilus HB8
Macromolecule	SsrA-binding protein (protein) tmRNA (nucleic acid)

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3V7E \| pdb_00003v7e	Download File View File

Crystal structure of YbxF bound to the SAM-I riboswitch aptamer

Baird, N.J., Zhang, J., Hamma, T., Ferre-D'Amare, A.R.

(2012) RNA 18: 759-770

Released	2012-03-07
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Bacillus subtilis Caldanaerobacter subterraneus subsp. tengcongensis
Macromolecule	Ribosome-associated protein L7Ae-like (protein) SAM-I riboswitch aptamer with an engineered helix P3 (nucleic acid)
Unique Ligands	MG, NCO, SAM

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4LCK \| pdb_00004lck	Download File View File

Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA

Zhang, J., Ferre-D'Amare, A.R.

(2013) Nature 500: 363-366

Released	2013-07-31
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Bacillus subtilis subsp. subtilis str. 168 Oceanobacillus iheyensis
Macromolecule	Ribosomal protein YbxF (protein) T-BOX RIBOSWITCH STEM I (nucleic acid) tRNA-Gly (nucleic acid)
Unique Ligands	MG, SR

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4PDB \| pdb_00004pdb	Download File View File

CRYSTAL STRUCTURE OF BACILLUS ANTHRACIS RIBOSOMAL PROTEIN S8 IN COMPLEX WITH AN RNA APTAMER

Davlieva, M., Shamoo, Y., Nikonowicz, E.P.

(2014) Nucleic Acids Res 42: 10795-10808

Released	2014-09-03
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Bacillus anthracis str. Sterne synthetic construct
Macromolecule	30S ribosomal protein S8 (protein) SELEX RNA aptamer (nucleic acid)

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4QG3 \| pdb_00004qg3	Download File View File

Crystal structure of mutant ribosomal protein G219V TthL1 in complex with 80nt 23S RNA from Thermus thermophilus

Gabdulkhakov, A.G., Nevskaya, N.A., Nikonov, S.V.

(2015) Acta Crystallogr D Biol Crystallogr 71: 376-386

Released	2015-02-11
Method	X-RAY DIFFRACTION 2 Å
Organisms	Thermus thermophilus
Macromolecule	50S ribosomal protein L1 (protein) fragment of 23S rRNA (nucleic acid)
Unique Ligands	BME, IPA, SO4, URE

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4QVI \| pdb_00004qvi	Download File View File

Crystal structure of mutant ribosomal protein M218L TthL1 in complex with 80nt 23S RNA from Thermus thermophilus

Gabdulkhakov, A.G., Nevskaya, N.A., NIkonov, S.V.

(2015) Acta Crystallogr D Biol Crystallogr 71: 376-386

Released	2015-02-11
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Thermus thermophilus
Macromolecule	50S ribosomal protein L1 (protein) fragment of 23S rRNA (nucleic acid)
Unique Ligands	ACT, MES, SO4
Unique branched monosaccharides	FRU, GLC

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4TZP \| pdb_00004tzp	Download File View File

As Grown, Untreated Co-crystals of the Ternary Complex Containing a T-box Stem I RNA, its cognate tRNAGly, and B. subtilis YbxF protein

Zhang, J., Ferre-D'Amare, A.R.

(2014) Structure 22: 1363-1371

Released	2014-09-10
Method	X-RAY DIFFRACTION 8.503 Å
Organisms	Bacillus subtilis Oceanobacillus iheyensis
Macromolecule	Ribosome-associated protein L7Ae-like (protein) engineered tRNA (nucleic acid) glyQ T-box Stem I (nucleic acid)

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4TZV \| pdb_00004tzv	Download File View File

Co-crystals of the Ternary Complex Containing a T-box Stem I RNA, its Cognate tRNAGly, and B. subtilis YbxF protein, treated by removing lithium sulfate post crystallization

Zhang, J., Ferre-D'Amare, A.R.

(2014) Structure 22: 1363-1371

Released	2014-09-10
Method	X-RAY DIFFRACTION 5.03 Å
Organisms	Bacillus subtilis Oceanobacillus iheyensis HTE831
Macromolecule	Ribosome-associated protein L7Ae-like (protein) T-box stem I (nucleic acid) engineered tRNA (nucleic acid)

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4TZW \| pdb_00004tzw	Download File View File

Co-crystals of the Ternary Complex Containing a T-box Stem I RNA, its Cognate tRNAGly, and B. subtilis YbxF protein, treated by removing lithium sulfate and replacing Mg2+ with Sr2+ post crystallization

Zhang, J., Ferre-D'Amare, A.R.

(2014) Structure 22: 1363-1371

Released	2014-09-10
Method	X-RAY DIFFRACTION 4.671 Å
Organisms	Bacillus subtilis Oceanobacillus iheyensis HTE831
Macromolecule	Ribosome-associated protein L7Ae-like (protein) T-box Stem I (nucleic acid) engineered tRNA (nucleic acid)
Unique Ligands	SR

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4TZZ \| pdb_00004tzz	Download File View File

Co-crystals of the Ternary Complex Containing a T-box Stem I RNA, its Cognate tRNAGly, and B. subtilis YbxF protein, treated by removing lithium sulfate and increasing PEG3350 concentration from 20% to 45% post crystallization

Zhang, J., Ferre-D'Amare, A.R.

(2014) Structure 22: 1363-1371

Released	2014-09-10
Method	X-RAY DIFFRACTION 3.64 Å
Organisms	Bacillus subtilis Oceanobacillus iheyensis
Macromolecule	Ribosome-associated protein L7Ae-like (protein) T-box Stem I RNA (nucleic acid) engineered tRNAGly (nucleic acid)
Unique Ligands	MG

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4V5Z \| pdb_00004v5z	Download File View File

Structure of a mammalian 80S ribosome obtained by docking homology models of the RNA and proteins into an 8.7 A cryo-EM map

Chandramouli, P., Akey, C.W.

(2008) Structure 16: 535-548

Released	2014-07-09
Method	ELECTRON MICROSCOPY 8.7 Å
Organisms	Canis lupus familiaris
Macromolecule	Unique protein chains: 50 Unique nucleic acid chains: 36

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6C4H \| pdb_00006c4h	Download File View File

Conformation of methylated GGQ in the peptidyl transferase center during translation termination (PTC region)

Zeng, F., Jin, H.

(2018) Sci Rep 8: 2349-2349

Released	2018-02-21
Method	ELECTRON MICROSCOPY 3.1 Å
Organisms	Escherichia coli
Macromolecule	Unique protein chains: 5 Unique nucleic acid chains: 2
Unique Ligands	MG

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3ID5 \| pdb_00003id5	Download File View File

Crystal structure of Sulfolobus solfataricus C/D RNP assembled with Nop5, fibrillarin, L7Ae and a split half C/D RNA

Ye, K.

(2009) Proc Natl Acad Sci U S A 106: 13808-13813

Released	2009-08-25
Method	X-RAY DIFFRACTION 4.01 Å
Organisms	Saccharolobus solfataricus
Macromolecule	50S ribosomal protein L7Ae (protein) Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase (protein) Pre mRNA splicing protein (protein) half C/D RNA (nucleic acid)
Unique Ligands	SAM

1 to 19 of 19 Structures

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

2R1G | pdb_00002r1g

Coordinates of the thermus thermophilus 30S components neighboring RbfA as obtained by fitting into the CRYO-EM map of A 30S-RBFA complex

2X7N | pdb_00002x7n

Mechanism of eIF6s anti-association activity

3EP2 | pdb_00003ep2

Model of Phe-tRNA(Phe) in the ribosomal pre-accommodated state revealed by cryo-EM

3EQ3 | pdb_00003eq3

Model of tRNA(Trp)-EF-Tu in the ribosomal pre-accommodated state revealed by cryo-EM

3EQ4 | pdb_00003eq4

Model of tRNA(Leu)-EF-Tu in the ribosomal pre-accommodated state revealed by cryo-EM

3IYQ | pdb_00003iyq

tmRNA-SmpB: a journey to the center of the bacterial ribosome

3IYR | pdb_00003iyr

tmRNA-SmpB: a journey to the center of the bacterial ribosome

3V7E | pdb_00003v7e

Crystal structure of YbxF bound to the SAM-I riboswitch aptamer

4LCK | pdb_00004lck

Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA

4PDB | pdb_00004pdb

CRYSTAL STRUCTURE OF BACILLUS ANTHRACIS RIBOSOMAL PROTEIN S8 IN COMPLEX WITH AN RNA APTAMER

4QG3 | pdb_00004qg3

Crystal structure of mutant ribosomal protein G219V TthL1 in complex with 80nt 23S RNA from Thermus thermophilus

4QVI | pdb_00004qvi

Crystal structure of mutant ribosomal protein M218L TthL1 in complex with 80nt 23S RNA from Thermus thermophilus

4TZP | pdb_00004tzp

As Grown, Untreated Co-crystals of the Ternary Complex Containing a T-box Stem I RNA, its cognate tRNAGly, and B. subtilis YbxF protein

4TZV | pdb_00004tzv

Co-crystals of the Ternary Complex Containing a T-box Stem I RNA, its Cognate tRNAGly, and B. subtilis YbxF protein, treated by removing lithium sulfate post crystallization

4TZW | pdb_00004tzw

Co-crystals of the Ternary Complex Containing a T-box Stem I RNA, its Cognate tRNAGly, and B. subtilis YbxF protein, treated by removing lithium sulfate and replacing Mg2+ with Sr2+ post crystallization

4TZZ | pdb_00004tzz

Co-crystals of the Ternary Complex Containing a T-box Stem I RNA, its Cognate tRNAGly, and B. subtilis YbxF protein, treated by removing lithium sulfate and increasing PEG3350 concentration from 20% to 45% post crystallization

4V5Z | pdb_00004v5z

Structure of a mammalian 80S ribosome obtained by docking homology models of the RNA and proteins into an 8.7 A cryo-EM map

6C4H | pdb_00006c4h

Conformation of methylated GGQ in the peptidyl transferase center during translation termination (PTC region)

3ID5 | pdb_00003id5

Crystal structure of Sulfolobus solfataricus C/D RNP assembled with Nop5, fibrillarin, L7Ae and a split half C/D RNA

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Symmetry Type

SCOP Classification

2R1G | pdb_00002r1g

2X7N | pdb_00002x7n

3EP2 | pdb_00003ep2

3EQ3 | pdb_00003eq3

3EQ4 | pdb_00003eq4

3IYQ | pdb_00003iyq

3IYR | pdb_00003iyr

3V7E | pdb_00003v7e

4LCK | pdb_00004lck

4PDB | pdb_00004pdb

4QG3 | pdb_00004qg3

4QVI | pdb_00004qvi

4TZP | pdb_00004tzp

4TZV | pdb_00004tzv

4TZW | pdb_00004tzw

4TZZ | pdb_00004tzz

4V5Z | pdb_00004v5z

6C4H | pdb_00006c4h

3ID5 | pdb_00003id5