PDBsum entry 4wt8

Ribosome

PDB id

4wt8

Loading ...

Contents

			Protein chains

					234 a.a.


					206 a.a.


					208 a.a.


					150 a.a.


					101 a.a.


					155 a.a.


					138 a.a.


					127 a.a.


					98 a.a.


					119 a.a.


					124 a.a.


					124 a.a.


					60 a.a.


					88 a.a.


					83 a.a.


					99 a.a.


					70 a.a.


					78 a.a.


					99 a.a.


					24 a.a.

			DNA/RNA

			Ligands

					PAR

PDB id:

4wt8

Links

Name:

Ribosome

Title:

Crystal structure of bactobolin a bound to 70s ribosome-trna

Structure:

mRNA. Chain: 2. 30s ribosomal protein s2. Chain: a. 30s ribosomal protein s3. Chain: c. 30s ribosomal protein s4. Chain: d. 30s ribosomal protein s5.

Source:

Thermus thermophilus. Organism_taxid: 300852. Strain: hb8 / atcc 27634 / dsm 579. Strain: hb8 / atcc 27634 / dsm 579

Resolution:

3.40Å

R-factor:

0.206

R-free:

0.241

Authors:

A.Amunts,K.Fiedorczuk,V.Ramakrishnan

Key ref:

A.Amunts et al. (2015). Bactobolin A binds to a site on the 70S ribosome distinct from previously seen antibiotics. J Mol Biol, 427, 753-755. PubMed id: 25562208 DOI: 10.1016/j.jmb.2014.12.018

Date:

29-Oct-14

Release date:

21-Jan-15

PROCHECK

	Headers

	References

Protein chain

P80371 (RS2_THET8) - Small ribosomal subunit protein uS2 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					256 a.a. 234 a.a.

Protein chain

P80372 (RS3_THET8) - Small ribosomal subunit protein uS3 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					239 a.a. 234 a.a.*

Protein chain

P80373 (RS4_THET8) - Small ribosomal subunit protein uS4 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					209 a.a. 234 a.a.*

Protein chain

Q5SHQ5 (RS5_THET8) - Small ribosomal subunit protein uS5 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					162 a.a. 234 a.a.*

Protein chain

Q5SLP8 (RS6_THET8) - Small ribosomal subunit protein bS6 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					101 a.a. 234 a.a.*

Protein chain

P17291 (RS7_THET8) - Small ribosomal subunit protein uS7 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					156 a.a. 234 a.a.*

Protein chain

P0DOY9 (RS8_THET8) - Small ribosomal subunit protein uS8 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					138 a.a. 234 a.a.*

Protein chain

P80374 (RS9_THET8) - Small ribosomal subunit protein uS9 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					128 a.a. 234 a.a.*

Protein chain

Q5SHN7 (RS10_THET8) - Small ribosomal subunit protein uS10 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					105 a.a. 234 a.a.*

Protein chain

P80376 (RS11_THET8) - Small ribosomal subunit protein uS11 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					129 a.a. 234 a.a.*

Protein chain

Q5SHN3 (RS12_THET8) - Small ribosomal subunit protein uS12 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					132 a.a. 234 a.a.*

Protein chain

P80377 (RS13_THET8) - Small ribosomal subunit protein uS13 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					126 a.a. 234 a.a.*

Protein chain

P0DOY6 (RS14Z_THET8) - Small ribosomal subunit protein uS14 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					61 a.a. 234 a.a.*

Protein chain

Q5SJ76 (RS15_THET8) - Small ribosomal subunit protein uS15 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					89 a.a. 234 a.a.*

Protein chain

Q5SJH3 (RS16_THET8) - Small ribosomal subunit protein bS16 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					88 a.a. 234 a.a.*

Protein chain

P0DOY7 (RS17_THET8) - Small ribosomal subunit protein uS17 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					105 a.a. 234 a.a.*

Protein chain

Q5SLQ0 (RS18_THET8) - Small ribosomal subunit protein bS18 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					88 a.a. 234 a.a.*

Protein chain

Q5SHP2 (RS19_THET8) - Small ribosomal subunit protein uS19 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					93 a.a. 234 a.a.*

Protein chain

P80380 (RS20_THET8) - Small ribosomal subunit protein bS20 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					106 a.a. 234 a.a.*

Protein chain

Q5SIH3 (RSHX_THET8) - Small ribosomal subunit protein bTHX from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					27 a.a. 234 a.a.*

Protein chain

Q5SHR2 (RL36_THET8) - Large ribosomal subunit protein bL36 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					37 a.a. 206 a.a.*

Protein chain

Q5SJE1 (RL31_THET8) - Large ribosomal subunit protein bL31 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					71 a.a. 206 a.a.*

Protein chain

P80339 (RL32_THET8) - Large ribosomal subunit protein bL32 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					60 a.a. 206 a.a.*

Protein chain

P35871 (RL33_THET8) - Large ribosomal subunit protein bL33 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					54 a.a. 206 a.a.*

Protein chain

P80340 (RL34_THET8) - Large ribosomal subunit protein bL34 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					49 a.a. 206 a.a.*

Protein chain

Q5SKU1 (RL35_THET8) - Large ribosomal subunit protein bL35 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					65 a.a. 206 a.a.*

Protein chain

P60493 (RL27_THET8) - Large ribosomal subunit protein bL27 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					85 a.a. 206 a.a.*

Protein chain

Q5SLP7 (RL1_THET8) - Large ribosomal subunit protein uL1 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					229 a.a. 206 a.a.*

Protein chain

P60405 (RL2_THET8) - Large ribosomal subunit protein uL2 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					276 a.a. 206 a.a.*

Protein chain

Q5SHN8 (RL3_THET8) - Large ribosomal subunit protein uL3 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					206 a.a. 206 a.a.*

Protein chain

Q5SHN9 (RL4_THET8) - Large ribosomal subunit protein uL4 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					210 a.a. 206 a.a.*

Protein chain

Q5SHQ0 (RL5_THET8) - Large ribosomal subunit protein uL5 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					182 a.a. 206 a.a.*

Protein chain

P0DOY8 (RL6_THET8) - Large ribosomal subunit protein uL6 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					180 a.a. 206 a.a.*

Protein chain

P60494 (RL28_THET8) - Large ribosomal subunit protein bL28 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					98 a.a. 206 a.a.*

Protein chain

Q5SLQ1 (RL9_THET8) - Large ribosomal subunit protein bL9 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					148 a.a. 206 a.a.*

Protein chain

Q5SHP6 (RL29_THET8) - Large ribosomal subunit protein uL29 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					72 a.a. 206 a.a.*

Protein chain

Q5SHQ6 (RL30_THET8) - Large ribosomal subunit protein uL30 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					60 a.a. 206 a.a.*

Protein chain

P60488 (RL13_THET8) - Large ribosomal subunit protein uL13 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					140 a.a. 206 a.a.*

Protein chain

Q5SHP8 (RL14_THET8) - Large ribosomal subunit protein uL14 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					122 a.a. 206 a.a.*

Protein chain

Q5SHQ7 (RL15_THET8) - Large ribosomal subunit protein uL15 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					150 a.a. 206 a.a.*

Protein chain

P60489 (RL16_THET8) - Large ribosomal subunit protein uL16 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					141 a.a. 206 a.a.*

Protein chain

Q9Z9H5 (RL17_THET8) - Large ribosomal subunit protein bL17 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					118 a.a. 206 a.a.*

Protein chain

Q5SHQ4 (RL18_THET8) - Large ribosomal subunit protein uL18 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					112 a.a. 206 a.a.*

Protein chain

P60490 (RL19_THET8) - Large ribosomal subunit protein bL19 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					146 a.a. 206 a.a.*

Protein chain

P60491 (RL20_THET8) - Large ribosomal subunit protein bL20 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					118 a.a. 206 a.a.*

Protein chain

P60492 (RL21_THET8) - Large ribosomal subunit protein bL21 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					101 a.a. 206 a.a.*

Protein chain

Q5SHP3 (RL22_THET8) - Large ribosomal subunit protein uL22 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					113 a.a. 206 a.a.*

Protein chain

Q5SHP0 (RL23_THET8) - Large ribosomal subunit protein uL23 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					96 a.a. 206 a.a.*

Protein chain

Q5SHP9 (RL24_THET8) - Large ribosomal subunit protein uL24 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					110 a.a. 206 a.a.*

Protein chain

Q5SHZ1 (RL25_THET8) - Large ribosomal subunit protein bL25 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					206 a.a. 206 a.a.*

Protein chain

Q5SHR2 (RL36_THET8) - Large ribosomal subunit protein bL36 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					37 a.a. 208 a.a.*

Protein chain

Q5SJE1 (RL31_THET8) - Large ribosomal subunit protein bL31 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					71 a.a. 208 a.a.*

Protein chain

P80339 (RL32_THET8) - Large ribosomal subunit protein bL32 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					60 a.a. 208 a.a.*

Protein chain

P35871 (RL33_THET8) - Large ribosomal subunit protein bL33 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					54 a.a. 208 a.a.*

Protein chain

P80340 (RL34_THET8) - Large ribosomal subunit protein bL34 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					49 a.a. 208 a.a.*

Protein chain

Q5SKU1 (RL35_THET8) - Large ribosomal subunit protein bL35 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					65 a.a. 208 a.a.*

Protein chain

P60493 (RL27_THET8) - Large ribosomal subunit protein bL27 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					85 a.a. 208 a.a.*

Protein chain

Q5SLP7 (RL1_THET8) - Large ribosomal subunit protein uL1 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					229 a.a. 208 a.a.*

Protein chain

P60405 (RL2_THET8) - Large ribosomal subunit protein uL2 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					276 a.a. 208 a.a.*

Protein chain

Q5SHN8 (RL3_THET8) - Large ribosomal subunit protein uL3 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					206 a.a. 208 a.a.*

Protein chain

Q5SHN9 (RL4_THET8) - Large ribosomal subunit protein uL4 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					210 a.a. 208 a.a.*

Protein chain

Q5SHQ0 (RL5_THET8) - Large ribosomal subunit protein uL5 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					182 a.a. 208 a.a.*

Protein chain

P0DOY8 (RL6_THET8) - Large ribosomal subunit protein uL6 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					180 a.a. 208 a.a.*

Protein chain

P60494 (RL28_THET8) - Large ribosomal subunit protein bL28 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					98 a.a. 208 a.a.*

Protein chain

Q5SLQ1 (RL9_THET8) - Large ribosomal subunit protein bL9 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					148 a.a. 208 a.a.*

Protein chain

Q5SHP6 (RL29_THET8) - Large ribosomal subunit protein uL29 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					72 a.a. 208 a.a.*

Protein chain

Q5SHQ6 (RL30_THET8) - Large ribosomal subunit protein uL30 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					60 a.a. 208 a.a.*

Protein chain

P60488 (RL13_THET8) - Large ribosomal subunit protein uL13 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					140 a.a. 208 a.a.*

Protein chain

Q5SHP8 (RL14_THET8) - Large ribosomal subunit protein uL14 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					122 a.a. 208 a.a.*

Protein chain

Q5SHQ7 (RL15_THET8) - Large ribosomal subunit protein uL15 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					150 a.a. 208 a.a.*

Protein chain

P60489 (RL16_THET8) - Large ribosomal subunit protein uL16 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					141 a.a. 208 a.a.*

Protein chain

Q9Z9H5 (RL17_THET8) - Large ribosomal subunit protein bL17 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					118 a.a. 208 a.a.*

Protein chain

Q5SHQ4 (RL18_THET8) - Large ribosomal subunit protein uL18 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					112 a.a. 208 a.a.*

Protein chain

P60490 (RL19_THET8) - Large ribosomal subunit protein bL19 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					146 a.a. 208 a.a.*

Protein chain

P60491 (RL20_THET8) - Large ribosomal subunit protein bL20 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					118 a.a. 208 a.a.*

Protein chain

P60492 (RL21_THET8) - Large ribosomal subunit protein bL21 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					101 a.a. 208 a.a.*

Protein chain

Q5SHP3 (RL22_THET8) - Large ribosomal subunit protein uL22 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					113 a.a. 208 a.a.*

Protein chain

Q5SHP0 (RL23_THET8) - Large ribosomal subunit protein uL23 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					96 a.a. 208 a.a.*

Protein chain

Q5SHP9 (RL24_THET8) - Large ribosomal subunit protein uL24 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					110 a.a. 208 a.a.*

Protein chain

Q5SHZ1 (RL25_THET8) - Large ribosomal subunit protein bL25 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: Struc:					206 a.a. 208 a.a.*

Protein chain

No UniProt id for this chain

Struc:					150 a.a.

Protein chain

No UniProt id for this chain

Struc:					101 a.a.

Protein chain

No UniProt id for this chain

Struc:					155 a.a.

Protein chain

No UniProt id for this chain

Struc:					138 a.a.

Protein chain

No UniProt id for this chain

Struc:					127 a.a.

Protein chain

No UniProt id for this chain

Struc:					98 a.a.

Protein chain

No UniProt id for this chain

Struc:					119 a.a.

Protein chain

No UniProt id for this chain

Struc:					124 a.a.

Protein chain

No UniProt id for this chain

Struc:					124 a.a.

Protein chain

No UniProt id for this chain

Struc:					60 a.a.

Protein chain

No UniProt id for this chain

Struc:					88 a.a.

Protein chain

No UniProt id for this chain

Struc:					83 a.a.

Protein chain

No UniProt id for this chain

Struc:					99 a.a.

Protein chain

No UniProt id for this chain

Struc:					70 a.a.

Protein chain

No UniProt id for this chain

Struc:					78 a.a.

Protein chain

No UniProt id for this chain

Struc:					99 a.a.

Protein chain

No UniProt id for this chain

Struc:					24 a.a.

Key:

PfamA domain

Secondary structure

* PDB and UniProt seqs differ at 6837 residue positions (black crosses)

DNA/RNA chains

		A-A-A-U-G-U-U-C-A 9 bases
		U-G-G-A-G-A-G-U-U-U-G-A-U-C-C-U-G-G-C-U-C-A-G-G-G-U-G-A-A-C-G-C-U-G-G-C-G-G-C- ... 1504 bases



		Enzyme reactions

Enzyme class:

Chains A, C, D: E.C.?

[IntEnz] [ExPASy] [KEGG] [BRENDA]

DOI no: 10.1016/j.jmb.2014.12.018	J Mol Biol 427:753-755 (2015)
PubMed id: 25562208

Bactobolin A binds to a site on the 70S ribosome distinct from previously seen antibiotics.
A.Amunts, K.Fiedorczuk, T.T.Truong, J.Chandler, E.Peter Greenberg, V.Ramakrishnan.

ABSTRACT

The ribosome is the target of a large number of antibiotics. Here, we report a 3.4-Å-resolution crystal structure of bactobolin A bound to 70S ribosome-tRNA complex. The antibiotic binds at a previously unseen site in the 50S subunit and displaces tRNA bound at the P-site. It thus likely has a similar mechanism of action as blasticidin S despite binding to a different site. The structure also rationalizes previously identified resistance mutations.