PDBsum entry 3pip

Ribosome/antibiotic

PDB id: 3pip

Contents

Protein chains

253 a.a. *

205 a.a. *

194 a.a. *

177 a.a. *

171 a.a. *

63 a.a. *

142 a.a. *

134 a.a. *

134 a.a. *

136 a.a. *

113 a.a. *

104 a.a. *

108 a.a. *

117 a.a. *

94 a.a. *

126 a.a. *

93 a.a. *

110 a.a. *

175 a.a. *

74 a.a. *

72 a.a. *

65 a.a. *

55 a.a. *

57 a.a. *

53 a.a. *

46 a.a. *

59 a.a. *

37 a.a. *

DNA/RNA

Ligands

LC2

LMA

Metals

_NA ×5

_MG ×73

__K ×4

* Residue conservation analysis

PDB id:

3pip

Name:

Ribosome/antibiotic

Title:

Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit

Structure:

Ribosomal 23s RNA. Chain: x. 5s ribosomal RNA. Chain: y. 50s ribosomal protein l2. Chain: a. 50s ribosomal protein l3. Chain: b. 50s ribosomal protein l4.

Source:

Deinococcus radiodurans r1. Organism_taxid: 243230. Deinococcus radiodurans. Organism_taxid: 1299. Organism_taxid: 1299

Resolution:

3.45Å R-factor: 0.257 R-free: 0.301

Authors:

M.J.Belousoff,T.Shapira,A.Bashan,E.Zimmerman,H.Kinashi,H.Rozenberg, A.Yonath

Key ref:

M.J.Belousoff et al. (2011). Crystal structure of the synergistic antibiotic pair, lankamycin and lankacidin, in complex with the large ribosomal subunit. Proc Natl Acad Sci U S A, 108, 2717-2722. PubMed id: 21282615

Date:

07-Nov-10 Release date: 23-Feb-11

Protein chain

Q9RXJ9  (RL2_DEIRA) -  Large ribosomal subunit protein uL2 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 275 a.a.

Struc: 253 a.a.

Protein chain

Q9RXK2  (RL3_DEIRA) -  Large ribosomal subunit protein uL3 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 211 a.a.

Struc: 205 a.a.

Protein chain

Q9RXK1  (RL4_DEIRA) -  Large ribosomal subunit protein uL4 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 205 a.a.

Struc: 194 a.a.

Protein chain

Q9RXJ0  (RL5_DEIRA) -  Large ribosomal subunit protein uL5 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 180 a.a.

Struc: 177 a.a.

Protein chain

Q9RSL3  (RL6_DEIRA) -  Large ribosomal subunit protein uL6 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 185 a.a.

Struc: 171 a.a.

Protein chain

Q9RSS7  (RL11_DEIRA) -  Large ribosomal subunit protein uL11 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 144 a.a.

Struc: 63 a.a.

Protein chain

Q9RXY1  (RL13_DEIRA) -  Large ribosomal subunit protein uL13 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 174 a.a.

Struc: 142 a.a.

Protein chain

Q9RXJ2  (RL14_DEIRA) -  Large ribosomal subunit protein uL14 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 134 a.a.

Struc: 134 a.a.

Protein chain

Q9RSK9  (RL15_DEIRA) -  Large ribosomal subunit protein uL15 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 156 a.a.

Struc: 134 a.a.

Protein chain

Q9RXJ5  (RL16_DEIRA) -  Large ribosomal subunit protein uL16 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 141 a.a.

Struc: 136 a.a.

Protein chain

Q9RSJ5  (RL17_DEIRA) -  Large ribosomal subunit protein bL17 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 116 a.a.

Struc: 113 a.a.

Protein chain

Q9RSL2  (RL18_DEIRA) -  Large ribosomal subunit protein uL18 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 114 a.a.

Struc: 104 a.a.

Protein chain

Q9RWB4  (RL19_DEIRA) -  Large ribosomal subunit protein bL19 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 166 a.a.

Struc: 108 a.a.

Protein chain

Q9RSW7  (RL20_DEIRA) -  Large ribosomal subunit protein bL20 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 118 a.a.

Struc: 117 a.a.

Protein chain

Q9RY64  (RL21_DEIRA) -  Large ribosomal subunit protein bL21 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 100 a.a.

Struc: 94 a.a.

Protein chain

Q9RXJ7  (RL22_DEIRA) -  Large ribosomal subunit protein uL22 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 134 a.a.

Struc: 126 a.a.

Protein chain

Q9RXK0  (RL23_DEIRA) -  Large ribosomal subunit protein uL23 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 95 a.a.

Struc: 93 a.a.

Protein chain

Q9RXJ1  (RL24_DEIRA) -  Large ribosomal subunit protein uL24 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 115 a.a.

Struc: 110 a.a.

Protein chain

Q9RX88  (RL25_DEIRA) -  Large ribosomal subunit protein bL25 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 237 a.a.

Struc: 175 a.a.

Protein chain

Q9RY65  (RL27_DEIRA) -  Large ribosomal subunit protein bL27 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 91 a.a.

Struc: 74 a.a.

Protein chain

Q9RRG8  (RL28_DEIRA) -  Large ribosomal subunit protein bL28 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 81 a.a.

Struc: 72 a.a.

Protein chain

Q9RXJ4  (RL29_DEIRA) -  Large ribosomal subunit protein uL29 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 67 a.a.

Struc: 65 a.a.

Protein chain

Q9RSL0  (RL30_DEIRA) -  Large ribosomal subunit protein uL30 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 55 a.a.

Struc: 55 a.a.

Protein chain

P49228  (RL32_DEIRA) -  Large ribosomal subunit protein bL32 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 60 a.a.

Struc: 57 a.a.

Protein chain

Q9RSS4  (RL33_DEIRA) -  Large ribosomal subunit protein bL33 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 55 a.a.

Struc: 53 a.a.

Protein chain

Q9RSH2  (RL34_DEIRA) -  Large ribosomal subunit protein bL34 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 47 a.a.

Struc: 46 a.a.

Protein chain

Q9RSW6  (RL35_DEIRA) -  Large ribosomal subunit protein bL35 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 66 a.a.

Struc: 59 a.a.

Protein chain

Q9RSK0  (RL36_DEIRA) -  Large ribosomal subunit protein bL36 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 37 a.a.

Struc: 37 a.a.

DNA/RNA chains

G-G-U-C-A-A-G-A-U-A-G-U-A-A-G-G-G-U-C-C-A-C-G-G-U-G-G-A-U-G-C-C-C-U-G-G-C-G-C- ... 2644 bases

A-C-C-C-C-C-G-U-G-C-C-C-A-U-A-G-C-A-C-U-G-U-G-G-A-A-C-C-A-C-C-C-C-A-C-C-C-C-A- 120 bases

Proc Natl Acad Sci U S A 108:2717-2722 (2011)

PubMed id: 21282615

Crystal structure of the synergistic antibiotic pair, lankamycin and lankacidin, in complex with the large ribosomal subunit.

M.J.Belousoff, T.Shapira, A.Bashan, E.Zimmerman, H.Rozenberg, K.Arakawa, H.Kinashi, A.Yonath.

ABSTRACT

No abstract given.