PDBsum entry 5gaf

Ribosome

PDB id: 5gaf

Contents

Protein chains

271 a.a.

209 a.a.

201 a.a.

177 a.a.

176 a.a.

149 a.a.

125 a.a.

134 a.a.

142 a.a.

123 a.a.

144 a.a.

136 a.a.

125 a.a.

117 a.a.

114 a.a.

117 a.a.

103 a.a.

110 a.a.

95 a.a.

102 a.a.

94 a.a.

76 a.a.

77 a.a.

62 a.a.

58 a.a.

56 a.a.

51 a.a.

46 a.a.

64 a.a.

38 a.a.

398 a.a.

18 a.a.

DNA/RNA

Ligands

GNP

Metals

_MG ×431

_ZN

PDB id:

5gaf

Name:

Ribosome

Title:

Rnc in complex with srp

Structure:

Srp 4.5s RNA. Chain: 1. tRNA ccaend. Chain: 2. 23s ribosomal RNA. Chain: a. Synonym: 23s rrna. 5s ribosomal RNA. Chain: b.

Source:

Escherichia coli. Organism_taxid: 562. Organism_taxid: 562

Authors:

A.Jomaa,D.Boehringer,M.Leibundgut,N.Ban

Key ref:

A.Jomaa et al. (2016). Structures of the E. coli translating ribosome with SRP and its receptor and with the translocon. Nat Commun, 7, 10471. PubMed id: 26804923 DOI: 10.1038/ncomms10471

Date:

25-Nov-15 Release date: 03-Feb-16

Protein chain

P60422  (RL2_ECOLI) -  Large ribosomal subunit protein uL2 from Escherichia coli (strain K12)

Seq: 273 a.a.

Struc: 271 a.a.

Protein chain

P60438  (RL3_ECOLI) -  Large ribosomal subunit protein uL3 from Escherichia coli (strain K12)

Seq: 209 a.a.

Struc: 209 a.a.

Protein chain

P60723  (RL4_ECOLI) -  Large ribosomal subunit protein uL4 from Escherichia coli (strain K12)

Seq: 201 a.a.

Struc: 201 a.a.

Protein chain

P62399  (RL5_ECOLI) -  Large ribosomal subunit protein uL5 from Escherichia coli (strain K12)

Seq: 179 a.a.

Struc: 177 a.a.

Protein chain

P0AG55  (RL6_ECOLI) -  Large ribosomal subunit protein uL6 from Escherichia coli (strain K12)

Seq: 177 a.a.

Struc: 176 a.a.

Protein chain

P0A7R1  (RL9_ECOLI) -  Large ribosomal subunit protein bL9 from Escherichia coli (strain K12)

Seq: 149 a.a.

Struc: 149 a.a.

Protein chain

P0A7J3  (RL10_ECOLI) -  Large ribosomal subunit protein uL10 from Escherichia coli (strain K12)

Seq: 165 a.a.

Struc: 125 a.a.*

Protein chain

P0A7J7  (RL11_ECOLI) -  Large ribosomal subunit protein uL11 from Escherichia coli (strain K12)

Seq: 142 a.a.

Struc: 134 a.a.

Protein chain

P0AA10  (RL13_ECOLI) -  Large ribosomal subunit protein uL13 from Escherichia coli (strain K12)

Seq: 142 a.a.

Struc: 142 a.a.

Protein chain

P0ADY3  (RL14_ECOLI) -  Large ribosomal subunit protein uL14 from Escherichia coli (strain K12)

Seq: 123 a.a.

Struc: 123 a.a.

Protein chain

P02413  (RL15_ECOLI) -  Large ribosomal subunit protein uL15 from Escherichia coli (strain K12)

Seq: 144 a.a.

Struc: 144 a.a.

Protein chain

P0ADY7  (RL16_ECOLI) -  Large ribosomal subunit protein uL16 from Escherichia coli (strain K12)

Seq: 136 a.a.

Struc: 136 a.a.

Protein chain

P0AG44  (RL17_ECOLI) -  Large ribosomal subunit protein bL17 from Escherichia coli (strain K12)

Seq: 127 a.a.

Struc: 125 a.a.

Protein chain

P0C018  (RL18_ECOLI) -  Large ribosomal subunit protein uL18 from Escherichia coli (strain K12)

Seq: 117 a.a.

Struc: 117 a.a.

Protein chain

P0A7K6  (RL19_ECOLI) -  Large ribosomal subunit protein bL19 from Escherichia coli (strain K12)

Seq: 115 a.a.

Struc: 114 a.a.

Protein chain

P0A7L3  (RL20_ECOLI) -  Large ribosomal subunit protein bL20 from Escherichia coli (strain K12)

Seq: 118 a.a.

Struc: 117 a.a.

Protein chain

P0AG48  (RL21_ECOLI) -  Large ribosomal subunit protein bL21 from Escherichia coli (strain K12)

Seq: 103 a.a.

Struc: 103 a.a.

Protein chain

P61175  (RL22_ECOLI) -  Large ribosomal subunit protein uL22 from Escherichia coli (strain K12)

Seq: 110 a.a.

Struc: 110 a.a.

Protein chain

P0ADZ0  (RL23_ECOLI) -  Large ribosomal subunit protein uL23 from Escherichia coli (strain K12)

Seq: 100 a.a.

Struc: 95 a.a.

Protein chain

P60624  (RL24_ECOLI) -  Large ribosomal subunit protein uL24 from Escherichia coli (strain K12)

Seq: 104 a.a.

Struc: 102 a.a.

Protein chain

P68919  (RL25_ECOLI) -  Large ribosomal subunit protein bL25 from Escherichia coli (strain K12)

Seq: 94 a.a.

Struc: 94 a.a.

Protein chain

P0A7L8  (RL27_ECOLI) -  Large ribosomal subunit protein bL27 from Escherichia coli (strain K12)

Seq: 85 a.a.

Struc: 76 a.a.

Protein chain

P0A7M2  (RL28_ECOLI) -  Large ribosomal subunit protein bL28 from Escherichia coli (strain K12)

Seq: 78 a.a.

Struc: 77 a.a.

Protein chain

P0A7M6  (RL29_ECOLI) -  Large ribosomal subunit protein uL29 from Escherichia coli (strain K12)

Seq: 63 a.a.

Struc: 62 a.a.

Protein chain

P0AG51  (RL30_ECOLI) -  Large ribosomal subunit protein uL30 from Escherichia coli (strain K12)

Seq: 59 a.a.

Struc: 58 a.a.

Protein chain

P0A7N4  (RL32_ECOLI) -  Large ribosomal subunit protein bL32 from Escherichia coli (strain K12)

Seq: 57 a.a.

Struc: 56 a.a.

Protein chain

P0A7N9  (RL33_ECOLI) -  Large ribosomal subunit protein bL33 from Escherichia coli (strain K12)

Seq: 55 a.a.

Struc: 51 a.a.

Protein chain

P0A7P5  (RL34_ECOLI) -  Large ribosomal subunit protein bL34 from Escherichia coli (strain K12)

Seq: 46 a.a.

Struc: 46 a.a.

Protein chain

P0A7Q1  (RL35_ECOLI) -  Large ribosomal subunit protein bL35 from Escherichia coli (strain K12)

Seq: 65 a.a.

Struc: 64 a.a.

Protein chain

P0A7Q6  (RL36_ECOLI) -  Large ribosomal subunit protein bL36A from Escherichia coli (strain K12)

Seq: 38 a.a.

Struc: 38 a.a.

Protein chain

P0AGD7  (SRP54_ECOLI) -  Signal recognition particle protein from Escherichia coli (strain K12)

Seq: 453 a.a.

Struc: 398 a.a.*

Protein chain

P00634  (PPB_ECOLI) -  Alkaline phosphatase from Escherichia coli (strain K12)

Seq: 471 a.a.

Struc: 18 a.a.*

* PDB and UniProt seqs differ at 25 residue positions (black crosses)

DNA/RNA chains

U-C-U-G-U-U-U-A-C-C-A-G-G-U-C-A-G-G-U-C-C-G-G-A-A-G-G-A-A-G-C-A-G-C-C-A-A-G-G- 43 bases

C-C-A 3 bases

G-G-U-U-A-A-G-C-G-A-C-U-A-A-G-C-G-U-A-C-A-C-G-G-U-G-G-A-U-G-C-C-C-U-G-G-C-A-G- ... 2883 bases

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

Enzyme reactions

• Enzyme class 1: Chain i: E.C.3.6.5.4 - signal-recognition-particle GTPase.
• Reaction: GTP + H2O = GDP + phosphate + H⁺
• Enzyme class 2: Chain k: E.C.3.1.3.1 - alkaline phosphatase.
• Reaction: a phosphate monoester + H2O = an alcohol + phosphate

phosphate monoester + H2O = alcohol (Bound ligand (Het Group name = GNP) matches with 81.82% similarity) + phosphate

• Cofactor: Mg(2+); Zn(2+)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1038/ncomms10471

Nat Commun 7:10471 (2016)

PubMed id: 26804923

Structures of the E. coli translating ribosome with SRP and its receptor and with the translocon.

A.Jomaa, D.Boehringer, M.Leibundgut, N.Ban.

ABSTRACT

Co-translational protein targeting to membranes is a universally conserved process. Central steps include cargo recognition by the signal recognition particle and handover to the Sec translocon. Here we present snapshots of key co-translational-targeting complexes solved by cryo-electron microscopy at near-atomic resolution, establishing the molecular contacts between the Escherichia coli translating ribosome, the signal recognition particle and the translocon. Our results reveal the conformational changes that regulate the latching of the signal sequence, the release of the heterodimeric domains of the signal recognition particle and its receptor, and the handover of the signal sequence to the translocon. We also observe that the signal recognition particle and the translocon insert-specific structural elements into the ribosomal tunnel to remodel it, possibly to sense nascent chains. Our work provides structural evidence for a conformational state of the signal recognition particle and its receptor primed for translocon binding to the ribosome-nascent chain complex.