PDBsum entry 5jb3

Translation

PDB id: 5jb3

Contents

Protein chains

133 a.a.

145 a.a.

158 a.a.

113 a.a.

190 a.a.

202 a.a.

99 a.a.

63 a.a.

186 a.a.

172 a.a.

241 a.a.

217 a.a.

125 a.a.

129 a.a.

127 a.a.

57 a.a.

123 a.a.

102 a.a.

148 a.a.

56 a.a.

67 a.a.

111 a.a.

144 a.a.

71 a.a.

50 a.a.

214 a.a.

135 a.a.

22 a.a.

83 a.a.

95 a.a.

409 a.a.

129 a.a.

254 a.a.

DNA/RNA

Ligands

MET

GNP

Metals

_ZN

_MG

PDB id:

5jb3

Name:

Translation

Title:

Cryo-em structure of a full archaeal ribosomal translation initiation complex in the p-remote conformation

Structure:

16s ribosomal RNA. Chain: 2. Other_details: 16s model from pyrococcus furiosus (PDB code 4v6u) used for fitting. 30s ribosomal protein s11. Chain: m. Other_details: 30s ribosomal protein us11 model from pyrococcus furiosus (PDB code 4v6u) used for fitting. 30s ribosomal protein s12.

Source:

Pyrococcus abyssi ge5. Organism_taxid: 272844. Escherichia coli. Organism_taxid: 562. Variant: a1u72. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Gene: mj0463.

Authors:

P.-D.Coureux,E.Schmitt,Y.Mechulam

Key ref:

P.D.Coureux et al. (2016). Cryo-EM study of start codon selection during archaeal translation initiation. Nat Commun, 7, 13366. PubMed id: 27819266 DOI: 10.1038/ncomms13366

Date:

13-Apr-16 Release date: 30-Nov-16

Protein chain

P62010  (RS11_PYRAB) -  Small ribosomal subunit protein uS11 from Pyrococcus abyssi (strain GE5 / Orsay)

Seq: 137 a.a.

Struc: 133 a.a.*

Protein chain

P61994  (RS12_PYRAB) -  Small ribosomal subunit protein uS12 from Pyrococcus abyssi (strain GE5 / Orsay)

Seq: 147 a.a.

Struc: 145 a.a.

Protein chain

Q8TZD9  (RS15_PYRFU) -  Small ribosomal subunit protein uS15 from Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

Seq: 158 a.a.

Struc: 158 a.a.

Protein chain

Q8U008  (RS17_PYRFU) -  Small ribosomal subunit protein uS17 from Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

Seq: 113 a.a.

Struc: 113 a.a.

Protein chain

Q8TZE1  (RS3A_PYRFU) -  Small ribosomal subunit protein eS1 from Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

Seq: 198 a.a.

Struc: 190 a.a.

Protein chain

Q8U0F0  (RS2_PYRFU) -  Small ribosomal subunit protein uS2 from Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

Seq: 202 a.a.

Struc: 202 a.a.

Protein chain

Q8U442  (RS24_PYRFU) -  Small ribosomal subunit protein eS24 from Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

Seq: 99 a.a.

Struc: 99 a.a.

Protein chain

Q8U474  (RS27_PYRFU) -  Small ribosomal subunit protein eS27 from Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

Seq: 63 a.a.

Struc: 63 a.a.

Protein chain

Q8U004  (RS3_PYRFU) -  Small ribosomal subunit protein uS3 from Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

Seq: 210 a.a.

Struc: 186 a.a.

Protein chain

P61992  (RS4_PYRAB) -  Small ribosomal subunit protein uS4 from Pyrococcus abyssi (strain GE5 / Orsay)

Seq: 180 a.a.

Struc: 172 a.a.

Protein chain

Q8U011  (RS4E_PYRFU) -  Small ribosomal subunit protein eS4 from Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

Seq: 243 a.a.

Struc: 241 a.a.

Protein chain

Q8U017  (RS5_PYRFU) -  Small ribosomal subunit protein uS5 from Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

Seq: 236 a.a.

Struc: 217 a.a.

Protein chain

Q8U3H8  (RS6E_PYRFU) -  Small ribosomal subunit protein eS6 from Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

Seq: 125 a.a.

Struc: 125 a.a.

Protein chain

Q8U014  (RS8_PYRFU) -  Small ribosomal subunit protein uS8 from Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

Seq: 130 a.a.

Struc: 129 a.a.

Protein chain

Q8U1Y5  (RS8E_PYRFU) -  Small ribosomal subunit protein eS8 from Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

Seq: 127 a.a.

Struc: 127 a.a.

Protein chain

No UniProt id for this chain

Struc: 57 a.a.

Protein chain

Q8U160  (RL7A_PYRFU) -  Large ribosomal subunit protein eL8 from Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

Seq: 123 a.a.

Struc: 123 a.a.

Protein chain

P61885  (RS10_PYRFU) -  Small ribosomal subunit protein uS10 from Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

Seq: 102 a.a.

Struc: 102 a.a.

Protein chain

Q8U0E2  (RS13_PYRFU) -  Small ribosomal subunit protein uS13 from Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

Seq: 148 a.a.

Struc: 148 a.a.

Protein chain

Q8U013  (RS14Z_PYRFU) -  Small ribosomal subunit protein uS14 from Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

Seq: 56 a.a.

Struc: 56 a.a.

Protein chain

Q8U0U1  (RS17E_PYRFU) -  Small ribosomal subunit protein eS17 from Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

Seq: 67 a.a.

Struc: 67 a.a.

Protein chain

Q8U002  (RS19_PYRFU) -  Small ribosomal subunit protein uS19 from Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

Seq: 132 a.a.

Struc: 111 a.a.

Protein chain

Q9V0G8  (RS19E_PYRAB) -  Small ribosomal subunit protein eS19 from Pyrococcus abyssi (strain GE5 / Orsay)

Seq: 150 a.a.

Struc: 144 a.a.*

Protein chain

Q8U159  (RS28_PYRFU) -  Small ribosomal subunit protein eS28 from Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

Seq: 71 a.a.

Struc: 71 a.a.

Protein chain

Q8U443  (RS27A_PYRFU) -  Small ribosomal subunit protein eS31 from Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

Seq: 50 a.a.

Struc: 50 a.a.

Protein chain

Q8U0M8  (RS7_PYRFU) -  Small ribosomal subunit protein uS7 from Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

Seq: 215 a.a.

Struc: 214 a.a.

Protein chain

Q8U0E7  (RS9_PYRFU) -  Small ribosomal subunit protein uS9 from Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

Seq: 135 a.a.

Struc: 135 a.a.

Protein chain

Q8U232  (RS32_PYRFU) -  Small ribosomal subunit protein eS32 from Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

Seq: 37 a.a.

Struc: 22 a.a.

Protein chain

Q57902  (SUI1_METJA) -  Protein translation factor SUI1 homolog from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)

Seq: 103 a.a.

Struc: 83 a.a.

Protein chain

Q9V138  (IF1A_PYRAB) -  Translation initiation factor 1A from Pyrococcus abyssi (strain GE5 / Orsay)

Seq: 113 a.a.

Struc: 95 a.a.

Protein chain

Q980A5  (IF2G_SULSO) -  Translation initiation factor 2 subunit gamma from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

Seq: 415 a.a.

Struc: 409 a.a.

Protein chain

Q97W59  (IF2B_SULSO) -  Translation initiation factor 2 subunit beta from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

Seq: 139 a.a.

Struc: 129 a.a.

Protein chain

Q97Z79  (IF2A_SULSO) -  Translation initiation factor 2 subunit alpha from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

Seq: 266 a.a.

Struc: 254 a.a.

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DNA/RNA chains

A-U-U-C-C-G-G-U-U-G-A-U-C-C-U-G-C-C-G-G-A-G-G-C-C-A-C-U-G-C-U-A-U-G-G-G-G-G-U- ... 1495 bases

G-C-G-G-G-G-U-G-G-A-G-C-A-G-C-C-U-G-G-H2U-A-G-C-U-C-G-U-C-G-G-G-OMC-U-C-A-U-A- 76 bases

U-G-G-A-G-G-U-G-A-U-U-U-A-A-A-U-G-C 18 bases

Enzyme reactions

• Enzyme class: Chain 7: E.C.3.6.5.3 - protein-synthesizing GTPase.
• Reaction: GTP + H2O = GDP + phosphate + H⁺

GTP + H2O = GDP (Bound ligand (Het Group name = GNP) matches with 81.82% similarity) + phosphate + H(+)

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

reference

DOI no: 10.1038/ncomms13366

Nat Commun 7:13366 (2016)

PubMed id: 27819266

Cryo-EM study of start codon selection during archaeal translation initiation.

P.D.Coureux, C.Lazennec-Schurdevin, A.Monestier, E.Larquet, L.Cladière, B.P.Klaholz, E.Schmitt, Y.Mechulam.

ABSTRACT

No abstract given.