PDBsum entry 8s8k

Ribosome

PDB id: 8s8k

Contents

Protein chains

219 a.a.

229 a.a.

220 a.a.

260 a.a.

230 a.a.

184 a.a.

188 a.a.

182 a.a.

153 a.a.

151 a.a.

129 a.a.

87 a.a.

129 a.a.

144 a.a.

134 a.a.

102 a.a.

81 a.a.

60 a.a.

25 a.a.

227 a.a.

206 a.a.

96 a.a.

117 a.a.

117 a.a.

141 a.a.

130 a.a.

145 a.a.

143 a.a.

106 a.a.

78 a.a.

64 a.a.

55 a.a.

74 a.a.

96 a.a.

86 a.a.

267 a.a.

470 a.a.

134 a.a.

93 a.a.

320 a.a.

DNA/RNA

Ligands

GCP

MET

Metals

_MG ×96

_ZN ×4

PDB id:

8s8k

Name:

Ribosome

Title:

Structure of a yeast 48s-auc preinitiation complex in swivelled conformation (model py48s-auc-swiv-eif1)

Structure:

18s ribosomal RNA. Chain: 2. Small ribosomal subunit protein us2. Chain: a. Synonym: 40s ribosomal protein s0. Small ribosomal subunit protein es1. Chain: b. Synonym: 40s ribosomal protein s1. Small ribosomal subunit protein us5.

Source:

Kluyveromyces lactis nrrl y-1140. Organism_taxid: 284590. Saccharomyces cerevisiae s288c. Organism_taxid: 559292. Gene: tif11, ymr260c, ym8156.02c. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: sui1, rfr1, ynl244c, n0905. Synthetic: yes.

Authors:

L.Villamayor-Belinchon,P.Sharma,J.L.Llacer,T.Hussain

Key ref:

L.Villamayor-Belinchon et al. (2024). Structural basis of auc codon discrimination during translation initiation in yeast.. Nucleic acids res, 52, 11317. PubMed id: 39193907

Date:

06-Mar-24 Release date: 06-Nov-24

Protein chain

Q6CN12  (RSSA_KLULA) -  Small ribosomal subunit protein uS2 from Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)

Seq: 254 a.a.

Struc: 219 a.a.

Protein chain

Q6CWD0  (RS3A_KLULA) -  Small ribosomal subunit protein eS1 from Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)

Seq: 255 a.a.

Struc: 229 a.a.

Protein chain

Q6CKL3  (Q6CKL3_KLULA) -  Small ribosomal subunit protein uS5 from Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)

Seq: 259 a.a.

Struc: 220 a.a.

Protein chain

Q6CWJ2  (Q6CWJ2_KLULA) -  40S ribosomal protein S4 from Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)

Seq: 261 a.a.

Struc: 260 a.a.

Protein chain

Q6CM04  (RS6_KLULA) -  Small ribosomal subunit protein eS6 from Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)

Seq: 236 a.a.

Struc: 230 a.a.

Protein chain

Q6CTD6  (Q6CTD6_KLULA) -  40S ribosomal protein S7 from Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)

Seq: 190 a.a.

Struc: 184 a.a.

Protein chain

Q6CMG3  (Q6CMG3_KLULA) -  40S ribosomal protein S8 from Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)

Seq: 201 a.a.

Struc: 188 a.a.

Protein chain

Q6CM18  (Q6CM18_KLULA) -  KLLA0E23673p from Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)

Seq: 188 a.a.

Struc: 182 a.a.

Protein chain

Q6CX80  (Q6CX80_KLULA) -  KLLA0A10483p from Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)

Seq: 156 a.a.

Struc: 153 a.a.

Protein chain

Q6CJK0  (Q6CJK0_KLULA) -  KLLA0F18040p from Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)

Seq: 151 a.a.

Struc: 151 a.a.

Protein chain

P27069  (RS14_KLULA) -  Small ribosomal subunit protein uS11 from Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)

Seq: 137 a.a.

Struc: 129 a.a.

Protein chain

Q6CXT6  (RS21_KLULA) -  Small ribosomal subunit protein eS21 from Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)

Seq: 87 a.a.

Struc: 87 a.a.

Protein chain

Q6CW21  (RS22_KLULA) -  Small ribosomal subunit protein uS8 from Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)

Seq: 130 a.a.

Struc: 129 a.a.

Protein chain

F2Z602  (F2Z602_KLULA) -  KLLA0B11231p from Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)

Seq: 145 a.a.

Struc: 144 a.a.

Protein chain

Q6CU44  (Q6CU44_KLULA) -  40S ribosomal protein S24 from Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)

Seq: 135 a.a.

Struc: 134 a.a.

Protein chain

Q6CS01  (Q6CS01_KLULA) -  40S ribosomal protein S26 from Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)

Seq: 119 a.a.

Struc: 102 a.a.

Protein chain

Q6CNL2  (Q6CNL2_KLULA) -  40S ribosomal protein S27 from Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)

Seq: 82 a.a.

Struc: 81 a.a.

Protein chain

Q6CUH5  (Q6CUH5_KLULA) -  40S ribosomal protein S30 from Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)

Seq: 63 a.a.

Struc: 60 a.a.

Protein chain

No UniProt id for this chain

Struc: 25 a.a.

Protein chain

Q6CRK7  (Q6CRK7_KLULA) -  40S ribosomal protein S3 from Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)

Seq: 237 a.a.

Struc: 227 a.a.

Protein chain

Q6CRA3  (Q6CRA3_KLULA) -  KLLA0D10659p from Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)

Seq: 227 a.a.

Struc: 206 a.a.

Protein chain

Q6CVZ5  (Q6CVZ5_KLULA) -  KLLA0B08173p from Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)

Seq: 106 a.a.

Struc: 96 a.a.

Protein chain

Q6CLU4  (Q6CLU4_KLULA) -  40S ribosomal protein S12 from Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)

Seq: 134 a.a.

Struc: 117 a.a.

Protein chain

Q6CKV4  (Q6CKV4_KLULA) -  KLLA0F07843p from Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)

Seq: 142 a.a.

Struc: 117 a.a.

Protein chain

Q875N2  (RS16_KLULA) -  Small ribosomal subunit protein uS9 from Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)

Seq: 143 a.a.

Struc: 141 a.a.

Protein chain

Q6CWU3  (Q6CWU3_KLULA) -  KLLA0B01474p from Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)

Seq: 136 a.a.

Struc: 130 a.a.

Protein chain

Q6CWT9  (Q6CWT9_KLULA) -  KLLA0B01562p from Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)

Seq: 146 a.a.

Struc: 145 a.a.

Protein chain

Q6CXM0  (Q6CXM0_KLULA) -  KLLA0A07194p from Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)

Seq: 144 a.a.

Struc: 143 a.a.

Protein chain

Q6CIM1  (Q6CIM1_KLULA) -  KLLA0F25542p from Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)

Seq: 117 a.a.

Struc: 106 a.a.

Protein chain

Q6CW78  (Q6CW78_KLULA) -  40S ribosomal protein S25 from Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)

Seq: 108 a.a.

Struc: 78 a.a.

Protein chain

P33285  (RS28_KLULA) -  Small ribosomal subunit protein eS28 from Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)

Seq: 67 a.a.

Struc: 64 a.a.

Protein chain

Q6CPG3  (RS29_KLULA) -  Small ribosomal subunit protein uS14 from Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)

Seq: 56 a.a.

Struc: 55 a.a.

Protein chain

P69061  (RS27A_KLULA) -  Ubiquitin-ribosomal protein eS31 fusion protein from Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)

Seq: 150 a.a.

Struc: 74 a.a.

Protein chain

P38912  (IF1A_YEAST) -  Eukaryotic translation initiation factor 1A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 153 a.a.

Struc: 96 a.a.

Protein chain

P32911  (SUI1_YEAST) -  Eukaryotic translation initiation factor eIF-1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 108 a.a.

Struc: 86 a.a.

Protein chain

P20459  (IF2A_YEAST) -  Eukaryotic translation initiation factor 2 subunit alpha from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 304 a.a.

Struc: 267 a.a.

Protein chain

P32481  (IF2G_YEAST) -  Eukaryotic translation initiation factor 2 subunit gamma from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 527 a.a.

Struc: 470 a.a.

Protein chain

P09064  (IF2B_YEAST) -  Eukaryotic translation initiation factor 2 subunit beta from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 285 a.a.

Struc: 134 a.a.

Protein chain

P32497  (EIF3C_YEAST) -  Eukaryotic translation initiation factor 3 subunit C from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 812 a.a.

Struc: 93 a.a.

Protein chain

Q6CNI7  (Q6CNI7_KLULA) -  KLLA0E12277p from Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)

Seq: 326 a.a.

Struc: 320 a.a.

DNA/RNA chains

U-A-U-C-U-G-G-U-U-G-A-U-C-C-U-G-C-C-A-G-U-A-G-U-C-A-U-A-U-G-C-U-U-G-U-C-U-C-A- ... 1798 bases

A-A-A-A-U-C 6 bases

A-G-C-G-C-C-G-U-1MG-2MG-C-G-C-A-G-H2U-G-G-A-A-G-C-G-C-M2G-C-A-G-G-G-C-U-C-A-U- 75 bases

Enzyme reactions

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

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

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