PDBsum entry 3j80

Ribosome

PDB id: 3j80

Contents

Protein chains

206 a.a.

214 a.a.

217 a.a.

260 a.a.

226 a.a.

184 a.a.

188 a.a.

182 a.a.

155 a.a.

150 a.a.

127 a.a.

87 a.a.

129 a.a.

144 a.a.

134 a.a.

97 a.a.

81 a.a.

53 a.a.

223 a.a.

206 a.a.

96 a.a.

122 a.a.

123 a.a.

141 a.a.

120 a.a.

145 a.a.

143 a.a.

106 a.a.

70 a.a.

63 a.a.

53 a.a.

69 a.a.

318 a.a.

25 a.a.

96 a.a.

86 a.a.

DNA/RNA

Metals

_MG ×67

_ZN ×3

PDB id:

3j80

Name:

Ribosome

Title:

Cryoem structure of 40s-eif1-eif1a preinitiation complex

Structure:

18s rrna. Chain: 2. Us2. Chain: a. Es1. Chain: b. Us5. Chain: c. Es4.

Source:

Kluyveromyces lactis. Organism_taxid: 28985. Saccharomyces cerevisiae. Yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562

Authors:

T.Hussain,J.L.Llacer,I.S.Fernandez,C.G.Savva,V.Ramakrishnan

Key ref:

T.Hussain et al. (2014). Structural changes enable start codon recognition by the eukaryotic translation initiation complex. Cell, 159, 597-607. PubMed id: 25417110 DOI: 10.1016/j.cell.2014.10.001

Date:

28-Aug-14 Release date: 05-Nov-14

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: 206 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: 214 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: 217 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: 226 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: 155 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: 150 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: 127 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: 97 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: 53 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: 223 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: 122 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: 123 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: 120 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: 70 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: 63 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: 53 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: 69 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: 318 a.a.

Protein chain

P0CX86  (RL41A_YEAST) -  Small ribosomal subunit protein eS32A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 25 a.a.

Struc: 25 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.

DNA/RNA chain

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- ... 1779 bases

DOI no: 10.1016/j.cell.2014.10.001

Cell 159:597-607 (2014)

PubMed id: 25417110

Structural changes enable start codon recognition by the eukaryotic translation initiation complex.

T.Hussain, J.L.Llácer, I.S.Fernández, A.Munoz, P.Martin-Marcos, C.G.Savva, J.R.Lorsch, A.G.Hinnebusch, V.Ramakrishnan.

ABSTRACT

During eukaryotic translation initiation, initiator tRNA does not insert fully into the P decoding site on the 40S ribosomal subunit. This conformation (POUT) is compatible with scanning mRNA for the AUG start codon. Base pairing with AUG is thought to promote isomerization to a more stable conformation (PIN) that arrests scanning and promotes dissociation of eIF1 from the 40S subunit. Here, we present a cryoEM reconstruction of a yeast preinitiation complex at 4.0 Å resolution with initiator tRNA in the PIN state, prior to eIF1 release. The structure reveals stabilization of the codon-anticodon duplex by the N-terminal tail of eIF1A, changes in the structure of eIF1 likely instrumental in its subsequent release, and changes in the conformation of eIF2. The mRNA traverses the entire mRNA cleft and makes connections to the regulatory domain of eIF2?, eIF1A, and ribosomal elements that allow recognition of context nucleotides surrounding the AUG codon.