PDBsum entry 3jap

Translation

PDB id: 3jap

Contents

Protein chains

208 a.a.

222 a.a.

217 a.a.

223 a.a.

260 a.a.

206 a.a.

226 a.a.

184 a.a.

188 a.a.

182 a.a.

96 a.a.

155 a.a.

117 a.a.

150 a.a.

127 a.a.

117 a.a.

141 a.a.

120 a.a.

145 a.a.

143 a.a.

106 a.a.

87 a.a.

129 a.a.

144 a.a.

134 a.a.

70 a.a.

98 a.a.

81 a.a.

62 a.a.

53 a.a.

54 a.a.

69 a.a.

318 a.a.

25 a.a.

111 a.a.

249 a.a.

396 a.a.

128 a.a.

90 a.a.

550 a.a.

634 a.a.

342 a.a.

31 a.a.

52 a.a.

DNA/RNA

Ligands

MET

GCP

Metals

_MG ×81

_ZN ×4

PDB id:

3jap

Name:

Translation

Title:

Structure of a partial yeast 48s preinitiation complex in closed conformation

Structure:

Met-trnai (u31:a39 variant). Chain: 1. Engineered: yes. 18s rrna. Chain: 2. mRNA. Chain: 3. Engineered: yes. Us2.

Source:

Synthetic: yes. Kluyveromyces lactis. Organism_taxid: 28985. Synthetic construct. Organism_taxid: 32630. Saccharomyces cerevisiae. Yeast. Organism_taxid: 4932. Expressed in: escherichia coli bl21.

Authors:

J.L.Llacer,T.Hussain,V.Ramakrishnan

Key ref:

J.L.Llácer et al. (2015). Conformational Differences between Open and Closed States of the Eukaryotic Translation Initiation Complex. Mol Cell, 59, 399-412. PubMed id: 26212456 DOI: 10.1016/j.molcel.2015.06.033

Date:

18-Jun-15 Release date: 12-Aug-15

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: 208 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: 222 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

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

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

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

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

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

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

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

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

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: 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

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

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

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: 98 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

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: 62 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

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: 54 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: 111 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: 249 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: 396 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: 128 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: 90 a.a.

Protein chain

P38249  (EIF3A_YEAST) -  Eukaryotic translation initiation factor 3 subunit A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 964 a.a.

Struc: 550 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: 634 a.a.*

Protein chain

P40217  (EIF3I_YEAST) -  Eukaryotic translation initiation factor 3 subunit I from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 347 a.a.

Struc: 342 a.a.

Protein chain

P06103  (EIF3B_YEAST) -  Eukaryotic translation initiation factor 3 subunit B from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 763 a.a.

Struc: 31 a.a.

Protein chain

A6ZZ25  (EIF3G_YEAS7) -  Eukaryotic translation initiation factor 3 subunit G from Saccharomyces cerevisiae (strain YJM789)

Seq: 274 a.a.

Struc: 52 a.a.

* PDB and UniProt seqs differ at 182 residue positions (black crosses)

DNA/RNA chains

A-G-C-G-C-C-G-U-G-G-C-G-C-A-G-U-G-G-A-A-G-C-G-C-G-C-A-G-G-U-C-U-C-A-U-A-A-A-C- 75 bases

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- ... 1780 bases

A-U-C-U-C-U-C-U-C-U-A-U-G-C 14 bases

Enzyme reactions

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

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

reference

DOI no: 10.1016/j.molcel.2015.06.033

Mol Cell 59:399-412 (2015)

PubMed id: 26212456

Conformational Differences between Open and Closed States of the Eukaryotic Translation Initiation Complex.

J.L.Llácer, T.Hussain, L.Marler, C.E.Aitken, A.Thakur, J.R.Lorsch, A.G.Hinnebusch, V.Ramakrishnan.

ABSTRACT

Translation initiation in eukaryotes begins with the formation of a pre-initiation complex (PIC) containing the 40S ribosomal subunit, eIF1, eIF1A, eIF3, ternary complex (eIF2-GTP-Met-tRNAi), and eIF5. The PIC, in an open conformation, attaches to the 5' end of the mRNA and scans to locate the start codon, whereupon it closes to arrest scanning. We present single particle cryo-electron microscopy (cryo-EM) reconstructions of 48S PICs from yeast in these open and closed states, at 6.0 Å and 4.9 Å, respectively. These reconstructions show eIF2β as well as a configuration of eIF3 that appears to encircle the 40S, occupying part of the subunit interface. Comparison of the complexes reveals a large conformational change in the 40S head from an open mRNA latch conformation to a closed one that constricts the mRNA entry channel and narrows the P site to enclose tRNAi, thus elucidating key events in start codon recognition.