J5_8S8J_005

3D structure

PDB id

8S8J (explore in PDB, NAKB, or RNA 3D Hub)

Description

Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model py48S-AUC-eIF5)

Experimental method

ELECTRON MICROSCOPY

Resolution

4.7 Å

Loop

Sequence

AUAGUUCCUUUACUACAU*AUGCUUAAAA*UG*CGAAU*AUGGUU

Length

41 nucleotides

Bulged bases

8S8J|1|2|U|128, 8S8J|1|2|C|130, 8S8J|1|2|C|131, 8S8J|1|2|U|132, 8S8J|1|2|U|133, 8S8J|1|2|U|134, 8S8J|1|2|A|135, 8S8J|1|2|C|136, 8S8J|1|2|C|139, 8S8J|1|2|A|140, 8S8J|1|2|U|177

QA status

Valid loop

Sequence variability

If this chain is mapped to an Rfam alignment, the link below will give its sequence variability.

R3DSVS

Structural variability across Equivalence Class

The link below will give the loop's structural variability across the equivalence class for this chain.

R3DMCS EC

Structural variability across Rfam

If this chain is mapped to an Rfam alignment, the link below will give the loop's structural variability between chains mapped to the same Rfam family.

R3DMCS Rfam

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

Not in a motif group

Basepair signature

Not available

Number of instances in this motif group

0

Unit IDs

8S8J|1|2|A|124
8S8J|1|2|U|125
8S8J|1|2|A|126
8S8J|1|2|G|127
8S8J|1|2|U|128
8S8J|1|2|U|129
8S8J|1|2|C|130
8S8J|1|2|C|131
8S8J|1|2|U|132
8S8J|1|2|U|133
8S8J|1|2|U|134
8S8J|1|2|A|135
8S8J|1|2|C|136
8S8J|1|2|U|137
8S8J|1|2|A|138
8S8J|1|2|C|139
8S8J|1|2|A|140
8S8J|1|2|U|141
*
8S8J|1|2|A|172
8S8J|1|2|U|173
8S8J|1|2|G|174
8S8J|1|2|C|175
8S8J|1|2|U|176
8S8J|1|2|U|177
8S8J|1|2|A|178
8S8J|1|2|A|179
8S8J|1|2|A|180
8S8J|1|2|A|181
*
8S8J|1|2|U|202
8S8J|1|2|G|203
*
8S8J|1|2|C|262
8S8J|1|2|G|263
8S8J|1|2|A|264
8S8J|1|2|A|265
8S8J|1|2|U|266
*
8S8J|1|2|A|287
8S8J|1|2|U|288
8S8J|1|2|G|289
8S8J|1|2|G|290
8S8J|1|2|U|291
8S8J|1|2|U|292

Current chains

Chain 2

18S ribosomal RNA

Nearby chains

Chain E

40S ribosomal protein S4

Chain G

Small ribosomal subunit protein eS6

Chain I

40S ribosomal protein S8