J5_8S8D_005

3D structure

PDB id

8S8D (explore in PDB, NAKB, or RNA 3D Hub)

Description

Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model py48S-AUC-2)

Experimental method

ELECTRON MICROSCOPY

Resolution

3.45 Å

Loop

Sequence

AUAGUUCCUUUACUACAU*AUGCUUAAAA*UG*CGAAU*AUGGUU

Length

41 nucleotides

Bulged bases

8S8D|1|2|C|131, 8S8D|1|2|U|132, 8S8D|1|2|U|134, 8S8D|1|2|A|135, 8S8D|1|2|C|136, 8S8D|1|2|C|139, 8S8D|1|2|A|140, 8S8D|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

8S8D|1|2|A|124
8S8D|1|2|U|125
8S8D|1|2|A|126
8S8D|1|2|G|127
8S8D|1|2|U|128
8S8D|1|2|U|129
8S8D|1|2|C|130
8S8D|1|2|C|131
8S8D|1|2|U|132
8S8D|1|2|U|133
8S8D|1|2|U|134
8S8D|1|2|A|135
8S8D|1|2|C|136
8S8D|1|2|U|137
8S8D|1|2|A|138
8S8D|1|2|C|139
8S8D|1|2|A|140
8S8D|1|2|U|141
*
8S8D|1|2|A|172
8S8D|1|2|U|173
8S8D|1|2|G|174
8S8D|1|2|C|175
8S8D|1|2|U|176
8S8D|1|2|U|177
8S8D|1|2|A|178
8S8D|1|2|A|179
8S8D|1|2|A|180
8S8D|1|2|A|181
*
8S8D|1|2|U|202
8S8D|1|2|G|203
*
8S8D|1|2|C|262
8S8D|1|2|G|263
8S8D|1|2|A|264
8S8D|1|2|A|265
8S8D|1|2|U|266
*
8S8D|1|2|A|287
8S8D|1|2|U|288
8S8D|1|2|G|289
8S8D|1|2|G|290
8S8D|1|2|U|291
8S8D|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