J5_8S8F_004

3D structure

PDB id

8S8F (explore in PDB, NAKB, or RNA 3D Hub)

Description

Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model py48S-AUC-3.2)

Experimental method

ELECTRON MICROSCOPY

Resolution

3.95 Å

Loop

Sequence

AUAGUUCCUUUACUACAU*AUGCUUAAAA*UG*CGAAU*AUGGUU

Length

41 nucleotides

Bulged bases

8S8F|1|2|U|128, 8S8F|1|2|C|131, 8S8F|1|2|U|132, 8S8F|1|2|U|134, 8S8F|1|2|A|135, 8S8F|1|2|C|136, 8S8F|1|2|C|139, 8S8F|1|2|A|140, 8S8F|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

8S8F|1|2|A|124
8S8F|1|2|U|125
8S8F|1|2|A|126
8S8F|1|2|G|127
8S8F|1|2|U|128
8S8F|1|2|U|129
8S8F|1|2|C|130
8S8F|1|2|C|131
8S8F|1|2|U|132
8S8F|1|2|U|133
8S8F|1|2|U|134
8S8F|1|2|A|135
8S8F|1|2|C|136
8S8F|1|2|U|137
8S8F|1|2|A|138
8S8F|1|2|C|139
8S8F|1|2|A|140
8S8F|1|2|U|141
*
8S8F|1|2|A|172
8S8F|1|2|U|173
8S8F|1|2|G|174
8S8F|1|2|C|175
8S8F|1|2|U|176
8S8F|1|2|U|177
8S8F|1|2|A|178
8S8F|1|2|A|179
8S8F|1|2|A|180
8S8F|1|2|A|181
*
8S8F|1|2|U|202
8S8F|1|2|G|203
*
8S8F|1|2|C|262
8S8F|1|2|G|263
8S8F|1|2|A|264
8S8F|1|2|A|265
8S8F|1|2|U|266
*
8S8F|1|2|A|287
8S8F|1|2|U|288
8S8F|1|2|G|289
8S8F|1|2|G|290
8S8F|1|2|U|291
8S8F|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