J5_8S8D_006

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

ACUUUGG*CUUUCCUUC*GGACUUU*AUGGAAUAGGA*UAAUGAU

Length

41 nucleotides

Bulged bases

8S8D|1|2|U|694, 8S8D|1|2|C|696, 8S8D|1|2|C|697, 8S8D|1|2|U|812, 8S8D|1|2|G|814, 8S8D|1|2|A|855

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|635
8S8D|1|2|C|636
8S8D|1|2|U|637
8S8D|1|2|U|638
8S8D|1|2|U|639
8S8D|1|2|G|640
8S8D|1|2|G|641
*
8S8D|1|2|C|692
8S8D|1|2|U|693
8S8D|1|2|U|694
8S8D|1|2|U|695
8S8D|1|2|C|696
8S8D|1|2|C|697
8S8D|1|2|U|698
8S8D|1|2|U|699
8S8D|1|2|C|700
*
8S8D|1|2|G|738
8S8D|1|2|G|739
8S8D|1|2|A|740
8S8D|1|2|C|741
8S8D|1|2|U|742
8S8D|1|2|U|743
8S8D|1|2|U|744
*
8S8D|1|2|A|806
8S8D|1|2|U|807
8S8D|1|2|G|808
8S8D|1|2|G|809
8S8D|1|2|A|810
8S8D|1|2|A|811
8S8D|1|2|U|812
8S8D|1|2|A|813
8S8D|1|2|G|814
8S8D|1|2|G|815
8S8D|1|2|A|816
*
8S8D|1|2|U|853
8S8D|1|2|A|854
8S8D|1|2|A|855
8S8D|1|2|U|856
8S8D|1|2|G|857
8S8D|1|2|A|858
8S8D|1|2|U|859

Current chains

Chain 2

18S ribosomal RNA

Nearby chains

Chain E

40S ribosomal protein S4

Chain H

40S ribosomal protein S7

Chain L

KLLA0A10483p

Chain N

KLLA0F18040p

Chain W

Small ribosomal subunit protein uS8