J4_8S8J_004

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

AAG*CGAAAG*CCAUAAACUAUG*UU

Length

23 nucleotides

Bulged bases

8S8J|1|2|A|622, 8S8J|1|2|A|1025, 8S8J|1|2|C|1027, 8S8J|1|2|U|1028, 8S8J|1|2|A|1029, 8S8J|1|2|U|1030

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

J4_8S8J_004 not in the Motif Atlas

Homologous match to J4_8CRE_022

Geometric discrepancy: 0.1592

The information below is about J4_8CRE_022

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_14595.4

Basepair signature

cWW-cWW-cWW-F-F-tHW-F-F-F-F-cWW-F

Number of instances in this motif group

7

Unit IDs

8S8J|1|2|A|621
8S8J|1|2|A|622
8S8J|1|2|G|623
*
8S8J|1|2|C|974
8S8J|1|2|G|975
8S8J|1|2|A|976
8S8J|1|2|A|977
8S8J|1|2|A|978
8S8J|1|2|G|979
*
8S8J|1|2|C|1020
8S8J|1|2|C|1021
8S8J|1|2|A|1022
8S8J|1|2|U|1023
8S8J|1|2|A|1024
8S8J|1|2|A|1025
8S8J|1|2|A|1026
8S8J|1|2|C|1027
8S8J|1|2|U|1028
8S8J|1|2|A|1029
8S8J|1|2|U|1030
8S8J|1|2|G|1031
*
8S8J|1|2|U|1102
8S8J|1|2|U|1103

Current chains

Chain 2

18S ribosomal RNA

Nearby chains

Chain N

KLLA0F18040p

Chain O

Small ribosomal subunit protein uS11

Chain W

Small ribosomal subunit protein uS8

Chain X

KLLA0B11231p

Chain a

40S ribosomal protein S26

Chain h

40S ribosomal protein L41-A