J4_3J81_004

3D structure

PDB id

3J81 (explore in PDB, NAKB, or RNA 3D Hub)

Description

CryoEM structure of a partial yeast 48S preinitiation complex

Experimental method

ELECTRON MICROSCOPY

Resolution

4 Å

Loop

Sequence

AAG*CGAAAG*CCAUAAACUAUG*UU

Length

23 nucleotides

Bulged bases

3J81|1|2|A|622, 3J81|1|2|A|1025, 3J81|1|2|C|1027, 3J81|1|2|U|1028, 3J81|1|2|A|1029, 3J81|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_3J81_004 not in the Motif Atlas

Homologous match to J4_8C3A_022

Geometric discrepancy: 0.1084

The information below is about J4_8C3A_022

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_61885.4

Basepair signature

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

Number of instances in this motif group

5

Unit IDs

3J81|1|2|A|621
3J81|1|2|A|622
3J81|1|2|G|623
*
3J81|1|2|C|974
3J81|1|2|G|975
3J81|1|2|A|976
3J81|1|2|A|977
3J81|1|2|A|978
3J81|1|2|G|979
*
3J81|1|2|C|1020
3J81|1|2|C|1021
3J81|1|2|A|1022
3J81|1|2|U|1023
3J81|1|2|A|1024
3J81|1|2|A|1025
3J81|1|2|A|1026
3J81|1|2|C|1027
3J81|1|2|U|1028
3J81|1|2|A|1029
3J81|1|2|U|1030
3J81|1|2|G|1031
*
3J81|1|2|U|1102
3J81|1|2|U|1103

Current chains

Chain 2

18S rRNA

Nearby chains

Chain L

uS17

Chain N

uS15

Chain O

uS11

Chain W

uS8

Chain X

uS12

Chain a

eS26

Chain h

eL41