J5_8YLD_009

3D structure

PDB id

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

Description

State 4a (S4a) of yeast 80S ribosome bound to 2 tRNAs and open eEF3 and eEF2 during translocation

Experimental method

ELECTRON MICROSCOPY

Resolution

3.9 Å

Loop

Sequence

CGAG*CGUAA*UGAACGUAG*CGA*UAAGAG

Length

27 nucleotides

Bulged bases

8YLD|1|A|U|719, 8YLD|1|A|A|784, 8YLD|1|A|G|785

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

J5_8YLD_009 not in the Motif Atlas

Homologous match to J5_8P9A_012

Geometric discrepancy: 0.1084

The information below is about J5_8P9A_012

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J5_56629.1

Basepair signature

cWW-F-F-tSS-F-cWW-cWW-F-F-cWW-F-cWW-F-F-F-F-F-F

Number of instances in this motif group

3

Unit IDs

8YLD|1|A|C|675
8YLD|1|A|G|676
8YLD|1|A|A|677
8YLD|1|A|G|678
*
8YLD|1|A|C|702
8YLD|1|A|G|703
8YLD|1|A|U|704
8YLD|1|A|A|705
8YLD|1|A|A|706
*
8YLD|1|A|U|713
8YLD|1|A|G|714
8YLD|1|A|A|715
8YLD|1|A|A|716
8YLD|1|A|C|717
8YLD|1|A|G|718
8YLD|1|A|U|719
8YLD|1|A|A|720
8YLD|1|A|G|721
*
8YLD|1|A|C|749
8YLD|1|A|G|750
8YLD|1|A|A|751
*
8YLD|1|A|U|782
8YLD|1|A|A|783
8YLD|1|A|A|784
8YLD|1|A|G|785
8YLD|1|A|A|786
8YLD|1|A|G|787

Current chains

Chain A

25S rRNA

Nearby chains

Chain F

Large ribosomal subunit protein uL4A

Chain N

Large ribosomal subunit protein eL13A

Chain S

Large ribosomal subunit protein eL18A

Chain c

Large ribosomal subunit protein uL15

Chain d

Large ribosomal subunit protein eL29

Chain k

Large ribosomal subunit protein eL36A