J5_8JDM_005

3D structure

PDB id

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

Description

Structure of the Human cytoplasmic Ribosome with human tRNA Tyr(GalQ34) and mRNA(UAU) (rotated state)

Experimental method

ELECTRON MICROSCOPY

Resolution

2.67 Å

Loop

Sequence

(PSU)UGA*UUUG*CA*(OMU)(OMG)*CAGAAAA

Length

19 nucleotides

Bulged bases

8JDM|1|D|G|3922, 8JDM|1|D|A|4376, 8JDM|1|D|G|4377, 8JDM|1|D|A|4378, 8JDM|1|D|A|4379

QA status

Modified nucleotides: PSU, OMU, OMG

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_8JDM_005 not in the Motif Atlas

Homologous match to J5_8P9A_015

Geometric discrepancy: 0.3193

The information below is about J5_8P9A_015

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J5_96125.1

Basepair signature

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

Number of instances in this motif group

6

Unit IDs

8JDM|1|D|PSU|3920
8JDM|1|D|U|3921
8JDM|1|D|G|3922
8JDM|1|D|A|3923
*
8JDM|1|D|U|4188
8JDM|1|D|U|4189
8JDM|1|D|U|4190
8JDM|1|D|G|4191
*
8JDM|1|D|C|4204
8JDM|1|D|A|4205
*
8JDM|1|D|OMU|4227
8JDM|1|D|OMG|4228
*
8JDM|1|D|C|4375
8JDM|1|D|A|4376
8JDM|1|D|G|4377
8JDM|1|D|A|4378
8JDM|1|D|A|4379
8JDM|1|D|A|4380
8JDM|1|D|A|4381

Current chains

Chain D

28S ribosomal RNA

Nearby chains

Chain B

Transfer RNA; tRNA

Chain G

60S ribosomal protein L8

Chain S

60S ribosomal protein L15

Chain V

60S ribosomal protein L18

Chain Y

60S ribosomal protein L21

Chain f

60S ribosomal protein L27a

Chain g

60S ribosomal protein L29

Chain t

60S ribosomal protein L36a