J3_8JDJ_030

3D structure

PDB id

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

Description

Structure of the Human cytoplasmic Ribosome with human tRNA Asp(Q34) and mRNA(GAU)

Experimental method

ELECTRON MICROSCOPY

Resolution

2.5 Å

Loop

Sequence

AGAUGG*CGUUCCGAAGGG*CGGCCGA(PSU)

Length

26 nucleotides

Bulged bases

8JDJ|1|D|C|2470, 8JDJ|1|D|A|2472, 8JDJ|1|D|G|2475, 8JDJ|1|D|G|2503, 8JDJ|1|D|C|2504

QA status

Modified nucleotides: PSU

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

J3_8JDJ_030 not in the Motif Atlas

Homologous match to J3_8CRE_016

Geometric discrepancy: 0.5997

The information below is about J3_8CRE_016

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_65403.1

Basepair signature

cWW-tSH-tHW-F-F-F-tHS-F-cWW-F-cWW-F-F-F-F

Number of instances in this motif group

1

Unit IDs

8JDJ|1|D|A|2451
8JDJ|1|D|G|2452
8JDJ|1|D|A|2453
8JDJ|1|D|U|2454
8JDJ|1|D|G|2455
8JDJ|1|D|G|2456
*
8JDJ|1|D|C|2465
8JDJ|1|D|G|2466
8JDJ|1|D|U|2467
8JDJ|1|D|U|2468
8JDJ|1|D|C|2469
8JDJ|1|D|C|2470
8JDJ|1|D|G|2471
8JDJ|1|D|A|2472
8JDJ|1|D|A|2473
8JDJ|1|D|G|2474
8JDJ|1|D|G|2475
8JDJ|1|D|G|2476
*
8JDJ|1|D|C|2501
8JDJ|1|D|G|2502
8JDJ|1|D|G|2503
8JDJ|1|D|C|2504
8JDJ|1|D|C|2505
8JDJ|1|D|G|2506
8JDJ|1|D|A|2507
8JDJ|1|D|PSU|2508

Current chains

Chain D

28S ribosomal RNA

Nearby chains

Chain F

5.8S ribosomal RNA; 5.8S rRNA

Chain G

60S ribosomal protein L8

Chain M

60S ribosomal protein L7a

Chain S

60S ribosomal protein L15

Chain c

60S ribosomal protein L23a

Chain o

60S ribosomal protein L37