J3_8JDK_030

3D structure

PDB id

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

Description

Structure of the Human cytoplasmic Ribosome with human tRNA Asp(ManQ34) and mRNA(GAU)

Experimental method

ELECTRON MICROSCOPY

Resolution

2.26 Å

Loop

Sequence

AGAUGG*CGUUCCGAAGGG*CGGCCGA(PSU)

Length

26 nucleotides

Bulged bases

8JDK|1|D|C|2470, 8JDK|1|D|A|2472, 8JDK|1|D|G|2475, 8JDK|1|D|G|2503, 8JDK|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_8JDK_030 not in the Motif Atlas

Homologous match to J3_8CRE_016

Geometric discrepancy: 0.5972

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

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