J3_8UD8_056

3D structure

PDB id

8UD8 (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of the A2503-C2,C8-dimethylated Thermus thermophilus 70S ribosome in complex with cresomycin, mRNA, deacylated A-site tRNAphe, aminoacylated P-site fMet-tRNAmet, and deacylated E-site tRNAphe at 2.70A resolution

Experimental method

X-RAY DIFFRACTION

Resolution

2.6 Å

Loop

Sequence

GC*GUGAAAAGAAC*GAGUGAAAUAGAGCC

Length

28 nucleotides

Bulged bases

8UD8|1|2A|U|504, 8UD8|1|2A|G|508

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

J3_8UD8_056 not in the Motif Atlas

Homologous match to J3_9DFE_002

Geometric discrepancy: 0.0528

The information below is about J3_9DFE_002

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_17917.1

Basepair signature

cWW-tWH-cSS-cWW-tSH-tHH-cWW-F-F-tWW-tSS-cSS-tWW-tSH-tWH-cSW-F-tHS-cWW-F

Number of instances in this motif group

9

Unit IDs

8UD8|1|2A|G|30
8UD8|1|2A|C|31
*
8UD8|1|2A|G|474
8UD8|1|2A|U|475
8UD8|1|2A|G|476
8UD8|1|2A|A|477
8UD8|1|2A|A|478
8UD8|1|2A|A|479
8UD8|1|2A|A|480
8UD8|1|2A|G|481
8UD8|1|2A|A|482
8UD8|1|2A|A|483
8UD8|1|2A|C|484
*
8UD8|1|2A|G|496
8UD8|1|2A|A|497
8UD8|1|2A|G|498
8UD8|1|2A|U|499
8UD8|1|2A|G|500
8UD8|1|2A|A|501
8UD8|1|2A|A|502
8UD8|1|2A|A|503
8UD8|1|2A|U|504
8UD8|1|2A|A|505
8UD8|1|2A|G|506
8UD8|1|2A|A|507
8UD8|1|2A|G|508
8UD8|1|2A|C|509
8UD8|1|2A|C|510

Current chains

Chain 2A

23S Ribosomal RNA

Nearby chains

Chain 2U

50S ribosomal protein L20

Chain 2W

50S ribosomal protein L22

Chain 2Y

50S ribosomal protein L24