J3_4V4Y_030

3D structure

PDB id

4V4Y (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of the 70S Thermus thermophilus ribosome with translocated and rotated Shine-Dalgarno Duplex.

Experimental method

X-RAY DIFFRACTION

Resolution

5.5 Å

Loop

Sequence

CCUCG*CGAUAGCGCACCAGUAC*GGAAAGG

Length

29 nucleotides

Bulged bases

4V4Y|1|BA|C|34, 4V4Y|1|BA|U|448, 4V4Y|1|BA|C|455, 4V4Y|1|BA|C|456, 4V4Y|1|BA|A|457

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_4V4Y_030 not in the Motif Atlas

Homologous match to J3_9DFE_003

Geometric discrepancy: 0.5932

The information below is about J3_9DFE_003

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_07616.1

Basepair signature

cWW-cSS-tSS-tSW-tHW-cWW-tWH-F-F-tHH-tSS-tWH-F-tHS-cWW-F-cSH

Number of instances in this motif group

10

Unit IDs

4V4Y|1|BA|C|31
4V4Y|1|BA|C|32
4V4Y|1|BA|U|33
4V4Y|1|BA|C|34
4V4Y|1|BA|G|35
*
4V4Y|1|BA|C|445
4V4Y|1|BA|G|446
4V4Y|1|BA|A|447
4V4Y|1|BA|U|448
4V4Y|1|BA|A|449
4V4Y|1|BA|G|450
4V4Y|1|BA|C|451
4V4Y|1|BA|G|452
4V4Y|1|BA|C|453
4V4Y|1|BA|A|454
4V4Y|1|BA|C|455
4V4Y|1|BA|C|456
4V4Y|1|BA|A|457
4V4Y|1|BA|G|458
4V4Y|1|BA|U|459
4V4Y|1|BA|A|460
4V4Y|1|BA|C|461
*
4V4Y|1|BA|G|468
4V4Y|1|BA|G|469
4V4Y|1|BA|A|470
4V4Y|1|BA|A|471
4V4Y|1|BA|A|472
4V4Y|1|BA|G|473
4V4Y|1|BA|G|474

Current chains

Chain BA

23S ribosomal RNA

Nearby chains

Chain B6

50S ribosomal protein L34

Chain BF

50S ribosomal protein L4

Chain BT

50S ribosomal protein L20

Chain BW

50S ribosomal protein L23