IL_4Y4O_250

3D structure

PDB id

4Y4O (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of the Thermus thermophilus 70S ribosome with rRNA modifications and bound to protein Y (YfiA) at 2.3A resolution

Experimental method

X-RAY DIFFRACTION

Resolution

2.3 Å

Loop

Sequence

CGAAA(5MU)UC(5MC)UUG*C(5MC)UG

Length

16 nucleotides

Bulged bases

4Y4O|1|2A|A|1938, 4Y4O|1|2A|U|1944, 4Y4O|1|2A|U|1963

QA status

Modified nucleotides: 5MU, 5MC

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

IL_4Y4O_250 not in the Motif Atlas

Geometric match to IL_4WF9_077

Geometric discrepancy: 0.1302

The information below is about IL_4WF9_077

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

IL_42218.2

Basepair signature

cWW-L-R-cHW-cWW-L-L-L-R-L

Number of instances in this motif group

5

Unit IDs

4Y4O|1|2A|C|1934
4Y4O|1|2A|G|1935
4Y4O|1|2A|A|1936
4Y4O|1|2A|A|1937
4Y4O|1|2A|A|1938
4Y4O|1|2A|5MU|1939
4Y4O|1|2A|U|1940
4Y4O|1|2A|C|1941
4Y4O|1|2A|5MC|1942
4Y4O|1|2A|U|1943
4Y4O|1|2A|U|1944
4Y4O|1|2A|G|1945
*
4Y4O|1|2A|C|1961
4Y4O|1|2A|5MC|1962
4Y4O|1|2A|U|1963
4Y4O|1|2A|G|1964

Current chains

Chain 2A

23S Ribosomal RNA

Nearby chains

Chain 2D

50S ribosomal protein L2

Chain 2a

Small subunit ribosomal RNA; SSU rRNA