J5_7XNY_004

3D structure

PDB id

7XNY (explore in PDB, NAKB, or RNA 3D Hub)

Description

High resolution cry-EM structure of the human 80S ribosome from SNORD127+/- Kasumi-1 cells

Experimental method

ELECTRON MICROSCOPY

Resolution

2.5 Å

Loop

Sequence

AGAAGACC*(OMG)GAUAACUG*CUU(5MC)GA(PSU)GUC*GG(UR3)(PSU)UAG*UAGUUU

Length

40 nucleotides

Bulged bases

7XNY|1|L1|A|3908, 7XNY|1|L1|A|4394, 7XNY|1|L1|PSU|4450, 7XNY|1|L1|G|4451, 7XNY|1|L1|U|4452, 7XNY|1|L1|U|4555, 7XNY|1|L1|U|4556

QA status

Modified nucleotides: OMG, 5MC, PSU, UR3

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

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

Not in a motif group

Basepair signature

Not available

Number of instances in this motif group

0

Unit IDs

7XNY|1|L1|A|3903
7XNY|1|L1|G|3904
7XNY|1|L1|A|3905
7XNY|1|L1|A|3906
7XNY|1|L1|G|3907
7XNY|1|L1|A|3908
7XNY|1|L1|C|3909
7XNY|1|L1|C|3910
*
7XNY|1|L1|OMG|4392
7XNY|1|L1|G|4393
7XNY|1|L1|A|4394
7XNY|1|L1|U|4395
7XNY|1|L1|A|4396
7XNY|1|L1|A|4397
7XNY|1|L1|C|4398
7XNY|1|L1|U|4399
7XNY|1|L1|G|4400
*
7XNY|1|L1|C|4444
7XNY|1|L1|U|4445
7XNY|1|L1|U|4446
7XNY|1|L1|5MC|4447
7XNY|1|L1|G|4448
7XNY|1|L1|A|4449
7XNY|1|L1|PSU|4450
7XNY|1|L1|G|4451
7XNY|1|L1|U|4452
7XNY|1|L1|C|4453
*
7XNY|1|L1|G|4528
7XNY|1|L1|G|4529
7XNY|1|L1|UR3|4530
7XNY|1|L1|PSU|4531
7XNY|1|L1|U|4532
7XNY|1|L1|A|4533
7XNY|1|L1|G|4534
*
7XNY|1|L1|U|4552
7XNY|1|L1|A|4553
7XNY|1|L1|G|4554
7XNY|1|L1|U|4555
7XNY|1|L1|U|4556
7XNY|1|L1|U|4557

Current chains

Chain L1

28S rRNA

Nearby chains

Chain LA

60S ribosomal protein L8

Chain LB

60S ribosomal protein L3

Chain LC

60S ribosomal protein L4

Chain LP

60S ribosomal protein L17

Chain Lb

60S ribosomal protein L29