J5_7XNX_004

3D structure

PDB id

7XNX (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

2.7 Å

Loop

Sequence

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

Length

40 nucleotides

Bulged bases

7XNX|1|L1|A|3908, 7XNX|1|L1|A|4394, 7XNX|1|L1|PSU|4450, 7XNX|1|L1|G|4451, 7XNX|1|L1|U|4555, 7XNX|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

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

60S ribosomal protein L29