J4_9SPF_010

3D structure

PDB id

9SPF (explore in PDB, NAKB, or RNA 3D Hub)

Description

CRYO-EM STRUCTURE OF HUMAN 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA CONTAINING N1-METHYLPSEUDOURIDINE

Experimental method

ELECTRON MICROSCOPY

Resolution

2.4 Å

Loop

Sequence

GAC(PSU)G*CAAAG*UGAUU*AUGA(A2M)C

Length

21 nucleotides

Bulged bases

None detected

QA status

Modified nucleotides: PSU, A2M

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

J4_9SPF_010 not in the Motif Atlas

Homologous match to J4_9PN5_006

Geometric discrepancy: 0.0686

The information below is about J4_9PN5_006

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_78485.4

Basepair signature

cWW-tSW-F-F-tHS-F-cWW-F-cWW-F-F-tHS-F-cWW

Number of instances in this motif group

8

Unit IDs

9SPF|1|L5|G|3634
9SPF|1|L5|A|3635
9SPF|1|L5|C|3636
9SPF|1|L5|PSU|3637
9SPF|1|L5|G|3638
*
9SPF|1|L5|C|3650
9SPF|1|L5|A|3651
9SPF|1|L5|A|3652
9SPF|1|L5|A|3653
9SPF|1|L5|G|3654
*
9SPF|1|L5|U|3690
9SPF|1|L5|G|3691
9SPF|1|L5|A|3692
9SPF|1|L5|U|3693
9SPF|1|L5|U|3694
*
9SPF|1|L5|A|3821
9SPF|1|L5|U|3822
9SPF|1|L5|G|3823
9SPF|1|L5|A|3824
9SPF|1|L5|A2M|3825
9SPF|1|L5|C|3826

Current chains

Chain L5

28S rRNA

Nearby chains

Chain LA

Large ribosomal subunit protein uL2

Chain Ln

60S ribosomal protein L41

Chain Lp

60S ribosomal protein L37a

Chain S2

Small subunit ribosomal RNA; SSU rRNA