HL_9XWO_037

3D structure

PDB id

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

Description

Cryo-EM structure of SecM-arrested 70S ribosome (short SecM)

Experimental method

ELECTRON MICROSCOPY

Resolution

2.89 Å

Loop

Sequence

CAG(H2U)(H2U)GG(H2U)AG

Length

10 nucleotides

Bulged bases

9XWO|1|Z|H2U|16, 9XWO|1|Z|H2U|17, 9XWO|1|Z|G|18, 9XWO|1|Z|G|19, 9XWO|1|Z|H2U|20

QA status

Modified nucleotides: H2U

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

HL_9XWO_037 not in the Motif Atlas

Homologous match to HL_1FIR_004

Geometric discrepancy: 0.1349

The information below is about HL_1FIR_004

Detailed Annotation

tRNA D-loop

Broad Annotation

No text annotation

Motif group

HL_20490.1

Basepair signature

cWW-cWS-F

Number of instances in this motif group

13

Unit IDs

9XWO|1|Z|C|13
9XWO|1|Z|A|14
9XWO|1|Z|G|15
9XWO|1|Z|H2U|16
9XWO|1|Z|H2U|17
9XWO|1|Z|G|18
9XWO|1|Z|G|19
9XWO|1|Z|H2U|20
9XWO|1|Z|A|21
9XWO|1|Z|G|22

Current chains

Chain Z

P-site tRNA (tRNAGly)

Nearby chains

Chain a

Large subunit ribosomal RNA; LSU rRNA

Chain f

Large ribosomal subunit protein uL5