J6_4D5Y_002

3D structure

PDB id

4D5Y (explore in PDB, NAKB, or RNA 3D Hub)

Description

Cryo-EM structures of ribosomal 80S complexes with termination factors and cricket paralysis virus IRES reveal the IRES in the translocated state

Experimental method

ELECTRON MICROSCOPY

Resolution

9 Å

Loop

Sequence

UUGAC*GUUUG*CA*UGUC*GCCUCACGAUCC*GGUGUCAGAAAA

Length

40 nucleotides

Bulged bases

4D5Y|1|2|G|3891, 4D5Y|1|2|U|4150, 4D5Y|1|2|C|4297, 4D5Y|1|2|A|4336, 4D5Y|1|2|A|4338, 4D5Y|1|2|A|4339

QA status

Valid loop

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

4D5Y|1|2|U|3889
4D5Y|1|2|U|3890
4D5Y|1|2|G|3891
4D5Y|1|2|A|3892
4D5Y|1|2|C|3893
*
4D5Y|1|2|G|4147
4D5Y|1|2|U|4148
4D5Y|1|2|U|4149
4D5Y|1|2|U|4150
4D5Y|1|2|G|4151
*
4D5Y|1|2|C|4164
4D5Y|1|2|A|4165
*
4D5Y|1|2|U|4187
4D5Y|1|2|G|4188
4D5Y|1|2|U|4189
4D5Y|1|2|C|4190
*
4D5Y|1|2|G|4291
4D5Y|1|2|C|4292
4D5Y|1|2|C|4293
4D5Y|1|2|U|4294
4D5Y|1|2|C|4295
4D5Y|1|2|A|4296
4D5Y|1|2|C|4297
4D5Y|1|2|G|4298
4D5Y|1|2|A|4299
4D5Y|1|2|U|4300
4D5Y|1|2|C|4301
4D5Y|1|2|C|4302
*
4D5Y|1|2|G|4330
4D5Y|1|2|G|4331
4D5Y|1|2|U|4332
4D5Y|1|2|G|4333
4D5Y|1|2|U|4334
4D5Y|1|2|C|4335
4D5Y|1|2|A|4336
4D5Y|1|2|G|4337
4D5Y|1|2|A|4338
4D5Y|1|2|A|4339
4D5Y|1|2|A|4340
4D5Y|1|2|A|4341

Current chains

Chain 2

28S Ribosomal RNA

Nearby chains

Chain A

60S RIBOSOMAL PROTEIN UL2

Chain N

60S RIBOSOMAL PROTEIN EL15

Chain Q

60S RIBOSOMAL PROTEIN EL18

Chain T

60S RIBOSOMAL PROTEIN EL21

Chain a

60S RIBOSOMAL PROTEIN UL15

Chain o

60S RIBOSOMAL PROTEIN EL44