J4_6SWC_004

3D structure

PDB id

6SWC (explore in PDB, NAKB, or RNA 3D Hub)

Description

IC2B model of cryo-EM structure of a full archaeal ribosomal translation initiation complex devoid of aIF1 in P. abyssi

Experimental method

ELECTRON MICROSCOPY

Resolution

3.3 Å

Loop

Sequence

G(4SU)GG*CGU*AAGAUCG*CC

Length

16 nucleotides

Bulged bases

6SWC|1|4|4SU|8, 6SWC|1|4|U|47, 6SWC|1|4|C|48

QA status

Modified nucleotides: 4SU

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_6SWC_004 not in the Motif Atlas

Homologous match to J4_7VNV_001

Geometric discrepancy: 0.3266

The information below is about J4_7VNV_001

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_70449.27

Basepair signature

cWW-F-cWW-cWW-cHS-F-cWW-cWW

Number of instances in this motif group

53

Unit IDs

6SWC|1|4|G|7
6SWC|1|4|4SU|8
6SWC|1|4|G|9
6SWC|1|4|G|10
*
6SWC|1|4|C|25
6SWC|1|4|G|26
6SWC|1|4|U|27
*
6SWC|1|4|A|43
6SWC|1|4|A|44
6SWC|1|4|G|45
6SWC|1|4|A|46
6SWC|1|4|U|47
6SWC|1|4|C|48
6SWC|1|4|G|49
*
6SWC|1|4|C|65
6SWC|1|4|C|66

Current chains

Chain 4

initiator Met-tRNA fMet from E. coli (A1U72 variant)

Nearby chains

Chain 2

Small subunit ribosomal RNA; SSU rRNA

Chain O

30S ribosomal protein S13