J5_7NRD_006

3D structure

PDB id

7NRD (explore in PDB, NAKB, or RNA 3D Hub)

Description

Structure of the yeast Gcn1 bound to a colliding stalled 80S ribosome with MBF1, A/P-tRNA and P/E-tRNA

Experimental method

ELECTRON MICROSCOPY

Resolution

4.36 Å

Loop

Sequence

UUGA*UUUG*CA*UG*CAGAAAA

Length

19 nucleotides

Bulged bases

7NRD|1|LA|G|2418, 7NRD|1|LA|A|2799, 7NRD|1|LA|G|2800, 7NRD|1|LA|A|2801, 7NRD|1|LA|A|2802

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

J5_7NRD_006 not in the Motif Atlas

Homologous match to J5_8P9A_015

Geometric discrepancy: 0.3173

The information below is about J5_8P9A_015

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J5_96125.1

Basepair signature

cWW-cWH-cWH-tSS-cWW-cWW-cWW-F-cWW

Number of instances in this motif group

6

Unit IDs

7NRD|1|LA|U|2416
7NRD|1|LA|U|2417
7NRD|1|LA|G|2418
7NRD|1|LA|A|2419
*
7NRD|1|LA|U|2611
7NRD|1|LA|U|2612
7NRD|1|LA|U|2613
7NRD|1|LA|G|2614
*
7NRD|1|LA|C|2627
7NRD|1|LA|A|2628
*
7NRD|1|LA|U|2650
7NRD|1|LA|G|2651
*
7NRD|1|LA|C|2798
7NRD|1|LA|A|2799
7NRD|1|LA|G|2800
7NRD|1|LA|A|2801
7NRD|1|LA|A|2802
7NRD|1|LA|A|2803
7NRD|1|LA|A|2804

Current chains

Chain LA

25S rRNA (3184-MER)

Nearby chains

Chain LD

60S ribosomal protein L2-A

Chain LP

60S ribosomal protein L15-A

Chain LS

60S ribosomal protein L18-A

Chain LV

60S ribosomal protein L21-A

Chain Lc

60S ribosomal protein L28

Chain Ld

60S ribosomal protein L29

Chain Lq

60S ribosomal protein L42-A

Chain Sm

Transfer RNA; tRNA