SMTL ID : 8s1u.1

YlmH bound to stalled 50S subunits with RqcH and PtRNA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.40 Å

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

15 x K: POTASSIUM ION(Non-functional Binders)(Non-covalent)

K.1: 4 residues within 4Å: Chain 6: G.2090, G.2476, C.2530, U.2533 Ligand excluded by PLIP K.2: 3 residues within 4Å: Chain 6: U.2051, G.2082, C.2645 Ligand excluded by PLIP K.3: 4 residues within 4Å: Chain 6: A.2080, G.2081, G.2082, A.2643 Ligand excluded by PLIP K.4: 6 residues within 4Å: Chain 6: G.2534, G.2605, C.2608, U.2609, G.2610, C.2639 Ligand excluded by PLIP K.5: 4 residues within 4Å: Chain 6: G.2279, G.2280, C.2525, A.2526 Ligand excluded by PLIP K.6: 4 residues within 4Å: Chain 6: U.874, A.2455, C.2456, G.2458 Ligand excluded by PLIP K.7: 5 residues within 4Å: Chain 6: A.637, U.638, G.709, G.710, U.711 Ligand excluded by PLIP K.8: 4 residues within 4Å: Chain 6: A.987, G.1231, G.1232 Chain P: G.32 Ligand excluded by PLIP K.9: 5 residues within 4Å: Chain 6: G.1255, C.1256, G.1273, U.1274, G.1275 Ligand excluded by PLIP K.10: 5 residues within 4Å: Chain 6: G.684, U.685, G.694, G.695, C.696 Ligand excluded by PLIP K.11: 4 residues within 4Å: Chain 6: A.2482, U.2535, A.2601, C.2602 Ligand excluded by PLIP K.12: 3 residues within 4Å: Chain 6: G.2082, G.2085, A.2606 Ligand excluded by PLIP K.13: 4 residues within 4Å: Chain 6: C.2710, U.2713, G.2714, U.2753 Ligand excluded by PLIP K.14: 5 residues within 4Å: Chain 6: U.615, G.617, A.619, A.2059, C.2528 Ligand excluded by PLIP K.15: 6 residues within 4Å: Chain 6: A.619, U.620, U.2529, C.2530, A.2532, U.2533 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Takada, H. et al., A role for the S4-domain containing protein YlmH in ribosome-associated quality control in Bacillus subtilis. Nucleic Acids Res. (2024)

Release Date

2024-06-12

Peptides

50S ribosomal protein L32: B
50S ribosomal protein L33 1: C
50S ribosomal protein L34: D
50S ribosomal protein L35: E
50S ribosomal protein L36: F
50S ribosomal protein L31: G
50S ribosomal protein L2: I
50S ribosomal protein L3: J
50S ribosomal protein L4: K
50S ribosomal protein L5: L
Large ribosomal subunit protein uL6: M
50S ribosomal protein L13: N
50S ribosomal protein L14: O
50S ribosomal protein L15: P
50S ribosomal protein L16: Q
50S ribosomal protein L17: R
50S ribosomal protein L18: S
50S ribosomal protein L19: T
Large ribosomal subunit protein bL20: U
50S ribosomal protein L21: V
50S ribosomal protein L22: W
Large ribosomal subunit protein uL23: X
50S ribosomal protein L24: Y
Putative RNA-binding protein YlmH: Z
Large ribosomal subunit protein bL27: 0
50S ribosomal protein L28: 1
50S ribosomal protein L29: 2
Large ribosomal subunit protein uL30: 3
Rqc2 homolog RqcH: 5

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
0

C
1

D
2

E
3

F
4

G
6

I
C

J
D

K
E

L
F

M
G

N
J

O
K

P
L

Q
M

R
N

S
O

T
P

U
Q

V
R

W
S

X
T

Y
U

Z
V

0
W

1
X

2
Y

3
Z

5
H

50S ribosomal protein L32

50S ribosomal protein L33 1

50S ribosomal protein L34

50S ribosomal protein L35

50S ribosomal protein L36

50S ribosomal protein L31

50S ribosomal protein L2

50S ribosomal protein L3

50S ribosomal protein L4

50S ribosomal protein L5

Large ribosomal subunit protein uL6

50S ribosomal protein L13

50S ribosomal protein L14

50S ribosomal protein L15

50S ribosomal protein L16

50S ribosomal protein L17

50S ribosomal protein L18

50S ribosomal protein L19

Large ribosomal subunit protein bL20

50S ribosomal protein L21

50S ribosomal protein L22

Large ribosomal subunit protein uL23

50S ribosomal protein L24

Putative RNA-binding protein YlmH

Large ribosomal subunit protein bL27

50S ribosomal protein L28

50S ribosomal protein L29

Large ribosomal subunit protein uL30

Rqc2 homolog RqcH

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