SMTL ID : 8v9l.1

Cryo-EM structure of the Mycobacterium smegmatis 70S ribosome in complex with hibernation factor Msmeg1130 (Balon) and MsmegEF-Tu(GDP) (Composite structure 6)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x U- U- U- U: poly-U mRNA(Non-functional Binders)

U-U-U-U.1: 7 residues within 4Å: Chain A: G.673, U.769, G.908 Chain W: A.35, A.36, A.37, A.38 Protein-ligand interaction information (PLIP) not available

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.2: 16 residues within 4Å: Chain V: V.21, D.22, H.23, G.24, K.25, T.26, T.27, D.53, P.85, N.138, K.139, D.141, A.142, S.175, A.176, L.177 17 PLIP interactions: 17 interactions with chain V Hydrogen bonds: V:D.22, V:D.22, V:H.23, V:G.24, V:G.24, V:K.25, V:T.26, V:T.26, V:T.27, V:T.27, V:P.85, V:N.138, V:K.139, V:A.176, V:L.177 Salt bridges: V:K.25, V:D.141

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain m: C.5, C.8, C.52, C.55 4 PLIP interactions: 4 interactions with chain m Metal complexes: m:C.5, m:C.8, m:C.52, m:C.55 ZN.4: 4 residues within 4Å: Chain r: C.15, C.18, C.42, C.45 4 PLIP interactions: 4 interactions with chain r Metal complexes: r:C.15, r:C.18, r:C.42, r:C.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Helena-Bueno, K. et al., A new family of bacterial ribosome hibernation factors. Nature (2024)

Release Date

2024-02-07

Peptides

30S Ribosomal Protein S2: B
30S ribosomal protein S3: C
30S ribosomal protein S4: D
Small ribosomal subunit protein uS5: E
30S ribosomal protein S6: F
30S ribosomal protein S7: G
Small ribosomal subunit protein uS8: H
30S ribosomal protein S9: I
30S ribosomal protein S10: J
30S ribosomal protein S11: K
30S ribosomal protein S12: L
30S ribosomal protein S13: M
Small ribosomal subunit protein uS14B: N
Small ribosomal subunit protein uS15: O
30S ribosomal protein S16: P
30S ribosomal protein S17: Q
Small ribosomal subunit protein bS18B: R
30S ribosomal protein S19: S
30S ribosomal protein S20: T
30S Ribosomal Protein S22: U
Elongation factor Tu: V
Ribosome hibernation factor Balon (MSMEG_1130): X
50S ribosomal protein L2: 0
50S ribosomal protein L3: 1
Large ribosomal subunit protein uL4: 2
Large ribosomal subunit protein uL5: 3
50S ribosomal protein L6: 4
50S ribosomal protein L9: 5
50S ribosomal protein L10: 6
50S ribosomal protein L11: 7
Large ribosomal subunit protein uL13: 8
50S ribosomal protein L14: 9
50S ribosomal protein L15: a
Large ribosomal subunit protein uL16: b
50S ribosomal protein L17: c
Large ribosomal subunit protein uL18: d
50S ribosomal protein L19: e
Large ribosomal subunit protein bL20: f
Large ribosomal subunit protein bL21: g
Large ribosomal subunit protein uL22: h
Large ribosomal subunit protein uL23: i
50S ribosomal protein L24: j
50S ribosomal protein L25: k
50S ribosomal protein L27: l
Large ribosomal subunit protein bL28: m
50S ribosomal protein L29: n
50S ribosomal protein L30: o
Large ribosomal subunit protein bL31: p
50S ribosomal protein L32: q
Large ribosomal subunit protein bL33A: r
50S ribosomal protein L34: s
50S ribosomal protein L35: t
50S ribosomal protein L36: u
50S Ribosomal Protein L27: v

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
b

C
c

D
d

E
e

F
f

G
g

H
h

I
i

J
j

K
k

L
l

M
m

N
n

O
o

P
p

Q
q

R
r

S
s

T
t

U
u

V
x

X
z

0
C

1
D

2
E

3
F

4
G

5
H

6
I

7
J

8
L

9
M

a
N

b
O

c
P

d
Q

e
R

f
S

g
T

h
U

i
V

j
W

k
X

l
Y

m
Z

n
1

o
2

p
3

q
4

r
5

s
6

t
7

u
8

v
9

30S Ribosomal Protein S2

30S ribosomal protein S3

30S ribosomal protein S4

Small ribosomal subunit protein uS5

30S ribosomal protein S6

30S ribosomal protein S7

Small ribosomal subunit protein uS8

30S ribosomal protein S9

30S ribosomal protein S10

30S ribosomal protein S11

30S ribosomal protein S12

30S ribosomal protein S13

Small ribosomal subunit protein uS14B

Small ribosomal subunit protein uS15

30S ribosomal protein S16

30S ribosomal protein S17

Small ribosomal subunit protein bS18B

30S ribosomal protein S19

30S ribosomal protein S20

30S Ribosomal Protein S22

Elongation factor Tu

Ribosome hibernation factor Balon (MSMEG_1130)

50S ribosomal protein L2

50S ribosomal protein L3

Large ribosomal subunit protein uL4

Large ribosomal subunit protein uL5

50S ribosomal protein L6

50S ribosomal protein L9

50S ribosomal protein L10

50S ribosomal protein L11

Large ribosomal subunit protein uL13

50S ribosomal protein L14

50S ribosomal protein L15

Large ribosomal subunit protein uL16

50S ribosomal protein L17

Large ribosomal subunit protein uL18

50S ribosomal protein L19

Large ribosomal subunit protein bL20

Large ribosomal subunit protein bL21

Large ribosomal subunit protein uL22

Large ribosomal subunit protein uL23

50S ribosomal protein L24

50S ribosomal protein L25

50S ribosomal protein L27

Large ribosomal subunit protein bL28

50S ribosomal protein L29

50S ribosomal protein L30

Large ribosomal subunit protein bL31

50S ribosomal protein L32

Large ribosomal subunit protein bL33A

50S ribosomal protein L34

50S ribosomal protein L35

50S ribosomal protein L36

50S Ribosomal Protein L27

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