SMTL ID : 8rdw.1

Cryo-EM structure of P. urativorans 70S ribosome in complex with hibernation factor Balon and EF-Tu(GDP) (structure 3).

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-mer

Ligands

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

GDP.1: 15 residues within 4Å: Chain D: V.21, D.22, G.24, K.25, T.26, T.27, Y.47, N.136, K.137, D.139, M.140, S.174, A.175, T.176 Ligands: MG.2 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:D.22, D:D.22, D:G.24, D:K.25, D:T.26, D:T.26, D:T.27, D:T.27, D:Y.47, D:N.136, D:K.137, D:S.174, D:A.175, D:T.176, D:T.176 Salt bridges: D:K.25, D:D.139

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain D: T.26, D.51 Ligands: GDP.1 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.26

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

2024-02-21

Peptides

Methyl-accepting chemotaxis protein: A
Large ribosomal subunit protein bL12: B
Small ribosomal subunit protein uS9: C
Elongation factor Tu: D
Small ribosomal subunit protein bS18: F
Small ribosomal subunit protein uS2: G
Small ribosomal subunit protein uS5: H
Small ribosomal subunit protein uS12: I
Large ribosomal subunit protein uL5: J
Large ribosomal subunit protein uL4: L
Large ribosomal subunit protein bL32: M
Large ribosomal subunit protein bL17: N
Large ribosomal subunit protein bL25: O
Large ribosomal subunit protein bL28: P
Large ribosomal subunit protein uL29: Q
Large ribosomal subunit protein uL22: R
Small ribosomal subunit protein bS6: S
Large ribosomal subunit protein bL27: T
Large ribosomal subunit protein uL24: U
Large ribosomal subunit protein bL31B: V
Small ribosomal subunit protein uS14: W
Small ribosomal subunit protein uS15: X
Small ribosomal subunit protein uS13: Y
Large ribosomal subunit protein bL20: 0
Small ribosomal subunit protein uS19: 1
Small ribosomal subunit protein uS8: 2
Large ribosomal subunit protein uL6: 3
Small ribosomal subunit protein uS7: 4
Small ribosomal subunit protein uS3: 5
Small ribosomal subunit protein uS11: 6
Small ribosomal subunit protein bS21: 7
Large ribosomal subunit protein uL30: 8
Large ribosomal subunit protein uL13: 9
Small ribosomal subunit protein uS10: a
Small ribosomal subunit protein uS17: b
Large ribosomal subunit protein bL34: c
Large ribosomal subunit protein bL21: d
Large ribosomal subunit protein uL18: e
Large ribosomal subunit protein uL15: f
Large ribosomal subunit protein uL14: g
Large ribosomal subunit protein uL3: h
Large ribosomal subunit protein uL16: i
Large ribosomal subunit protein bL35: j
Large ribosomal subunit protein bL19: k
Small ribosomal subunit protein bS16: l
Large ribosomal subunit protein bL33: m
Large ribosomal subunit protein uL2: n
Small ribosomal subunit protein uS4: o
Large ribosomal subunit protein uL23: p
Small ribosomal subunit protein bS20: q
Large ribosomal subunit protein bL36: r
Large ribosomal subunit protein bL9: s

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

C
F

D
H

F
R3

G
A4

H
E5

I
L6

J
F7

L
E9

M
aA

N
MB

O
UC

P
WD

Q
XE

R
RF

S
FG

T
VH

U
TI

V
fJ

W
HK

X
OL

Y
MM

0
PO

1
SP

2
BQ

3
GR

4
GS

5
CT

6
KU

7
NV

8
YW

9
IX

a
JY

b
QZ

c
Ba

d
Qb

e
Nc

f
Kd

g
Je

h
Af

i
Lg

j
dh

k
Oi

l
Pj

m
bk

n
Cl

o
Dm

p
Sn

q
To

r
ep

s
C1

Methyl-accepting chemotaxis protein

Large ribosomal subunit protein bL12

Small ribosomal subunit protein uS9

Elongation factor Tu

Small ribosomal subunit protein bS18

Small ribosomal subunit protein uS2

Small ribosomal subunit protein uS5

Small ribosomal subunit protein uS12

Large ribosomal subunit protein uL5

Large ribosomal subunit protein uL4

Large ribosomal subunit protein bL32

Large ribosomal subunit protein bL17

Large ribosomal subunit protein bL25

Large ribosomal subunit protein bL28

Large ribosomal subunit protein uL29

Large ribosomal subunit protein uL22

Small ribosomal subunit protein bS6

Large ribosomal subunit protein bL27

Large ribosomal subunit protein uL24

Large ribosomal subunit protein bL31B

Small ribosomal subunit protein uS14

Small ribosomal subunit protein uS15

Small ribosomal subunit protein uS13

Large ribosomal subunit protein bL20

Small ribosomal subunit protein uS19

Small ribosomal subunit protein uS8

Large ribosomal subunit protein uL6

Small ribosomal subunit protein uS7

Small ribosomal subunit protein uS3

Small ribosomal subunit protein uS11

Small ribosomal subunit protein bS21

Large ribosomal subunit protein uL30

Large ribosomal subunit protein uL13

Small ribosomal subunit protein uS10

Small ribosomal subunit protein uS17

Large ribosomal subunit protein bL34

Large ribosomal subunit protein bL21

Large ribosomal subunit protein uL18

Large ribosomal subunit protein uL15

Large ribosomal subunit protein uL14

Large ribosomal subunit protein uL3

Large ribosomal subunit protein uL16

Large ribosomal subunit protein bL35

Large ribosomal subunit protein bL19

Small ribosomal subunit protein bS16

Large ribosomal subunit protein bL33

Large ribosomal subunit protein uL2

Small ribosomal subunit protein uS4

Large ribosomal subunit protein uL23

Small ribosomal subunit protein bS20

Large ribosomal subunit protein bL36

Large ribosomal subunit protein bL9

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