SMTL ID : 5jb3.1

Cryo-EM structure of a full archaeal ribosomal translation initiation complex in the P-REMOTE conformation

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-mer

Ligands

1 x MET: METHIONINE(Non-covalent)

MET.1: 9 residues within 4Å: Chain 3: A.76 Chain 7: Y.51, R.219, R.280, F.281, G.282, L.294, V.295, A.296 3 PLIP interactions: 3 interactions with chain 7 Hydrophobic interactions: 7:Y.51 Hydrogen bonds: 7:G.282, 7:V.295

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain 7: T.23, D.93 Ligands: GNP.3 1 PLIP interactions: 1 interactions with chain 7 Metal complexes: 7:T.23

1 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Non-covalent)

GNP.3: 28 residues within 4Å: Chain 7: H.17, V.18, D.19, H.20, G.21, K.22, T.23, T.24, K.36, M.45, T.46, D.93, A.94, P.95, G.96, H.97, N.149, K.150, D.152, V.153, S.184, A.185, L.186 Chain 8: S.122, Y.124, Q.133, P.135 Ligands: MG.2 21 PLIP interactions: 19 interactions with chain 7, 2 interactions with chain 8 Hydrogen bonds: 7:D.19, 7:D.19, 7:H.20, 7:G.21, 7:K.22, 7:K.22, 7:K.22, 7:T.23, 7:T.23, 7:T.24, 7:T.24, 7:T.46, 7:G.96, 7:H.97, 7:N.149, 7:L.186, 8:S.122, 8:Q.133 Salt bridges: 7:K.36, 7:D.152 pi-Cation interactions: 7:K.150

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 5 residues within 4Å: Chain 8: C.106, S.111, D.113, T.114, C.127 1 PLIP interactions: 1 interactions with chain 8 Metal complexes: 8:C.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Coureux, P.D. et al., Cryo-EM study of start codon selection during archaeal translation initiation. Nat Commun (2016)

Release Date

2016-11-30

Peptides

30S ribosomal protein S11: B
30S ribosomal protein S12: C
30S ribosomal protein S15: D
30S ribosomal protein S17P: E
30S ribosomal protein S3Ae: F
30S ribosomal protein S2: G
30S ribosomal protein S24e: H
30S ribosomal protein S27e: I
30S ribosomal protein S3: J
30S ribosomal protein S4: K
30S ribosomal protein S4e: L
30S ribosomal protein S5: M
30S ribosomal protein S6e: N
30S ribosomal protein S8: O
30S ribosomal protein S8e: P
30S ribosomal protein SX: Q
50S ribosomal protein L7Ae: R
30S ribosomal protein S10: S
30S ribosomal protein S13: T
30S ribosomal protein S14 type Z: U
30S ribosomal protein S17e: V
30S ribosomal protein S19: W
30S ribosomal protein S19e: X
30S ribosomal protein S28e: Y
30S ribosomal protein S27ae: Z
30S ribosomal protein S7: 0
30S ribosomal protein S9: 1
30S ribosomal protein eL41: 2
Protein translation factor SUI1 homolog: 5
Translation initiation factor 1A: 6
Translation initiation factor 2 subunit gamma: 7
Translation initiation factor 2 subunit beta: 8
Translation initiation factor 2 subunit alpha: 9

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
M

C
N

D
Q

E
R

F
A

G
B

H
V

I
W

J
Z

K
D

L
E

M
F

N
G

O
I

P
J

Q
C

R
3

S
L

T
O

U
P

V
S

W
T

X
U

Y
X

Z
Y

0
H

1
K

2
0

5
1

6
6

7
7

8
8

9
9

30S ribosomal protein S11

30S ribosomal protein S12

30S ribosomal protein S15

30S ribosomal protein S17P

30S ribosomal protein S3Ae

30S ribosomal protein S2

30S ribosomal protein S24e

30S ribosomal protein S27e

30S ribosomal protein S3

30S ribosomal protein S4

30S ribosomal protein S4e

30S ribosomal protein S5

30S ribosomal protein S6e

30S ribosomal protein S8

30S ribosomal protein S8e

30S ribosomal protein SX

50S ribosomal protein L7Ae

30S ribosomal protein S10

30S ribosomal protein S13

30S ribosomal protein S14 type Z

30S ribosomal protein S17e

30S ribosomal protein S19

30S ribosomal protein S19e

30S ribosomal protein S28e

30S ribosomal protein S27ae

30S ribosomal protein S7

30S ribosomal protein S9

30S ribosomal protein eL41

Protein translation factor SUI1 homolog

Translation initiation factor 1A

Translation initiation factor 2 subunit gamma

Translation initiation factor 2 subunit beta

Translation initiation factor 2 subunit alpha

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