SMTL ID : 3jap.1

Structure of a partial yeast 48S preinitiation complex in closed conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

81 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.1: 1 residues within 4Å: Chain B: G.361 No protein-ligand interaction detected (PLIP) MG.2: 3 residues within 4Å: Chain B: A.93, C.401, G.402 No protein-ligand interaction detected (PLIP) MG.3: 3 residues within 4Å: Chain B: G.551, A.554, A.555 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain B: U.44, U.45, A.100 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain B: G.623, A.1007 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain B: G.556, C.582, A.584 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain B: C.49, G.387 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain B: U.986, A.987 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain B: G.1312, C.1314, C.1401 No protein-ligand interaction detected (PLIP) MG.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain B: U.910, A.911 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain B: A.1744, G.1749, U.1752 No protein-ligand interaction detected (PLIP) MG.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain B: A.399, A.400 Chain L: K.23 No protein-ligand interaction detected (PLIP) MG.15: 2 residues within 4Å: Chain B: G.16, U.607 No protein-ligand interaction detected (PLIP) MG.16: 3 residues within 4Å: Chain B: G.376, A.377, U.378 No protein-ligand interaction detected (PLIP) MG.17: 2 residues within 4Å: Chain B: U.27, A.28 No protein-ligand interaction detected (PLIP) MG.18: 4 residues within 4Å: Chain B: G.370, A.603, A.604, G.606 No protein-ligand interaction detected (PLIP) MG.19: 4 residues within 4Å: Chain B: U.978, G.979, A.980, U.986 No protein-ligand interaction detected (PLIP) MG.20: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.21: 4 residues within 4Å: Chain B: A.43, U.44, A.46, A.47 No protein-ligand interaction detected (PLIP) MG.22: 5 residues within 4Å: Chain B: U.1742, A.1743, A.1744, G.1748, G.1749 No protein-ligand interaction detected (PLIP) MG.23: 4 residues within 4Å: Chain B: U.617, A.618, A.619, A.620 No protein-ligand interaction detected (PLIP) MG.24: 2 residues within 4Å: Chain B: G.560, G.561 No protein-ligand interaction detected (PLIP) MG.25: 3 residues within 4Å: Chain B: U.617, A.618, G.1773 No protein-ligand interaction detected (PLIP) MG.26: 4 residues within 4Å: Chain B: C.1309, G.1310, A.1311, G.1312 No protein-ligand interaction detected (PLIP) MG.27: 1 residues within 4Å: Chain B: A.1008 No protein-ligand interaction detected (PLIP) MG.28: 5 residues within 4Å: Chain B: C.99, A.100, U.101, A.359, C.360 No protein-ligand interaction detected (PLIP) MG.29: 1 residues within 4Å: Chain B: G.20 No protein-ligand interaction detected (PLIP) MG.30: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.31: 1 residues within 4Å: Chain B: U.1751 No protein-ligand interaction detected (PLIP) MG.32: 2 residues within 4Å: Chain B: U.94, G.95 No protein-ligand interaction detected (PLIP) MG.33: 2 residues within 4Å: Chain B: G.1708, U.1709 No protein-ligand interaction detected (PLIP) MG.34: 3 residues within 4Å: Chain B: U.1611, G.1773, G.1774 No protein-ligand interaction detected (PLIP) MG.35: 2 residues within 4Å: Chain B: G.63, U.64 No protein-ligand interaction detected (PLIP) MG.36: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.37: 2 residues within 4Å: Chain B: A.459, G.460 No protein-ligand interaction detected (PLIP) MG.38: 2 residues within 4Å: Chain B: U.465, G.466 No protein-ligand interaction detected (PLIP) MG.39: 1 residues within 4Å: Chain B: C.624 No protein-ligand interaction detected (PLIP) MG.40: 3 residues within 4Å: Chain B: G.967, G.968, G.996 No protein-ligand interaction detected (PLIP) MG.41: 2 residues within 4Å: Chain B: U.1395, G.1399 No protein-ligand interaction detected (PLIP) MG.42: 1 residues within 4Å: Chain B: G.548 No protein-ligand interaction detected (PLIP) MG.43: 2 residues within 4Å: Chain B: A.104, G.355 No protein-ligand interaction detected (PLIP) MG.44: 1 residues within 4Å: Chain B: G.1029 No protein-ligand interaction detected (PLIP) MG.45: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.46: 3 residues within 4Å: Chain B: G.402, G.403, C.404 No protein-ligand interaction detected (PLIP) MG.47: 2 residues within 4Å: Chain B: U.1285, U.1287 No protein-ligand interaction detected (PLIP) MG.48: 2 residues within 4Å: Chain B: A.960, A.961 No protein-ligand interaction detected (PLIP) MG.49: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.50: 3 residues within 4Å: Chain B: U.742, A.743, G.744 No protein-ligand interaction detected (PLIP) MG.51: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.52: 3 residues within 4Å: Chain B: C.809, A.826, G.827 No protein-ligand interaction detected (PLIP) MG.53: 2 residues within 4Å: Chain B: C.529, C.530 No protein-ligand interaction detected (PLIP) MG.54: 4 residues within 4Å: Chain B: G.1276, U.1285, A.1304 Ligands: MG.55 No protein-ligand interaction detected (PLIP) MG.55: 2 residues within 4Å: Chain F: K.121 Ligands: MG.54 No protein-ligand interaction detected (PLIP) MG.56: 1 residues within 4Å: Chain B: G.920 No protein-ligand interaction detected (PLIP) MG.57: 2 residues within 4Å: Chain B: U.971, G.993 No protein-ligand interaction detected (PLIP) MG.58: 1 residues within 4Å: Chain B: A.212 No protein-ligand interaction detected (PLIP) MG.59: 3 residues within 4Å: Chain B: G.1521, G.1522, G.1523 No protein-ligand interaction detected (PLIP) MG.60: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.61: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.62: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.63: 3 residues within 4Å: Chain B: G.884, U.991 Chain R: K.129 No protein-ligand interaction detected (PLIP) MG.64: 2 residues within 4Å: Chain B: G.1101, G.1109 No protein-ligand interaction detected (PLIP) MG.65: 2 residues within 4Å: Chain B: U.1036, U.1037 No protein-ligand interaction detected (PLIP) MG.66: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.67: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.68: 4 residues within 4Å: Chain B: C.1141, A.1175, U.1265, U.1267 No protein-ligand interaction detected (PLIP) MG.69: 3 residues within 4Å: Chain B: A.1450, A.1456 Chain W: N.85 No protein-ligand interaction detected (PLIP) MG.70: 3 residues within 4Å: Chain 8: T.86, P.88 Chain B: G.1426 No protein-ligand interaction detected (PLIP) MG.71: 2 residues within 4Å: Chain B: C.1159, C.1438 No protein-ligand interaction detected (PLIP) MG.72: 2 residues within 4Å: Chain B: G.1182, G.1183 No protein-ligand interaction detected (PLIP) MG.73: 3 residues within 4Å: Chain B: C.1412, U.1413, U.1418 No protein-ligand interaction detected (PLIP) MG.74: 2 residues within 4Å: Chain B: A.1178, C.1179 No protein-ligand interaction detected (PLIP) MG.75: 2 residues within 4Å: Chain B: G.1250, U.1251 No protein-ligand interaction detected (PLIP) MG.76: 5 residues within 4Å: Chain B: C.1256, A.1408, G.1409, G.1410 Ligands: MG.79 No protein-ligand interaction detected (PLIP) MG.77: 4 residues within 4Å: Chain B: G.1522, G.1523, C.1549, A.1550 No protein-ligand interaction detected (PLIP) MG.78: 4 residues within 4Å: Chain B: A.1464, G.1465, G.1502, U.1503 No protein-ligand interaction detected (PLIP) MG.79: 7 residues within 4Å: Chain B: G.1255, C.1256, A.1408, G.1409, G.1410 Ligands: MG.76 Chain b: N.17 No protein-ligand interaction detected (PLIP) MG.80: 3 residues within 4Å: Chain B: A.1184, A.1185, C.1580 No protein-ligand interaction detected (PLIP) MG.85: 4 residues within 4Å: Ligands: GCP.86 Chain d: S.114, T.137, D.193 1 PLIP interactions: 1 interactions with chain d Metal complexes: d:T.137

4 x ZN: ZINC ION(Non-covalent)

ZN.81: 4 residues within 4Å: Chain 3: C.23, C.26, C.74, C.77 3 PLIP interactions: 3 interactions with chain 3 Metal complexes: 3:C.23, 3:C.26, 3:C.77 ZN.82: 5 residues within 4Å: Chain 4: C.37, C.56, S.58, C.59, T.61 2 PLIP interactions: 2 interactions with chain 4 Metal complexes: 4:C.59, 4:C.59 ZN.83: 3 residues within 4Å: Chain 8: C.121, C.124, C.139 3 PLIP interactions: 3 interactions with chain 8 Metal complexes: 8:C.121, 8:C.124, 8:C.139 ZN.87: 5 residues within 4Å: Chain e: C.236, T.238, C.259, C.262, S.264 3 PLIP interactions: 3 interactions with chain e Metal complexes: e:C.236, e:C.262, e:S.264

1 x MET: METHIONINE(Non-covalent)

MET.84: 9 residues within 4Å: Chain A: A.75 Chain d: Y.142, F.321, F.381, A.382, E.383, L.395, I.396, G.397 2 PLIP interactions: 2 interactions with chain d Hydrogen bonds: d:E.383, d:E.383

1 x GCP: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER(Non-covalent)

GCP.86: 25 residues within 4Å: Ligands: MG.85 Chain d: H.108, A.110, H.111, G.112, K.113, S.114, T.115, R.127, I.136, T.137, D.193, C.194, P.195, G.196, N.249, D.252, S.284, A.285, Q.286 Chain e: T.238, C.262, S.264, T.265, R.266 16 PLIP interactions: 3 interactions with chain e, 13 interactions with chain d Hydrogen bonds: e:T.265, e:T.265, e:T.265, d:A.110, d:H.111, d:G.112, d:K.113, d:K.113, d:S.114, d:T.115, d:T.137, d:G.196, d:N.249, d:A.285, d:Q.286 Salt bridges: d:D.252

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Llacer, J.L. et al., Conformational Differences between Open and Closed States of the Eukaryotic Translation Initiation Complex. Mol.Cell (2015)

Release Date

2015-08-12

Peptides

uS2: D
eS1: E
uS5: F
uS3: G
eS4: H
uS7: I
eS6: J
eS7: K
eS8: L
uS4: M
eS10: N
uS17: O
eS12: P
uS15: Q
uS11: R
uS19: S
uS9: T
eS17: U
uS13: V
eS19: W
uS10: X
eS21: Y
uS8: Z
uS12: 0
eS24: 1
eS25: 2
eS26: 3
eS27: 4
eS28: 5
uS14: 6
eS30: 7
eS31: 8
RACK1: 9
eL41: a
eIF1A: b
eIF2 alpha: c
eIF2 gamma: d
eIF2 beta: e
eIF1: f
eIF3a: g
eIF3c: h
eIF3i: i
eIF3b: j
eIF3g: k

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

D
A

E
B

F
C

G
D

H
E

I
F

J
G

K
H

L
I

M
J

N
K

O
L

P
M

Q
N

R
O

S
P

T
Q

U
R

V
S

W
T

X
U

Y
V

Z
W

0
X

1
Y

2
Z

3
a

4
b

5
c

6
d

7
e

8
f

9
g

a
h

b
i

c
j

d
k

e
l

f
m

g
o

h
p

i
q

j
r

k
s

uS2

eS1

uS5

uS3

eS4

uS7

eS6

eS7

eS8

uS4

eS10

uS17

eS12

uS15

uS11

uS19

uS9

eS17

uS13

eS19

uS10

eS21

uS8

uS12

eS24

eS25

eS26

eS27

eS28

uS14

eS30

eS31

RACK1

eL41

eIF1A

eIF2 alpha

eIF2 gamma

eIF2 beta

eIF1

eIF3a

eIF3c

eIF3i

eIF3b

eIF3g

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