SMTL ID : 3j81.1

CryoEM structure of a partial yeast 48S preinitiation complex

Coordinates

PDB Format

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-mer

Ligands

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

MG.1: 2 residues within 4Å: Chain A: G.361, G.362 No protein-ligand interaction detected (PLIP) MG.2: 5 residues within 4Å: Chain A: A.93, G.95, C.401, G.402 Chain F: R.3 No protein-ligand interaction detected (PLIP) MG.3: 5 residues within 4Å: Chain A: G.551, G.552, C.553, A.554, A.555 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain A: A.100, C.360 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain A: G.623, A.1025 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain A: C.582, A.584, G.585 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain A: C.49, A.424 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain A: A.993, U.1004, A.1005 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain A: A.1329, G.1330, C.1419 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain A: U.8, U.9, A.11 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain A: U.928, A.929 No protein-ligand interaction detected (PLIP) MG.12: 5 residues within 4Å: Chain A: A.1761, A.1762, G.1767, U.1770, C.1783 No protein-ligand interaction detected (PLIP) MG.13: 2 residues within 4Å: Chain A: G.547, G.548 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain A: G.391, A.400, C.401 No protein-ligand interaction detected (PLIP) MG.15: 4 residues within 4Å: Chain A: G.16, U.607, G.609, C.613 No protein-ligand interaction detected (PLIP) MG.16: 5 residues within 4Å: Chain A: G.361, G.362, G.376, A.377, U.378 No protein-ligand interaction detected (PLIP) MG.17: 2 residues within 4Å: Chain A: A.28, U.29 No protein-ligand interaction detected (PLIP) MG.18: 3 residues within 4Å: Chain A: G.370, A.604, G.606 No protein-ligand interaction detected (PLIP) MG.19: 4 residues within 4Å: Chain A: A.998, U.999, A.1003, U.1004 No protein-ligand interaction detected (PLIP) MG.20: 2 residues within 4Å: Chain A: C.426, G.428 No protein-ligand interaction detected (PLIP) MG.21: 2 residues within 4Å: Chain A: U.44, A.47 No protein-ligand interaction detected (PLIP) MG.22: 5 residues within 4Å: Chain A: U.1760, A.1761, A.1762, G.1766, G.1767 No protein-ligand interaction detected (PLIP) MG.23: 4 residues within 4Å: Chain A: U.617, A.618, A.619, A.620 No protein-ligand interaction detected (PLIP) MG.24: 2 residues within 4Å: Chain A: G.560, A.579 No protein-ligand interaction detected (PLIP) MG.25: 2 residues within 4Å: Chain A: A.618, A.619 No protein-ligand interaction detected (PLIP) MG.26: 3 residues within 4Å: Chain A: C.1327, G.1328, G.1330 No protein-ligand interaction detected (PLIP) MG.27: 1 residues within 4Å: Chain A: A.622 No protein-ligand interaction detected (PLIP) MG.28: 4 residues within 4Å: Chain A: C.99, A.100, U.101, C.360 No protein-ligand interaction detected (PLIP) MG.29: 1 residues within 4Å: Chain A: G.20 No protein-ligand interaction detected (PLIP) MG.30: 2 residues within 4Å: Chain A: G.1109, G.1110 No protein-ligand interaction detected (PLIP) MG.31: 2 residues within 4Å: Chain A: U.1769, A.1793 No protein-ligand interaction detected (PLIP) MG.32: 1 residues within 4Å: Chain A: G.95 No protein-ligand interaction detected (PLIP) MG.33: 5 residues within 4Å: Chain A: G.1671, G.1672, C.1673, G.1726, U.1727 No protein-ligand interaction detected (PLIP) MG.34: 3 residues within 4Å: Chain A: U.1629, G.1792, A.1793 No protein-ligand interaction detected (PLIP) MG.35: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.36: 3 residues within 4Å: Chain A: G.458, A.459, G.460 No protein-ligand interaction detected (PLIP) MG.37: 2 residues within 4Å: Chain A: G.466, A.467 No protein-ligand interaction detected (PLIP) MG.38: 4 residues within 4Å: Chain A: A.622, C.624, C.1028, U.1031 No protein-ligand interaction detected (PLIP) MG.39: 3 residues within 4Å: Chain A: G.985, G.986, G.1014 No protein-ligand interaction detected (PLIP) MG.40: 1 residues within 4Å: Chain A: G.1417 No protein-ligand interaction detected (PLIP) MG.41: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.42: 3 residues within 4Å: Chain A: A.104, C.353, G.354 No protein-ligand interaction detected (PLIP) MG.43: 3 residues within 4Å: Chain A: G.1064, A.1065 Chain C: Q.157 No protein-ligand interaction detected (PLIP) MG.44: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.45: 5 residues within 4Å: Chain A: G.402, G.403, C.404, G.421, G.422 No protein-ligand interaction detected (PLIP) MG.46: 3 residues within 4Å: Chain A: U.1302, U.1303, G.1304 No protein-ligand interaction detected (PLIP) MG.47: 2 residues within 4Å: Chain A: A.979, U.1015 No protein-ligand interaction detected (PLIP) MG.48: 1 residues within 4Å: Chain A: U.58 No protein-ligand interaction detected (PLIP) MG.49: 3 residues within 4Å: Chain A: U.760, A.761, G.762 No protein-ligand interaction detected (PLIP) MG.50: 2 residues within 4Å: Chain A: A.1139, G.1140 No protein-ligand interaction detected (PLIP) MG.51: 3 residues within 4Å: Chain A: C.827, U.843, A.844 No protein-ligand interaction detected (PLIP) MG.52: 3 residues within 4Å: Chain A: A.514, C.529, C.530 No protein-ligand interaction detected (PLIP) MG.53: 3 residues within 4Å: Chain A: U.1302, U.1303 Ligands: MG.54 No protein-ligand interaction detected (PLIP) MG.54: 2 residues within 4Å: Chain A: A.1296 Ligands: MG.53 No protein-ligand interaction detected (PLIP) MG.55: 1 residues within 4Å: Chain A: G.938 No protein-ligand interaction detected (PLIP) MG.56: 2 residues within 4Å: Chain A: U.989, G.1011 No protein-ligand interaction detected (PLIP) MG.57: 2 residues within 4Å: Chain A: A.212, G.213 No protein-ligand interaction detected (PLIP) MG.58: 3 residues within 4Å: Chain A: C.1475, G.1539, G.1540 No protein-ligand interaction detected (PLIP) MG.59: 2 residues within 4Å: Chain A: G.335, G.336 No protein-ligand interaction detected (PLIP) MG.60: 2 residues within 4Å: Chain A: C.1635, G.1637 No protein-ligand interaction detected (PLIP) MG.61: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.62: 1 residues within 4Å: Chain A: U.379 No protein-ligand interaction detected (PLIP) MG.63: 3 residues within 4Å: Chain A: G.991, U.1009 Chain P: K.129 No protein-ligand interaction detected (PLIP) MG.64: 1 residues within 4Å: Chain A: U.1117 No protein-ligand interaction detected (PLIP) MG.65: 1 residues within 4Å: Chain A: U.1055 No protein-ligand interaction detected (PLIP) MG.66: 2 residues within 4Å: Chain A: G.885, G.925 No protein-ligand interaction detected (PLIP) MG.67: 1 residues within 4Å: Chain A: G.1393 No protein-ligand interaction detected (PLIP) MG.68: 4 residues within 4Å: Chain A: C.1159, A.1193, U.1283, U.1285 No protein-ligand interaction detected (PLIP) MG.69: 3 residues within 4Å: Chain A: A.1468, A.1474, G.1540 No protein-ligand interaction detected (PLIP) MG.70: 2 residues within 4Å: Chain A: G.1444, A.1445 No protein-ligand interaction detected (PLIP) MG.71: 3 residues within 4Å: Chain A: G.1176, A.1202, C.1456 No protein-ligand interaction detected (PLIP) MG.72: 3 residues within 4Å: Chain A: G.1199, G.1200, G.1201 No protein-ligand interaction detected (PLIP) MG.73: 2 residues within 4Å: Chain A: U.1272, C.1430 No protein-ligand interaction detected (PLIP) MG.74: 3 residues within 4Å: Chain A: A.1196, C.1197, C.1464 No protein-ligand interaction detected (PLIP) MG.75: 3 residues within 4Å: Chain A: G.1268, U.1269, U.1433 No protein-ligand interaction detected (PLIP) MG.76: 4 residues within 4Å: Chain A: G.1273, C.1274, A.1426, G.1427 No protein-ligand interaction detected (PLIP) MG.77: 4 residues within 4Å: Chain A: U.1537, G.1538, G.1540, G.1541 No protein-ligand interaction detected (PLIP) MG.78: 3 residues within 4Å: Chain A: G.1483, G.1520, U.1521 No protein-ligand interaction detected (PLIP) MG.79: 5 residues within 4Å: Chain A: C.1274, A.1426, G.1427, G.1428 Chain b: R.14 No protein-ligand interaction detected (PLIP) MG.80: 2 residues within 4Å: Chain A: A.1202, A.1203 No protein-ligand interaction detected (PLIP) MG.81: 3 residues within 4Å: Chain A: U.64, A.168 Chain H: Q.176 No protein-ligand interaction detected (PLIP)

3 x ZN: ZINC ION(Non-covalent)

ZN.82: 5 residues within 4Å: Chain 1: C.23, N.25, C.26, C.74, C.77 3 PLIP interactions: 3 interactions with chain 1 Metal complexes: 1:C.23, 1:C.26, 1:C.74 ZN.83: 2 residues within 4Å: Chain 2: G.39, T.61 No protein-ligand interaction detected (PLIP) ZN.84: 6 residues within 4Å: Chain 4: C.121, C.124, C.139, C.142, T.145, F.146 1 PLIP interactions: 1 interactions with chain 4 Metal complexes: 4:C.124

1 x MET: METHIONINE(Covalent)

MET.85: 6 residues within 4Å: Chain 9: A.75 Chain e: G.141, Y.142, A.143, N.144, E.383 1 PLIP interactions: 1 interactions with chain e Hydrophobic interactions: e:Y.142

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hussain, T. et al., Structural changes enable start codon recognition by the eukaryotic translation initiation complex. Cell(Cambridge,Mass.) (2014)

Release Date

2014-11-05

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

C
B

D
C

E
D

F
E

G
F

H
G

I
H

J
I

K
J

L
K

M
L

N
M

O
N

P
O

Q
P

R
Q

S
R

T
S

U
T

V
U

W
V

X
W

Y
X

Z
Y

0
Z

1
a

2
b

3
c

4
f

5
g

6
d

7
e

8
h

b
i

c
j

d
m

e
k

f
l

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

eS31

RACK1

uS14

eS30

eL41

eIF1A

eIF2 alpha

eIF1

eIF2 gamma

eIF2 beta

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