SMTL ID : 3jam.1

CryoEM structure of 40S-eIF1A-eIF1 complex from yeast

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-mer

Ligands

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

MG.1: 1 residues within 4Å: Chain A: G.361 No protein-ligand interaction detected (PLIP) MG.2: 2 residues within 4Å: Chain A: G.95, G.402 No protein-ligand interaction detected (PLIP) MG.3: 3 residues within 4Å: Chain A: G.551, 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: 1 residues within 4Å: Chain A: G.556 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: 2 residues within 4Å: Chain A: A.993, G.994 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, G.10, 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.1762, G.1766, G.1767, U.1769, U.1770 No protein-ligand interaction detected (PLIP) MG.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.14: 2 residues within 4Å: Chain A: A.386, A.400 No protein-ligand interaction detected (PLIP) MG.15: 3 residues within 4Å: Chain A: G.16, G.609, C.613 No protein-ligand interaction detected (PLIP) MG.16: 4 residues within 4Å: Chain A: G.361, G.376, A.377, U.378 No protein-ligand interaction detected (PLIP) MG.17: 2 residues within 4Å: Chain A: A.28, A.436 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: 2 residues within 4Å: Chain A: A.998, U.1004 No protein-ligand interaction detected (PLIP) MG.20: 3 residues within 4Å: Chain A: C.426, A.427, G.428 No protein-ligand interaction detected (PLIP) MG.21: 3 residues within 4Å: Chain A: A.43, 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: U.562, A.579 No protein-ligand interaction detected (PLIP) MG.25: 3 residues within 4Å: Chain A: U.617, A.618, A.619 No protein-ligand interaction detected (PLIP) MG.26: 3 residues within 4Å: Chain A: G.1328, A.1329, G.1330 No protein-ligand interaction detected (PLIP) MG.27: 3 residues within 4Å: Chain A: A.622, C.1028, U.1031 No protein-ligand interaction detected (PLIP) MG.28: 4 residues within 4Å: Chain A: A.100, U.101, U.102, C.360 No protein-ligand interaction detected (PLIP) MG.29: 2 residues within 4Å: Chain A: G.20 Chain Y: K.110 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: 1 residues within 4Å: Chain A: U.1769 No protein-ligand interaction detected (PLIP) MG.32: 2 residues within 4Å: Chain A: G.95, G.96 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: 4 residues within 4Å: Chain A: G.1628, U.1629, G.1792, A.1793 No protein-ligand interaction detected (PLIP) MG.35: 4 residues within 4Å: Chain A: U.169, U.266, C.267 Chain H: Q.176 No protein-ligand interaction detected (PLIP) MG.36: 2 residues within 4Å: Chain A: A.459, G.460 No protein-ligand interaction detected (PLIP) MG.37: 2 residues within 4Å: Chain A: U.465, G.466 No protein-ligand interaction detected (PLIP) MG.38: 1 residues within 4Å: Chain A: G.1417 No protein-ligand interaction detected (PLIP) MG.39: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.40: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.41: 1 residues within 4Å: Chain A: U.1303 No protein-ligand interaction detected (PLIP) MG.42: 2 residues within 4Å: Chain A: A.979, U.1015 No protein-ligand interaction detected (PLIP) MG.43: 3 residues within 4Å: Chain A: U.88, G.89, C.90 No protein-ligand interaction detected (PLIP) MG.44: 2 residues within 4Å: Chain A: A.761, G.762 No protein-ligand interaction detected (PLIP) MG.45: 3 residues within 4Å: Chain A: U.8, A.1139, G.1140 No protein-ligand interaction detected (PLIP) MG.46: 2 residues within 4Å: Chain A: A.514, C.530 No protein-ligand interaction detected (PLIP) MG.47: 1 residues within 4Å: Chain A: G.1294 No protein-ligand interaction detected (PLIP) MG.48: 1 residues within 4Å: Chain A: G.938 No protein-ligand interaction detected (PLIP) MG.49: 2 residues within 4Å: Chain A: U.989, C.990 No protein-ligand interaction detected (PLIP) MG.50: 2 residues within 4Å: Chain A: A.212, G.213 No protein-ligand interaction detected (PLIP) MG.51: 1 residues within 4Å: Chain M: K.56 No protein-ligand interaction detected (PLIP) MG.52: 2 residues within 4Å: Chain A: G.876, U.935 No protein-ligand interaction detected (PLIP) MG.53: 1 residues within 4Å: Chain A: G.382 No protein-ligand interaction detected (PLIP) MG.54: 2 residues within 4Å: Chain A: G.1393, G.1394 No protein-ligand interaction detected (PLIP) MG.55: 2 residues within 4Å: Chain A: C.1159, U.1283 No protein-ligand interaction detected (PLIP) MG.56: 2 residues within 4Å: Chain A: A.1468 Chain U: N.85 No protein-ligand interaction detected (PLIP) MG.57: 2 residues within 4Å: Chain A: A.1202, C.1456 No protein-ligand interaction detected (PLIP) MG.58: 3 residues within 4Å: Chain A: G.1201, A.1599, C.1601 No protein-ligand interaction detected (PLIP) MG.59: 2 residues within 4Å: Chain A: G.1271, C.1430 No protein-ligand interaction detected (PLIP) MG.60: 4 residues within 4Å: Chain A: A.1196, C.1197, C.1464 Chain V: K.74 No protein-ligand interaction detected (PLIP) MG.61: 3 residues within 4Å: Chain A: G.1268, U.1269, G.1434 No protein-ligand interaction detected (PLIP) MG.62: 3 residues within 4Å: Chain A: G.1273, C.1274, G.1427 No protein-ligand interaction detected (PLIP) MG.63: 3 residues within 4Å: Chain A: G.1538, G.1540, C.1567 No protein-ligand interaction detected (PLIP) MG.64: 2 residues within 4Å: Chain A: U.1519, U.1521 No protein-ligand interaction detected (PLIP) MG.65: 4 residues within 4Å: Chain A: C.1274, A.1426, G.1427, G.1428 No protein-ligand interaction detected (PLIP) MG.66: 3 residues within 4Å: Chain A: A.1202, A.1203, C.1598 No protein-ligand interaction detected (PLIP) MG.67: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.68: 2 residues within 4Å: Chain A: U.118 Chain J: N.52 No protein-ligand interaction detected (PLIP) MG.69: 2 residues within 4Å: Chain A: C.249, A.250 No protein-ligand interaction detected (PLIP) MG.70: 1 residues within 4Å: Chain A: C.423 No protein-ligand interaction detected (PLIP) MG.71: 2 residues within 4Å: Chain A: A.603, A.604 No protein-ligand interaction detected (PLIP) MG.72: 3 residues within 4Å: Chain A: A.634, A.635, A.806 No protein-ligand interaction detected (PLIP) MG.73: 1 residues within 4Å: Chain A: G.1035 No protein-ligand interaction detected (PLIP) MG.74: 3 residues within 4Å: Chain A: G.895, A.915, U.917 No protein-ligand interaction detected (PLIP) MG.75: 2 residues within 4Å: Chain 1: G.16 Chain A: G.942 No protein-ligand interaction detected (PLIP) MG.76: 2 residues within 4Å: Chain A: A.967, U.968 No protein-ligand interaction detected (PLIP) MG.77: 2 residues within 4Å: Chain A: A.971, G.972 No protein-ligand interaction detected (PLIP) MG.78: 1 residues within 4Å: Chain A: A.1142 No protein-ligand interaction detected (PLIP) MG.79: 1 residues within 4Å: Chain A: G.513 No protein-ligand interaction detected (PLIP) MG.82: 3 residues within 4Å: Chain 6: Y.85, T.86, T.87 No protein-ligand interaction detected (PLIP)

3 x ZN: ZINC ION(Non-covalent)

ZN.80: 4 residues within 4Å: Chain 1: C.23, C.26, C.74, C.77 4 PLIP interactions: 4 interactions with chain 1 Metal complexes: 1:C.23, 1:C.26, 1:C.74, 1:C.77 ZN.81: 4 residues within 4Å: Chain 2: C.37, G.39, C.40, C.59 No protein-ligand interaction detected (PLIP) ZN.83: 5 residues within 4Å: Chain 6: C.121, I.128, C.139, K.141, C.142 No protein-ligand interaction detected (PLIP)

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: 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
uS14: 4
eS30: 5
eS31: 6
RACK1: 7
eL41: 8
eIF1A: 9
eIF1: a

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
d

5
e

6
f

7
g

8
h

9
i

a
j

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

eIF1

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