SMTL ID : 6gaz.1

Unique features of mammalian mitochondrial translation initiation revealed by cryo-EM. This file contains the 28S ribosomal subunit.

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 GSP: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE(Non-covalent)

GSP.1: 19 residues within 4Å: Chain A: H.118, V.119, D.120, H.121, G.122, K.123, T.124, T.125, T.144, G.167, H.168, N.218, K.219, D.221, S.254, A.255, L.256 Ligands: MG.2, NA.3 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:H.118, A:D.120, A:H.121, A:G.122, A:K.123, A:K.123, A:T.124, A:T.125, A:T.125, A:T.144, A:T.144, A:G.167, A:N.218, A:K.219, A:K.219, A:A.255, A:L.256 Water bridges: A:T.124, A:T.144 Salt bridges: A:K.123, A:D.221

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

MG.2: 3 residues within 4Å: Chain A: T.124, T.144 Ligands: GSP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.124, A:T.144, H2O.1, H2O.1 MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain C: G.232, A.234, A.235, A.236 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Chain C: U.938 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain C: C.416, A.419, A.442, U.443 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Chain C: C.494 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Chain C: A.250 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain C: C.422, A.434 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain C: A.157, C.162 Ligands: MG.76 No protein-ligand interaction detected (PLIP) MG.13: 5 residues within 4Å: Chain C: U.28, A.42, U.43, A.183, A.184 No protein-ligand interaction detected (PLIP) MG.14: 1 residues within 4Å: Chain C: A.29 No protein-ligand interaction detected (PLIP) MG.15: 5 residues within 4Å: Chain C: U.924, A.925, A.926, G.930, G.931 No protein-ligand interaction detected (PLIP) MG.16: 1 residues within 4Å: Chain C: G.178 No protein-ligand interaction detected (PLIP) MG.17: 1 residues within 4Å: Chain C: A.840 No protein-ligand interaction detected (PLIP) MG.18: 3 residues within 4Å: Chain 6: N.24 Chain C: G.955, A.957 No protein-ligand interaction detected (PLIP) MG.19: 1 residues within 4Å: Chain C: G.444 No protein-ligand interaction detected (PLIP) MG.20: 3 residues within 4Å: Chain C: U.495, A.496, A.510 No protein-ligand interaction detected (PLIP) MG.21: 1 residues within 4Å: Chain C: G.398 No protein-ligand interaction detected (PLIP) MG.22: 1 residues within 4Å: Chain C: G.381 No protein-ligand interaction detected (PLIP) MG.23: 3 residues within 4Å: Chain C: A.406, U.407, C.451 No protein-ligand interaction detected (PLIP) MG.24: 5 residues within 4Å: Chain C: A.925, A.926, A.934, G.947 Ligands: MG.64 No protein-ligand interaction detected (PLIP) MG.25: 3 residues within 4Å: Chain C: U.302, U.397, G.398 No protein-ligand interaction detected (PLIP) MG.26: 1 residues within 4Å: Chain C: G.807 No protein-ligand interaction detected (PLIP) MG.27: 2 residues within 4Å: Chain C: G.550, G.551 No protein-ligand interaction detected (PLIP) MG.28: 4 residues within 4Å: Chain C: A.47, A.170, C.171, A.172 No protein-ligand interaction detected (PLIP) MG.29: 1 residues within 4Å: Chain M: I.87 No protein-ligand interaction detected (PLIP) MG.30: 1 residues within 4Å: Chain C: A.659 No protein-ligand interaction detected (PLIP) MG.31: 3 residues within 4Å: Chain C: A.72, G.73, G.147 No protein-ligand interaction detected (PLIP) MG.32: 2 residues within 4Å: Chain C: U.112, C.497 No protein-ligand interaction detected (PLIP) MG.33: 3 residues within 4Å: Chain C: A.569, G.683, U.684 No protein-ligand interaction detected (PLIP) MG.34: 1 residues within 4Å: Chain C: A.350 No protein-ligand interaction detected (PLIP) MG.35: 4 residues within 4Å: Chain C: C.584, C.585, U.586, G.706 No protein-ligand interaction detected (PLIP) MG.36: 2 residues within 4Å: Chain C: U.230, G.231 No protein-ligand interaction detected (PLIP) MG.37: 4 residues within 4Å: Chain C: A.549, G.550, G.551, G.781 No protein-ligand interaction detected (PLIP) MG.38: 4 residues within 4Å: Chain C: U.614, A.681, G.682, G.683 No protein-ligand interaction detected (PLIP) MG.39: 4 residues within 4Å: Chain C: C.589, U.610, G.700, G.701 No protein-ligand interaction detected (PLIP) MG.40: 2 residues within 4Å: Chain C: C.585, G.705 No protein-ligand interaction detected (PLIP) MG.41: 4 residues within 4Å: Chain C: G.845, C.846 Chain T: A.4, C.5 No protein-ligand interaction detected (PLIP) MG.42: 4 residues within 4Å: Chain C: U.292, A.293, A.294, A.295 No protein-ligand interaction detected (PLIP) MG.43: 1 residues within 4Å: Chain C: A.794 No protein-ligand interaction detected (PLIP) MG.44: 1 residues within 4Å: Ligands: MG.107 No protein-ligand interaction detected (PLIP) MG.45: 1 residues within 4Å: Chain C: U.932 No protein-ligand interaction detected (PLIP) MG.46: 3 residues within 4Å: Chain C: A.613, U.614, G.682 No protein-ligand interaction detected (PLIP) MG.47: 3 residues within 4Å: Chain C: U.242, G.243, A.259 No protein-ligand interaction detected (PLIP) MG.48: 2 residues within 4Å: Chain C: C.576, C.577 No protein-ligand interaction detected (PLIP) MG.49: 2 residues within 4Å: Chain C: G.173 Chain Y: D.32 No protein-ligand interaction detected (PLIP) MG.50: 4 residues within 4Å: Chain C: A.367, A.368, A.384 Chain K: H.185 No protein-ligand interaction detected (PLIP) MG.51: 2 residues within 4Å: Chain C: A.99, A.100 No protein-ligand interaction detected (PLIP) MG.52: 3 residues within 4Å: Chain C: U.761, G.762 Chain M: K.59 No protein-ligand interaction detected (PLIP) MG.53: 1 residues within 4Å: Chain C: C.422 No protein-ligand interaction detected (PLIP) MG.54: 1 residues within 4Å: Chain C: G.190 No protein-ligand interaction detected (PLIP) MG.55: 2 residues within 4Å: Chain C: C.262, G.263 No protein-ligand interaction detected (PLIP) MG.56: 1 residues within 4Å: Chain C: A.329 No protein-ligand interaction detected (PLIP) MG.57: 2 residues within 4Å: Chain C: A.297, U.299 No protein-ligand interaction detected (PLIP) MG.58: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.59: 1 residues within 4Å: Chain C: U.70 No protein-ligand interaction detected (PLIP) MG.60: 5 residues within 4Å: Chain C: G.7, U.8, G.17, G.18, C.19 No protein-ligand interaction detected (PLIP) MG.61: 1 residues within 4Å: Chain C: U.559 No protein-ligand interaction detected (PLIP) MG.62: 2 residues within 4Å: Chain C: G.298, A.454 No protein-ligand interaction detected (PLIP) MG.63: 4 residues within 4Å: Chain C: A.630, A.653, A.654, G.655 No protein-ligand interaction detected (PLIP) MG.64: 6 residues within 4Å: Chain C: A.926, G.930, G.931, A.933, A.934 Ligands: MG.24 No protein-ligand interaction detected (PLIP) MG.65: 2 residues within 4Å: Chain C: A.392, A.393 No protein-ligand interaction detected (PLIP) MG.66: 3 residues within 4Å: Chain C: G.836, C.837, G.956 No protein-ligand interaction detected (PLIP) MG.67: 4 residues within 4Å: Chain C: C.927, A.928, G.930, A.933 No protein-ligand interaction detected (PLIP) MG.68: 1 residues within 4Å: Chain C: U.433 No protein-ligand interaction detected (PLIP) MG.69: 2 residues within 4Å: Chain C: G.17, G.18 No protein-ligand interaction detected (PLIP) MG.70: 3 residues within 4Å: Chain C: U.10, G.11, G.12 No protein-ligand interaction detected (PLIP) MG.71: 2 residues within 4Å: Chain C: U.9, G.520 No protein-ligand interaction detected (PLIP) MG.72: 4 residues within 4Å: Chain C: C.191, U.194, G.195, U.206 No protein-ligand interaction detected (PLIP) MG.73: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.74: 2 residues within 4Å: Chain C: G.323, U.447 No protein-ligand interaction detected (PLIP) MG.75: 1 residues within 4Å: Chain C: G.413 No protein-ligand interaction detected (PLIP) MG.76: 5 residues within 4Å: Chain C: C.156, A.157, C.161, C.162 Ligands: MG.12 No protein-ligand interaction detected (PLIP) MG.77: 4 residues within 4Å: Chain C: U.556, G.557, U.714, G.715 No protein-ligand interaction detected (PLIP) MG.78: 2 residues within 4Å: Chain C: C.416, C.417 No protein-ligand interaction detected (PLIP) MG.79: 6 residues within 4Å: Chain 4: N.48 Chain C: G.55, U.56, A.57, G.61, C.62 No protein-ligand interaction detected (PLIP) MG.80: 1 residues within 4Å: Chain C: A.420 No protein-ligand interaction detected (PLIP) MG.81: 3 residues within 4Å: Chain C: C.685, A.686, U.690 No protein-ligand interaction detected (PLIP) MG.82: 1 residues within 4Å: Chain C: A.84 No protein-ligand interaction detected (PLIP) MG.83: 1 residues within 4Å: Chain C: A.673 No protein-ligand interaction detected (PLIP) MG.84: 4 residues within 4Å: Chain C: C.244, G.255 Chain L: P.73, N.74 No protein-ligand interaction detected (PLIP) MG.85: 2 residues within 4Å: Chain C: G.491, U.492 No protein-ligand interaction detected (PLIP) MG.86: 1 residues within 4Å: Chain C: C.174 No protein-ligand interaction detected (PLIP) MG.87: 3 residues within 4Å: Chain C: G.530, U.531, A.929 No protein-ligand interaction detected (PLIP) MG.88: 1 residues within 4Å: Chain C: A.297 No protein-ligand interaction detected (PLIP) MG.89: 2 residues within 4Å: Chain C: G.628, A.657 No protein-ligand interaction detected (PLIP) MG.90: 3 residues within 4Å: Chain C: A.720, G.750, A.751 No protein-ligand interaction detected (PLIP) MG.91: 2 residues within 4Å: Chain C: G.377, A.379 No protein-ligand interaction detected (PLIP) MG.92: 1 residues within 4Å: Chain C: U.671 No protein-ligand interaction detected (PLIP) MG.93: 3 residues within 4Å: Chain C: A.663, U.664, C.667 No protein-ligand interaction detected (PLIP) MG.94: 1 residues within 4Å: Chain C: A.39 No protein-ligand interaction detected (PLIP) MG.95: 3 residues within 4Å: Chain C: A.74, A.75, U.145 No protein-ligand interaction detected (PLIP) MG.96: 3 residues within 4Å: Chain C: G.568, A.569, U.570 No protein-ligand interaction detected (PLIP) MG.97: 2 residues within 4Å: Chain 6: K.25 Chain C: U.959 No protein-ligand interaction detected (PLIP) MG.98: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.99: 1 residues within 4Å: Chain C: G.643 No protein-ligand interaction detected (PLIP) MG.100: 1 residues within 4Å: Chain C: A.639 No protein-ligand interaction detected (PLIP) MG.101: 2 residues within 4Å: Chain C: A.218, A.274 No protein-ligand interaction detected (PLIP) MG.102: 1 residues within 4Å: Chain C: G.263 No protein-ligand interaction detected (PLIP) MG.103: 2 residues within 4Å: Chain C: A.573, G.682 No protein-ligand interaction detected (PLIP) MG.104: 1 residues within 4Å: Chain C: A.611 No protein-ligand interaction detected (PLIP) MG.105: 4 residues within 4Å: Chain C: A.748, C.749, G.750, A.775 No protein-ligand interaction detected (PLIP) MG.106: 2 residues within 4Å: Chain C: C.609, G.689 No protein-ligand interaction detected (PLIP) MG.107: 3 residues within 4Å: Chain A: R.352 Chain C: A.184 Ligands: MG.44 No protein-ligand interaction detected (PLIP) MG.108: 2 residues within 4Å: Chain C: A.539, A.787 No protein-ligand interaction detected (PLIP) MG.109: 2 residues within 4Å: Chain A: E.382 Chain C: U.31 No protein-ligand interaction detected (PLIP) MG.110: 2 residues within 4Å: Chain C: G.548, A.549 No protein-ligand interaction detected (PLIP) MG.111: 5 residues within 4Å: Chain D: H.92, D.223, N.225, D.239, D.240 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:H.92, D:D.223, D:D.239, D:D.240, D:D.240 MG.114: 1 residues within 4Å: Chain T: G.3 No protein-ligand interaction detected (PLIP) MG.117: 2 residues within 4Å: Chain 1: T.134 Ligands: GTP.116 4 PLIP interactions: 1 interactions with chain 1, 3 Ligand-Water interactions Metal complexes: 1:T.134, H2O.1, H2O.1, H2O.1 MG.118: 2 residues within 4Å: Chain 7: N.139 Chain C: U.492 No protein-ligand interaction detected (PLIP)

1 x NA: SODIUM ION(Non-functional Binders)

NA.3: 3 residues within 4Å: Chain A: D.120, G.142 Ligands: GSP.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.142

1 x SPM: SPERMINE(Non-functional Binders)

SPM.5: 9 residues within 4Å: Chain C: U.299, G.300, U.301, U.397, G.398, A.399, C.400, A.462, U.463 No protein-ligand interaction detected (PLIP)

3 x ZN: ZINC ION(Non-covalent)

ZN.112: 4 residues within 4Å: Chain G: C.105 Chain Q: C.66, C.69, C.101 4 PLIP interactions: 3 interactions with chain Q, 1 interactions with chain G Metal complexes: Q:C.66, Q:C.69, Q:C.101, G:C.105 ZN.115: 4 residues within 4Å: Chain O: C.26 Chain X: C.139, C.141, C.149 4 PLIP interactions: 3 interactions with chain X, 1 interactions with chain O Metal complexes: X:C.139, X:C.141, X:C.149, O:C.26 ZN.119: 4 residues within 4Å: Chain 9: C.94, C.105, C.108, C.143 4 PLIP interactions: 4 interactions with chain 9 Metal complexes: 9:C.94, 9:C.105, 9:C.108, 9:C.143

1 x FME: N-FORMYLMETHIONINE(Non-covalent)

FME.113: 6 residues within 4Å: Chain A: A.560, G.575, H.608, H.609, D.621 Chain S: A.71 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.609

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.116: 20 residues within 4Å: Chain 1: H.66, R.85, F.86, C.97, L.98, M.99, R.101, K.129, G.130, T.131, G.132, K.133, T.134, L.135, T.312, Y.347, P.387, G.388, E.391 Ligands: MG.117 16 PLIP interactions: 16 interactions with chain 1 Hydrogen bonds: 1:C.97, 1:M.99, 1:G.130, 1:T.131, 1:T.131, 1:G.132, 1:K.133, 1:T.134, 1:T.134, 1:T.134, 1:L.135, 1:T.312, 1:T.312 Water bridges: 1:T.134 Salt bridges: 1:K.133, 1:K.133

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kummer, E. et al., Unique features of mammalian mitochondrial translation initiation revealed by cryo-EM. Nature (2018)

Release Date

2018-08-08

Peptides

Translation initiation factor IF-2, mitochondrial: A
Mitochondrial ribosomal protein L19: B
Mitochondrial ribosomal protein S2: D
Mitochondrial ribosomal protein S24: E
Mitochondrial ribosomal protein S5: F
Mitochondrial ribosomal protein S6: G
Mitochondrial ribosomal protein S7: H
Mitochondrial ribosomal protein S9: I
Mitochondrial ribosomal protein S10: J
Mitochondrial ribosomal protein S11: K
Mitochondrial ribosomal protein S12: L
Mitochondrial ribosomal protein S14: M
Mitochondrial ribosomal protein S15: N
bS16m, MRPS16: O
Mitochondrial ribosomal protein S17: P
Mitochondrial ribosomal protein S18C: Q
Mitochondrial ribosomal protein S21: R
unassigned secondary structure elements: U
Mitochondrial ribosomal protein S22: V
Mitochondrial ribosomal protein S23: W
Mitochondrial ribosomal protein S25: X
Mitochondrial ribosomal protein S26: Y
Mitochondrial ribosomal protein S27: Z
Mitoribosomal protein ms28, mrps28: 0
Death associated protein 3: 1
mS31, MRPS31: 2
Mitochondrial ribosomal protein S33: 3
Mitochondrial ribosomal protein S34: 4
Mitochondrial ribosomal protein S35: 5
Mitochondrial ribosomal protein S37: 6
Aurora kinase A interacting protein 1: 7
Mitochondrial ribosomal protein S39: 8
28S ribosomal protein S18b, mitochondrial: 9

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
BC

B
BT

D
AB

E
AC

F
AE

G
AF

H
AG

I
AI

J
AJ

K
AK

L
AL

M
AN

N
AO

O
AP

P
AQ

Q
AR

R
AU

U
AZ

V
Aa

W
Ab

X
Ac

Y
Ad

Z
Ae

0
Af

1
Ag

2
Ah

3
Ai

4
Aj

5
Ak

6
Am

7
An

8
Ao

9
Ap

Translation initiation factor IF-2, mitochondrial

Mitochondrial ribosomal protein L19

Mitochondrial ribosomal protein S2

Mitochondrial ribosomal protein S24

Mitochondrial ribosomal protein S5

Mitochondrial ribosomal protein S6

Mitochondrial ribosomal protein S7

Mitochondrial ribosomal protein S9

Mitochondrial ribosomal protein S10

Mitochondrial ribosomal protein S11

Mitochondrial ribosomal protein S12

Mitochondrial ribosomal protein S14

Mitochondrial ribosomal protein S15

bS16m, MRPS16

Mitochondrial ribosomal protein S17

Mitochondrial ribosomal protein S18C

Mitochondrial ribosomal protein S21

unassigned secondary structure elements

Mitochondrial ribosomal protein S22

Mitochondrial ribosomal protein S23

Mitochondrial ribosomal protein S25

Mitochondrial ribosomal protein S26

Mitochondrial ribosomal protein S27

Mitoribosomal protein ms28, mrps28

Death associated protein 3

mS31, MRPS31

Mitochondrial ribosomal protein S33

Mitochondrial ribosomal protein S34

Mitochondrial ribosomal protein S35

Mitochondrial ribosomal protein S37

Aurora kinase A interacting protein 1

Mitochondrial ribosomal protein S39

28S ribosomal protein S18b, mitochondrial

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