SMTL ID : 6rw4.1

Structure of human mitochondrial 28S ribosome in complex with mitochondrial IF3

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-mer

Ligands

1 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 16 residues within 4Å: Chain A: A.134, A.135, A.136, U.301, U.302, G.398, A.399, A.400, C.401, A.402 Chain J: R.38 Chain L: L.194, Y.195, Y.196, R.197 Ligands: MG.36 4 PLIP interactions: 1 interactions with chain J, 3 interactions with chain L Salt bridges: J:R.38 Hydrogen bonds: L:Y.196, L:Y.196, L:Y.196

1 x SPM: SPERMINE(Non-functional Binders)

SPM.2: 14 residues within 4Å: Chain A: U.297, G.298, U.299, U.397, G.398, A.399, A.400, C.401, A.402, C.403, A.404, A.463, C.464 Ligands: MG.17 No protein-ligand interaction detected (PLIP)

1 x SRY: STREPTOMYCIN(Non-covalent)

SRY.3: 14 residues within 4Å: Chain A: U.7, U.8, U.9, C.251, G.252, C.518, A.519, A.520, A.521, A.908, C.909 Chain J: K.71, K.72, P.73 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:K.71

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

MG.4: 4 residues within 4Å: Chain A: A.71, G.72, A.143, G.144 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain A: A.291, A.292, A.293 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain A: A.380, G.381, A.457 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain A: A.406, A.407, C.452, C.453 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain A: C.419, A.420, A.421, C.441 No protein-ligand interaction detected (PLIP) MG.9: 4 residues within 4Å: Chain A: C.423, U.424, A.435, G.939 No protein-ligand interaction detected (PLIP) MG.10: 4 residues within 4Å: Chain A: C.417, A.420, A.443, U.444 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain A: U.612, A.679, G.680, G.681 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain A: A.619 Chain H: H.130 No protein-ligand interaction detected (PLIP) MG.13: 1 residues within 4Å: Chain A: A.787 No protein-ligand interaction detected (PLIP) MG.14: 5 residues within 4Å: Chain A: U.916, A.917, A.918, G.922, G.923 No protein-ligand interaction detected (PLIP) MG.15: 6 residues within 4Å: Chain A: A.918, G.922, G.923, A.925, A.926 Ligands: K.73 No protein-ligand interaction detected (PLIP) MG.16: 4 residues within 4Å: Chain 2: N.23 Chain A: G.947, G.948, A.949 No protein-ligand interaction detected (PLIP) MG.17: 3 residues within 4Å: Chain A: G.398, A.462 Ligands: SPM.2 No protein-ligand interaction detected (PLIP) MG.18: 2 residues within 4Å: Chain A: U.300, G.398 No protein-ligand interaction detected (PLIP) MG.19: 2 residues within 4Å: Chain A: A.658, A.659 No protein-ligand interaction detected (PLIP) MG.20: 4 residues within 4Å: Chain A: C.591, C.607, U.608, G.698 No protein-ligand interaction detected (PLIP) MG.21: 1 residues within 4Å: Chain A: G.11 No protein-ligand interaction detected (PLIP) MG.22: 2 residues within 4Å: Chain A: A.154, C.159 No protein-ligand interaction detected (PLIP) MG.23: 2 residues within 4Å: Chain A: C.168, A.169 No protein-ligand interaction detected (PLIP) MG.24: 6 residues within 4Å: Chain A: G.231, C.233, A.234, A.235 Chain D: G.195 Chain G: H.51 3 PLIP interactions: 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:H.51, H2O.1, H2O.2 MG.25: 3 residues within 4Å: Chain A: A.671, A.672, G.673 No protein-ligand interaction detected (PLIP) MG.26: 1 residues within 4Å: Chain A: G.296 No protein-ligand interaction detected (PLIP) MG.27: 5 residues within 4Å: Chain A: G.6, U.7, A.16, G.17, C.18 No protein-ligand interaction detected (PLIP) MG.28: 4 residues within 4Å: Chain A: U.27, U.42, A.180, C.181 No protein-ligand interaction detected (PLIP) MG.29: 3 residues within 4Å: Chain A: A.83, A.84, A.85 No protein-ligand interaction detected (PLIP) MG.30: 3 residues within 4Å: Chain A: A.98, A.99, A.100 No protein-ligand interaction detected (PLIP) MG.31: 2 residues within 4Å: Chain A: U.111, C.499 No protein-ligand interaction detected (PLIP) MG.32: 4 residues within 4Å: Chain A: C.168, C.171, A.172, G.173 No protein-ligand interaction detected (PLIP) MG.33: 4 residues within 4Å: Chain A: C.248, C.250, C.251 Chain J: Q.116 No protein-ligand interaction detected (PLIP) MG.34: 2 residues within 4Å: Chain A: C.261, G.262 No protein-ligand interaction detected (PLIP) MG.35: 5 residues within 4Å: Chain A: A.28, G.29, C.30, G.273, U.274 No protein-ligand interaction detected (PLIP) MG.36: 5 residues within 4Å: Chain A: A.295, A.399, A.400, G.487 Ligands: NAD.1 No protein-ligand interaction detected (PLIP) MG.37: 2 residues within 4Å: Chain A: G.426, G.427 No protein-ligand interaction detected (PLIP) MG.38: 2 residues within 4Å: Chain A: C.411, G.445 No protein-ligand interaction detected (PLIP) MG.39: 4 residues within 4Å: Chain A: G.296, A.455, A.456, A.457 No protein-ligand interaction detected (PLIP) MG.40: 2 residues within 4Å: Chain A: G.491, A.492 No protein-ligand interaction detected (PLIP) MG.41: 2 residues within 4Å: Chain A: C.496, G.929 No protein-ligand interaction detected (PLIP) MG.42: 2 residues within 4Å: Chain A: U.497, A.512 No protein-ligand interaction detected (PLIP) MG.43: 2 residues within 4Å: Chain A: G.500, A.501 No protein-ligand interaction detected (PLIP) MG.44: 3 residues within 4Å: Chain A: U.560, C.569, G.570 No protein-ligand interaction detected (PLIP) MG.45: 3 residues within 4Å: Chain A: G.570, A.571, U.682 No protein-ligand interaction detected (PLIP) MG.46: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.47: 5 residues within 4Å: Chain A: C.586, C.587, U.588, C.705, A.706 No protein-ligand interaction detected (PLIP) MG.48: 3 residues within 4Å: Chain A: C.587, G.703, G.704 No protein-ligand interaction detected (PLIP) MG.49: 3 residues within 4Å: Chain A: U.612, G.680, G.681 No protein-ligand interaction detected (PLIP) MG.50: 3 residues within 4Å: Chain A: A.662, G.668, U.669 No protein-ligand interaction detected (PLIP) MG.51: 3 residues within 4Å: Chain A: A.745, G.746, G.765 No protein-ligand interaction detected (PLIP) MG.52: 3 residues within 4Å: Chain A: A.740, C.741, G.742 No protein-ligand interaction detected (PLIP) MG.53: 2 residues within 4Å: Chain A: G.754 Chain K: K.59 No protein-ligand interaction detected (PLIP) MG.54: 3 residues within 4Å: Chain A: A.367, A.368, G.384 No protein-ligand interaction detected (PLIP) MG.55: 2 residues within 4Å: Chain A: A.67, G.68 No protein-ligand interaction detected (PLIP) MG.56: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.57: 2 residues within 4Å: Chain A: G.175, A.176 No protein-ligand interaction detected (PLIP) MG.58: 1 residues within 4Å: Chain A: A.204 No protein-ligand interaction detected (PLIP) MG.59: 4 residues within 4Å: Chain A: G.294, A.295, U.297, C.458 No protein-ligand interaction detected (PLIP) MG.60: 2 residues within 4Å: Chain A: A.209, G.210 No protein-ligand interaction detected (PLIP) MG.78: 6 residues within 4Å: Chain B: H.93, D.224, N.226, D.240, D.241 Chain W: K.119 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.93, B:D.224, B:D.240, B:D.241 MG.83: 4 residues within 4Å: Chain X: K.134, T.135, S.311 Ligands: ATP.82 3 PLIP interactions: 1 interactions with chain X, 2 Ligand-Water interactions Metal complexes: X:T.135, H2O.3, H2O.3 MG.85: 2 residues within 4Å: Chain 3: R.135, N.139 No protein-ligand interaction detected (PLIP)

17 x K: POTASSIUM ION(Non-functional Binders)(Non-covalent)

K.61: 5 residues within 4Å: Chain A: C.55, C.60, C.61, C.195, G.196 Ligand excluded by PLIP K.62: 4 residues within 4Å: Chain A: G.70, A.71, G.72, G.144 Ligand excluded by PLIP K.63: 5 residues within 4Å: Chain A: C.243, C.253, G.254 Chain J: P.73, N.74 Ligand excluded by PLIP K.64: 6 residues within 4Å: Chain A: C.458, C.459, U.460, U.945, U.946, G.947 Ligand excluded by PLIP K.65: 4 residues within 4Å: Chain A: A.551, G.552, G.553, G.774 Ligand excluded by PLIP K.66: 4 residues within 4Å: Chain A: A.551, G.552, G.714, G.715 Ligand excluded by PLIP K.67: 2 residues within 4Å: Chain A: G.552, G.553 Ligand excluded by PLIP K.68: 6 residues within 4Å: Chain A: A.609, U.610, C.683, U.688, G.689, U.690 Ligand excluded by PLIP K.69: 6 residues within 4Å: Chain A: A.611, C.615, G.616, C.617, G.681, U.682 Ligand excluded by PLIP K.70: 5 residues within 4Å: Chain A: C.683, A.684, G.686, G.687, U.688 Ligand excluded by PLIP K.71: 3 residues within 4Å: Chain A: A.718, G.742, A.743 Ligand excluded by PLIP K.72: 4 residues within 4Å: Chain A: G.529, C.530, G.829, U.830 Ligand excluded by PLIP K.73: 5 residues within 4Å: Chain A: A.917, A.918, A.926, G.939 Ligands: MG.15 Ligand excluded by PLIP K.74: 5 residues within 4Å: Chain A: G.842, U.843, C.844, G.912, U.913 Ligand excluded by PLIP K.75: 5 residues within 4Å: Chain A: C.153, A.154, C.157, C.158, C.159 Ligand excluded by PLIP K.76: 6 residues within 4Å: Chain A: C.188, A.190, U.191, A.192, U.203, A.205 Ligand excluded by PLIP K.77: 4 residues within 4Å: Chain A: U.241, G.242, C.257, A.258 Ligand excluded by PLIP

1 x ZN: ZINC ION(Non-covalent)

ZN.79: 5 residues within 4Å: Chain O: C.94, C.105, C.108, C.143, Q.146 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.94, O:C.105, O:C.108, O:C.143

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.80: 8 residues within 4Å: Chain E: C.105, G.107, I.108 Chain P: K.64, C.65, C.68, C.100, K.103 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain P, Metal complexes: E:C.105, P:C.65, P:C.68, P:C.100 FES.81: 7 residues within 4Å: Chain M: G.25, C.26, R.29 Chain T: C.139, C.141, C.149, P.150 4 PLIP interactions: 3 interactions with chain T, 1 interactions with chain M, Metal complexes: T:C.139, T:C.141, T:C.149, M:C.26

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.82: 25 residues within 4Å: Chain X: H.67, P.84, R.86, F.87, Q.90, C.98, L.99, M.100, R.102, K.130, G.131, T.132, G.133, K.134, T.135, L.136, S.311, Q.312, T.313, Y.348, Y.360, P.388, S.389, E.392 Ligands: MG.83 14 PLIP interactions: 14 interactions with chain X Hydrogen bonds: X:Q.90, X:M.100, X:M.100, X:G.131, X:T.132, X:G.133, X:K.134, X:T.135, X:L.136, X:T.313, X:T.313, X:Y.348 Salt bridges: X:K.134, X:K.134

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

GNP.84: 13 residues within 4Å: Chain X: Y.173, R.177, Y.208, V.209, W.210, D.238, G.241, I.242, K.245, A.288, H.291, N.292, K.295 14 PLIP interactions: 14 interactions with chain X Hydrogen bonds: X:Y.173, X:R.177, X:R.177, X:V.209, X:V.209, X:V.209, X:H.291, X:N.292, X:K.295 Salt bridges: X:D.238, X:K.245, X:K.295 pi-Stacking: X:Y.173, X:Y.173

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Khawaja, A. et al., Distinct pre-initiation steps in human mitochondrial translation. Nat Commun (2020)

Release Date

2020-06-03

Peptides

28S ribosomal protein S2, mitochondrial: B
28S ribosomal protein S24, mitochondrial: C
28S ribosomal protein S5, mitochondrial: D
28S ribosomal protein S6, mitochondrial: E
28S ribosomal protein S7, mitochondrial: F
28S ribosomal protein S9, mitochondrial: G
28S ribosomal protein S10, mitochondrial: H
28S ribosomal protein S11, mitochondrial: I
28S ribosomal protein S12, mitochondrial: J
28S ribosomal protein S14, mitochondrial: K
28S ribosomal protein S15, mitochondrial: L
28S ribosomal protein S16, mitochondrial: M
28S ribosomal protein S17, mitochondrial: N
28S ribosomal protein S18b, mitochondrial: O
28S ribosomal protein S18c, mitochondrial: P
28S ribosomal protein S21, mitochondrial: Q
28S ribosomal protein S22, mitochondrial: R
28S ribosomal protein S23, mitochondrial: S
28S ribosomal protein S25, mitochondrial: T
28S ribosomal protein S26, mitochondrial: U
28S ribosomal protein S27, mitochondrial: V
28S ribosomal protein S28, mitochondrial: W
28S ribosomal protein S29, mitochondrial: X
28S ribosomal protein S31, mitochondrial: Y
28S ribosomal protein S33, mitochondrial: Z
28S ribosomal protein S34, mitochondrial: 0
28S ribosomal protein S35, mitochondrial: 1
Coiled-coil-helix-coiled-coil-helix domain-containing protein 1: 2
Aurora kinase A-interacting protein: 3
Pentatricopeptide repeat domain-containing protein 3, mitochondrial: 4
Translation initiation factor IF-3, mitochondrial: 5

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Q
Q

R
R

S
S

T
T

U
U

V
V

W
W

X
X

Y
Y

Z
Z

0
0

1
1

2
2

3
3

4
4

5
8

28S ribosomal protein S2, mitochondrial

28S ribosomal protein S24, mitochondrial

28S ribosomal protein S5, mitochondrial

28S ribosomal protein S6, mitochondrial

28S ribosomal protein S7, mitochondrial

28S ribosomal protein S9, mitochondrial

28S ribosomal protein S10, mitochondrial

28S ribosomal protein S11, mitochondrial

28S ribosomal protein S12, mitochondrial

28S ribosomal protein S14, mitochondrial

28S ribosomal protein S15, mitochondrial

28S ribosomal protein S16, mitochondrial

28S ribosomal protein S17, mitochondrial

28S ribosomal protein S18b, mitochondrial

28S ribosomal protein S18c, mitochondrial

28S ribosomal protein S21, mitochondrial

28S ribosomal protein S22, mitochondrial

28S ribosomal protein S23, mitochondrial

28S ribosomal protein S25, mitochondrial

28S ribosomal protein S26, mitochondrial

28S ribosomal protein S27, mitochondrial

28S ribosomal protein S28, mitochondrial

28S ribosomal protein S29, mitochondrial

28S ribosomal protein S31, mitochondrial

28S ribosomal protein S33, mitochondrial

28S ribosomal protein S34, mitochondrial

28S ribosomal protein S35, mitochondrial

Coiled-coil-helix-coiled-coil-helix domain-containing protein 1

Aurora kinase A-interacting protein

Pentatricopeptide repeat domain-containing protein 3, mitochondrial

Translation initiation factor IF-3, mitochondrial

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