SMTL ID : 8qrn.1

mt-SSU in GTPBP8 knock-out cells, state 4

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 A- U- A: mRNA(Non-functional Binders)

A-U-A.1: 11 residues within 4Å: Chain 5: X.31, A.32, U.33, A.34 Chain A: G.532, C.837, G.838, C.839, C.840, U.916, G.923 Protein-ligand interaction information (PLIP) not available

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

NAD.2: 13 residues within 4Å: Chain A: A.134, A.135, A.136, U.301, U.302, A.399, A.400, C.401 Chain J: R.38 Chain L: L.194, Y.195, Y.196 Ligands: MG.36 2 PLIP interactions: 1 interactions with chain L, 1 interactions with chain J Hydrogen bonds: L:Y.196 Salt bridges: J:R.38

1 x SPM: SPERMINE(Non-functional Binders)

SPM.3: 9 residues within 4Å: Chain A: U.297, G.298, U.299, U.397, G.398, A.399, A.400, C.401, A.463 No protein-ligand interaction detected (PLIP)

1 x SRY: STREPTOMYCIN(Non-covalent)

SRY.4: 12 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 1 PLIP interactions: 1 interactions with chain J Salt bridges: J:K.71

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

MG.5: 3 residues within 4Å: Chain A: A.71, G.72, G.144 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain A: A.291, A.292, A.293 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Chain A: G.381 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain A: A.407, C.452, C.453 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain A: A.420, C.441 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain A: C.423, U.424, A.435 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain A: A.443, U.444 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Chain A: A.619 No protein-ligand interaction detected (PLIP) MG.13: 1 residues within 4Å: Chain A: A.787 No protein-ligand interaction detected (PLIP) MG.14: 4 residues within 4Å: Chain A: U.916, A.917, A.918, G.923 No protein-ligand interaction detected (PLIP) MG.15: 5 residues within 4Å: Chain A: A.918, G.923, A.925, A.926 Ligands: K.71 No protein-ligand interaction detected (PLIP) MG.16: 4 residues within 4Å: Chain 2: N.23 Chain A: U.946, G.947, G.948 No protein-ligand interaction detected (PLIP) MG.17: 1 residues within 4Å: Chain A: G.398 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: 3 residues within 4Å: Chain A: A.658, A.659, G.660 No protein-ligand interaction detected (PLIP) MG.20: 4 residues within 4Å: Chain A: A.590, C.591, U.608, G.698 No protein-ligand interaction detected (PLIP) MG.21: 2 residues within 4Å: Chain A: U.8, U.9 No protein-ligand interaction detected (PLIP) MG.22: 3 residues within 4Å: Chain A: A.154, C.159, A.160 No protein-ligand interaction detected (PLIP) MG.23: 3 residues within 4Å: Chain A: A.167, C.168, A.169 No protein-ligand interaction detected (PLIP) MG.24: 4 residues within 4Å: Chain A: G.231, C.233, A.234, A.235 No protein-ligand interaction detected (PLIP) MG.25: 1 residues within 4Å: Chain A: A.671 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: 3 residues within 4Å: Chain A: U.27, U.42, C.181 No protein-ligand interaction detected (PLIP) MG.29: 2 residues within 4Å: Chain A: A.84, A.85 No protein-ligand interaction detected (PLIP) MG.30: 2 residues within 4Å: Chain A: 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: 3 residues within 4Å: Chain A: 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: 3 residues within 4Å: Chain A: G.29, G.273, U.274 No protein-ligand interaction detected (PLIP) MG.36: 2 residues within 4Å: Chain A: A.400 Ligands: NAD.2 No protein-ligand interaction detected (PLIP) MG.37: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.38: 2 residues within 4Å: Chain A: G.410, G.445 No protein-ligand interaction detected (PLIP) MG.39: 5 residues within 4Å: Chain A: A.295, G.296, A.455, A.456, A.457 No protein-ligand interaction detected (PLIP) MG.40: 1 residues within 4Å: Chain A: A.492 No protein-ligand interaction detected (PLIP) MG.41: 1 residues within 4Å: Chain A: C.496 No protein-ligand interaction detected (PLIP) MG.42: 3 residues within 4Å: Chain A: U.497, A.498, A.512 No protein-ligand interaction detected (PLIP) MG.43: 1 residues within 4Å: Chain A: G.500 No protein-ligand interaction detected (PLIP) MG.44: 3 residues within 4Å: Chain A: U.560, U.561, G.570 No protein-ligand interaction detected (PLIP) MG.45: 3 residues within 4Å: Chain A: U.796, A.797, G.798 No protein-ligand interaction detected (PLIP) MG.46: 2 residues within 4Å: Chain A: C.586, C.587 No protein-ligand interaction detected (PLIP) MG.47: 4 residues within 4Å: Chain A: A.611, U.612, G.680, G.681 No protein-ligand interaction detected (PLIP) MG.48: 3 residues within 4Å: Chain A: C.667, G.668, U.669 No protein-ligand interaction detected (PLIP) MG.49: 2 residues within 4Å: Chain A: G.765, U.766 No protein-ligand interaction detected (PLIP) MG.50: 2 residues within 4Å: Chain A: A.740, C.741 No protein-ligand interaction detected (PLIP) MG.51: 1 residues within 4Å: Chain A: G.754 No protein-ligand interaction detected (PLIP) MG.52: 3 residues within 4Å: Chain A: A.367, A.368, G.384 No protein-ligand interaction detected (PLIP) MG.53: 2 residues within 4Å: Chain A: C.66, A.67 No protein-ligand interaction detected (PLIP) MG.54: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.55: 1 residues within 4Å: Chain A: G.175 No protein-ligand interaction detected (PLIP) MG.56: 1 residues within 4Å: Chain A: A.204 No protein-ligand interaction detected (PLIP) MG.57: 4 residues within 4Å: Chain A: G.294, A.295, U.297, C.458 No protein-ligand interaction detected (PLIP) MG.58: 2 residues within 4Å: Chain A: A.209, G.210 No protein-ligand interaction detected (PLIP) MG.76: 5 residues within 4Å: Chain B: H.93, D.224, N.226, D.240, D.241 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.93, B:D.224, B:D.240, B:D.241 MG.80: 2 residues within 4Å: Chain X: T.135 Ligands: ATP.81 1 PLIP interactions: 1 interactions with chain X Metal complexes: X:T.135 MG.83: 1 residues within 4Å: Chain 3: N.139 No protein-ligand interaction detected (PLIP) MG.86: 3 residues within 4Å: Chain 6: T.158, T.178 Ligands: GTP.85 2 PLIP interactions: 2 interactions with chain 6 Metal complexes: 6:T.158, 6:T.178

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

K.59: 5 residues within 4Å: Chain A: C.55, C.60, C.61, C.195, G.196 Ligand excluded by PLIP K.60: 4 residues within 4Å: Chain A: G.70, A.71, G.72, G.144 Ligand excluded by PLIP K.61: 5 residues within 4Å: Chain A: C.243, C.253, G.254 Chain J: P.73, N.74 Ligand excluded by PLIP K.62: 5 residues within 4Å: Chain A: C.458, U.460, U.945, U.946, G.947 Ligand excluded by PLIP K.63: 4 residues within 4Å: Chain A: A.551, G.552, G.553, G.774 Ligand excluded by PLIP K.64: 3 residues within 4Å: Chain A: A.551, G.552, G.715 Ligand excluded by PLIP K.65: 3 residues within 4Å: Chain A: G.552, G.553, A.554 Ligand excluded by PLIP K.66: 4 residues within 4Å: Chain A: U.610, C.683, U.688, G.689 Ligand excluded by PLIP K.67: 5 residues within 4Å: Chain A: C.615, G.616, C.617, G.681, U.682 Ligand excluded by PLIP K.68: 3 residues within 4Å: Chain A: C.683, G.686, G.687 Ligand excluded by PLIP K.69: 2 residues within 4Å: Chain A: C.725, G.742 Ligand excluded by PLIP K.70: 5 residues within 4Å: Chain A: G.528, G.529, C.530, G.829, U.830 Ligand excluded by PLIP K.71: 5 residues within 4Å: Chain A: A.917, A.918, A.926, G.939 Ligands: MG.15 Ligand excluded by PLIP K.72: 5 residues within 4Å: Chain A: G.842, U.843, C.844, G.912, U.913 Ligand excluded by PLIP K.73: 4 residues within 4Å: Chain A: C.153, A.154, C.158, C.159 Ligand excluded by PLIP K.74: 5 residues within 4Å: Chain A: C.188, A.190, U.191, A.192, U.203 Ligand excluded by PLIP K.75: 3 residues within 4Å: Chain A: G.240, U.241, A.258 Ligand excluded by PLIP K.87: 5 residues within 4Å: Chain 6: D.154, G.175, G.176, I.177 Ligands: GTP.85 Ligand excluded by PLIP

1 x ZN: ZINC ION(Non-covalent)

ZN.77: 4 residues within 4Å: Chain O: C.94, C.105, C.108, C.143 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.78: 4 residues within 4Å: Chain E: C.105 Chain P: C.65, C.68, C.100 4 PLIP interactions: 3 interactions with chain P, 1 interactions with chain E, Metal complexes: P:C.65, P:C.68, P:C.100, E:C.105 FES.79: 5 residues within 4Å: Chain M: C.26, R.29 Chain T: C.139, C.141, C.149 4 PLIP interactions: 1 interactions with chain M, 3 interactions with chain T, Metal complexes: M:C.26, T:C.139, T:C.141, T:C.149

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

ATP.81: 18 residues within 4Å: Chain X: P.84, L.99, M.100, R.102, K.130, G.131, T.132, G.133, K.134, T.135, L.136, S.311, T.313, Y.348, P.388, S.389, E.392 Ligands: MG.80 13 PLIP interactions: 13 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 Salt bridges: X:K.134, X:K.134

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

GNP.82: 11 residues within 4Å: Chain X: Y.173, R.177, Y.208, V.209, D.238, G.241, I.242, K.245, H.291, N.292, K.295 13 PLIP interactions: 13 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:D.238, X:H.291, X:N.292, X:K.295 Salt bridges: X:D.238, X:K.245, X:K.295

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

FME.84: 5 residues within 4Å: Chain 5: A.71 Chain 6: L.593, H.642, H.643, D.655 2 PLIP interactions: 2 interactions with chain 6 Hydrogen bonds: 6:H.642, 6:H.643

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

GTP.85: 20 residues within 4Å: Chain 6: H.152, V.153, D.154, H.155, G.156, K.157, T.158, T.159, G.176, I.177, T.178, G.201, N.252, K.253, D.255, S.288, A.289, L.290 Ligands: MG.86, K.87 18 PLIP interactions: 18 interactions with chain 6 Hydrogen bonds: 6:D.154, 6:H.155, 6:G.156, 6:K.157, 6:T.158, 6:T.159, 6:T.159, 6:T.178, 6:G.201, 6:N.252, 6:K.253, 6:K.253, 6:A.289, 6:L.290 Salt bridges: 6:K.157, 6:K.157, 6:D.255 pi-Cation interactions: 6:K.253

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cipullo, M. et al., GTPBP8 plays a role in mitoribosome formation in human mitochondria. Nat Commun (2024)

Release Date

2024-06-26

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-2, mitochondrial: 6

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

6
7

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-2, mitochondrial

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