SMTL ID : 6hiy.1

Cryo-EM structure of the Trypanosoma brucei mitochondrial ribosome - This entry contains the body of the small mitoribosomal subunit in complex with mt-IF-3

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

1 x UNK- UNK- UNK- UNK- UNK- UNK- UNK- UNK: Unknown protein(Non-covalent)

UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK.1: 7 residues within 4Å: Chain 9: E.553, D.554, A.557, Q.559, T.568, E.571, H.581 3 PLIP interactions: 3 interactions with chain 9 Hydrophobic interactions: 9:D.554, 9:Q.559, 9:E.571

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.291, C.294, C.304, H.323 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.291, A:C.294, A:C.304, A:H.323 ZN.3: 4 residues within 4Å: Chain K: C.98, C.101, C.119, C.122 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.98, K:C.101, K:C.119, K:C.122 ZN.4: 4 residues within 4Å: Chain K: C.175, C.178, C.211, C.214 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.175, K:C.178, K:C.211, K:C.214 ZN.8: 4 residues within 4Å: Chain 8: H.55, C.59, C.82, C.85 4 PLIP interactions: 4 interactions with chain 8 Metal complexes: 8:H.55, 8:C.59, 8:C.82, 8:C.85

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

MG.5: 3 residues within 4Å: Chain U: D.405, N.429 Chain a: A.91 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain N: H.12 Chain T: F.3 Chain W: H.39 2 PLIP interactions: 1 interactions with chain W, 1 interactions with chain N Metal complexes: W:H.39, N:H.12 MG.7: 3 residues within 4Å: Chain 0: R.363 Chain B: G.766 Chain Q: M.67 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Chain 9: D.30 1 PLIP interactions: 1 interactions with chain 9 Metal complexes: 9:D.30 MG.10: 1 residues within 4Å: Chain a: A.27 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain a: U.65, A.131 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain a: U.65, U.66, A.133 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain a: A.60, A.61, A.155 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain a: A.68, A.93, U.94 No protein-ligand interaction detected (PLIP) MG.15: 2 residues within 4Å: Chain a: U.69, A.91 No protein-ligand interaction detected (PLIP) MG.16: 4 residues within 4Å: Chain a: G.141, U.142, U.143, G.147 No protein-ligand interaction detected (PLIP) MG.17: 3 residues within 4Å: Chain a: U.231, G.232, U.246 No protein-ligand interaction detected (PLIP) MG.18: 2 residues within 4Å: Chain a: C.237, U.251 No protein-ligand interaction detected (PLIP) MG.19: 3 residues within 4Å: Chain a: U.338, U.339, A.355 No protein-ligand interaction detected (PLIP) MG.20: 2 residues within 4Å: Chain a: A.571, A.572 No protein-ligand interaction detected (PLIP) MG.21: 2 residues within 4Å: Chain a: U.562, U.563 No protein-ligand interaction detected (PLIP) MG.22: 1 residues within 4Å: Chain a: A.603 No protein-ligand interaction detected (PLIP) MG.23: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.24: 2 residues within 4Å: Chain a: U.592, A.593 No protein-ligand interaction detected (PLIP) MG.25: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.26: 3 residues within 4Å: Chain a: A.280, U.281, A.367 No protein-ligand interaction detected (PLIP) MG.27: 2 residues within 4Å: Ligands: MG.33 Chain a: U.596 No protein-ligand interaction detected (PLIP) MG.28: 2 residues within 4Å: Chain a: G.158, G.159 No protein-ligand interaction detected (PLIP) MG.29: 2 residues within 4Å: Chain a: C.238, U.241 No protein-ligand interaction detected (PLIP) MG.30: 4 residues within 4Å: Chain a: C.582, A.583, G.584, U.588 No protein-ligand interaction detected (PLIP) MG.31: 6 residues within 4Å: Ligands: MG.32 Chain a: G.584, A.587, U.588, A.590, A.591 No protein-ligand interaction detected (PLIP) MG.32: 5 residues within 4Å: Ligands: MG.31 Chain a: A.583, G.584, A.591, A.604 No protein-ligand interaction detected (PLIP) MG.33: 2 residues within 4Å: Ligands: MG.27 Chain a: A.604 No protein-ligand interaction detected (PLIP) MG.34: 3 residues within 4Å: Chain a: A.222, A.224, A.225 No protein-ligand interaction detected (PLIP) MG.35: 3 residues within 4Å: Chain a: G.229, A.248, U.250 No protein-ligand interaction detected (PLIP) MG.36: 2 residues within 4Å: Chain 6: Q.11 Chain a: A.33 No protein-ligand interaction detected (PLIP) MG.37: 4 residues within 4Å: Chain 1: Y.9 Chain a: G.542, A.586, U.613 No protein-ligand interaction detected (PLIP) MG.38: 2 residues within 4Å: Chain a: A.386, U.387 No protein-ligand interaction detected (PLIP) MG.39: 2 residues within 4Å: Chain a: A.385, U.544 No protein-ligand interaction detected (PLIP) MG.40: 3 residues within 4Å: Chain 1: K.13 Chain 4: D.68 Chain a: A.541 No protein-ligand interaction detected (PLIP) MG.41: 3 residues within 4Å: Chain 3: R.10 Chain a: A.75, A.76 No protein-ligand interaction detected (PLIP)

2 x SPD: SPERMIDINE(Non-covalent)

SPD.42: 11 residues within 4Å: Chain 0: R.572, D.578, N.581 Chain 6: Y.13, P.15 Chain a: A.218, U.259, U.261, A.262, A.263, A.264 2 PLIP interactions: 2 interactions with chain 0 Hydrogen bonds: 0:R.572, 0:N.581 SPD.43: 11 residues within 4Å: Chain 6: D.10, T.12 Chain T: F.2, G.71, G.72 Chain a: A.27, U.28, G.239, A.266, U.267, U.268 2 PLIP interactions: 1 interactions with chain 6, 1 interactions with chain T Hydrogen bonds: 6:T.12, T:F.2

1 x SPM: SPERMINE(Non-covalent)

SPM.44: 11 residues within 4Å: Chain U: Q.297 Chain W: T.127 Chain a: U.66, U.67, U.95, U.96, U.97, U.126, G.127, A.128, U.129 1 PLIP interactions: 1 interactions with chain U Hydrogen bonds: U:Q.297

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ramrath, D.J.F. et al., Evolutionary shift toward protein-based architecture in trypanosomal mitochondrial ribosomes. Science (2018)

Release Date

2018-09-26

Peptides

mS48: A
mS51: B
mS56: C
mS59: D
mS60: E
mS61: F
mS62: G
mS63: H
mS64: I
mS65: J
mS66: K
mS68: L
mS73: M
mS74: N
mS55m: O
bS6m: P
uS8m: Q
uS9m: R
uS11m: S
uS12m: T
uS15m: U
bS16m: V
uS17m: W
bS18m: X
uS21m: Y
mt-IF-3: Z
mS22: 0
mS23: 1
mS26: 2
mS34: 3
mS37: 4
mS38: 5
mS41: 6
mS42: 7
mS43: 8
mS47: 9
Unknown protein: b
Unknown protein: c
Unknown protein: d

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
DA

B
DD

C
DI

D
DL

E
DM

F
DN

G
DO

H
DP

I
DQ

J
DR

K
DS

L
DU

M
DZ

N
Da

O
CE

P
CF

Q
CH

R
CI

S
CK

T
CL

U
CO

V
CP

W
CQ

X
CR

Y
CU

Z
CZ

0
Ca

1
Cb

2
Cd

3
Cj

4
Cm

5
Cn

6
Cp

7
Cq

8
Cr

9
Cv

b
UQ

c
US

d
UT

mS48

mS51

mS56

mS59

mS60

mS61

mS62

mS63

mS64

mS65

mS66

mS68

mS73

mS74

mS55m

bS6m

uS8m

uS9m

uS11m

uS12m

uS15m

bS16m

uS17m

bS18m

uS21m

mt-IF-3

mS22

mS23

mS26

mS34

mS37

mS38

mS41

mS42

mS43

mS47

Unknown protein

Unknown protein

Unknown protein

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