SMTL ID : 6hiw.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

3 x UNK- UNK- UNK- UNK- UNK: Unknown Protein(Non-covalent)

UNK-UNK-UNK-UNK-UNK.1: 6 residues within 4Å: Chain P: E.244, T.464, Q.473 Chain W: H.94, R.95, Y.174 7 PLIP interactions: 4 interactions with chain W, 3 interactions with chain P Hydrophobic interactions: W:Y.174, P:Q.473 Hydrogen bonds: W:H.94, W:Y.174, W:Y.174, P:E.244, P:E.244 UNK-UNK-UNK-UNK-UNK.2: 8 residues within 4Å: Chain O: V.743, V.754, L.755, T.756, V.757, S.758, Y.762, P.796 10 PLIP interactions: 10 interactions with chain O Hydrophobic interactions: O:V.743, O:V.754, O:L.755, O:T.756 Hydrogen bonds: O:V.754, O:V.754, O:T.756, O:T.756, O:S.758, O:S.758 UNK-UNK-UNK-UNK-UNK.3: 6 residues within 4Å: Chain t: E.553, D.554, A.557, Q.559, L.575, H.581 3 PLIP interactions: 3 interactions with chain t Hydrophobic interactions: t:D.554, t:Q.559, t:L.575

4 x ZN: ZINC ION(Non-covalent)

ZN.4: 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.5: 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.6: 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.12: 4 residues within 4Å: Chain s: H.55, C.59, C.82, C.85 4 PLIP interactions: 4 interactions with chain s Metal complexes: s:H.55, s:C.59, s:C.82, s:C.85

1 x UTP: URIDINE 5'-TRIPHOSPHATE(Non-covalent)

UTP.7: 12 residues within 4Å: Chain R: R.188 Chain U: R.132, K.171, F.202, K.205, R.209, E.234, R.236, K.283, L.284, R.285 Chain u: U.429 16 PLIP interactions: 14 interactions with chain U, 2 interactions with chain R Hydrogen bonds: U:K.205, U:E.234, U:R.236, U:R.285, R:R.188 Salt bridges: U:R.132, U:R.132, U:K.171, U:K.205, U:K.205, U:K.205, U:R.209, U:R.236, U:R.285, R:R.188 pi-Cation interactions: U:R.236

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

MG.8: 4 residues within 4Å: Chain 8: F.3 Chain N: H.12 Chain c: H.39, V.41 2 PLIP interactions: 1 interactions with chain c, 1 interactions with chain N Metal complexes: c:H.39, N:H.12 MG.9: 3 residues within 4Å: Chain 4: M.67 Chain B: G.766 Chain h: R.363 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Ligands: GTP.10 Chain k: S.156, T.358 4 PLIP interactions: 1 interactions with chain k, 3 Ligand-Water interactions Metal complexes: k:S.156, H2O.1, H2O.1, H2O.1 MG.13: 2 residues within 4Å: Chain t: D.30 Chain u: U.383 1 PLIP interactions: 1 interactions with chain t Metal complexes: t:D.30 MG.14: 1 residues within 4Å: Chain u: A.27 No protein-ligand interaction detected (PLIP) MG.15: 2 residues within 4Å: Chain u: U.65, A.131 No protein-ligand interaction detected (PLIP) MG.16: 3 residues within 4Å: Chain u: U.65, U.66, A.133 No protein-ligand interaction detected (PLIP) MG.17: 3 residues within 4Å: Chain u: A.60, A.61, A.155 No protein-ligand interaction detected (PLIP) MG.18: 3 residues within 4Å: Chain u: A.68, A.93, U.94 No protein-ligand interaction detected (PLIP) MG.19: 2 residues within 4Å: Chain u: U.69, A.91 No protein-ligand interaction detected (PLIP) MG.20: 3 residues within 4Å: Chain a: D.405, N.429 Chain u: A.91 No protein-ligand interaction detected (PLIP) MG.21: 4 residues within 4Å: Chain u: G.141, U.142, U.143, G.147 No protein-ligand interaction detected (PLIP) MG.22: 3 residues within 4Å: Chain u: U.231, G.232, U.246 No protein-ligand interaction detected (PLIP) MG.23: 2 residues within 4Å: Chain u: C.237, U.251 No protein-ligand interaction detected (PLIP) MG.24: 3 residues within 4Å: Chain u: U.338, U.339, A.355 No protein-ligand interaction detected (PLIP) MG.25: 2 residues within 4Å: Chain u: A.571, A.572 No protein-ligand interaction detected (PLIP) MG.26: 2 residues within 4Å: Chain u: U.563, U.564 No protein-ligand interaction detected (PLIP) MG.27: 1 residues within 4Å: Chain u: A.603 No protein-ligand interaction detected (PLIP) MG.28: 1 residues within 4Å: Chain u: U.606 No protein-ligand interaction detected (PLIP) MG.29: 2 residues within 4Å: Chain u: U.592, A.593 No protein-ligand interaction detected (PLIP) MG.30: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.31: 3 residues within 4Å: Chain u: A.280, U.281, A.367 No protein-ligand interaction detected (PLIP) MG.32: 3 residues within 4Å: Ligands: MG.38 Chain u: A.595, U.596 No protein-ligand interaction detected (PLIP) MG.33: 2 residues within 4Å: Chain u: G.158, G.159 No protein-ligand interaction detected (PLIP) MG.34: 2 residues within 4Å: Chain u: C.238, U.241 No protein-ligand interaction detected (PLIP) MG.35: 4 residues within 4Å: Chain u: C.582, A.583, G.584, U.588 No protein-ligand interaction detected (PLIP) MG.36: 6 residues within 4Å: Ligands: MG.37 Chain u: G.584, A.587, U.588, A.590, A.591 No protein-ligand interaction detected (PLIP) MG.37: 5 residues within 4Å: Ligands: MG.36 Chain u: A.583, G.584, A.591, A.604 No protein-ligand interaction detected (PLIP) MG.38: 2 residues within 4Å: Ligands: MG.32 Chain p: Q.170 No protein-ligand interaction detected (PLIP) MG.39: 3 residues within 4Å: Chain u: A.222, A.224, A.225 No protein-ligand interaction detected (PLIP) MG.40: 3 residues within 4Å: Chain u: G.229, A.248, U.250 No protein-ligand interaction detected (PLIP) MG.41: 3 residues within 4Å: Chain c: Q.15 Chain q: Q.11 Chain u: A.33 No protein-ligand interaction detected (PLIP) MG.42: 4 residues within 4Å: Chain i: Y.9 Chain u: G.542, A.586, U.613 No protein-ligand interaction detected (PLIP) MG.43: 2 residues within 4Å: Chain u: A.386, U.387 No protein-ligand interaction detected (PLIP) MG.44: 2 residues within 4Å: Chain u: A.385, U.544 No protein-ligand interaction detected (PLIP) MG.45: 3 residues within 4Å: Chain i: K.13 Chain o: D.68 Chain u: A.541 No protein-ligand interaction detected (PLIP) MG.46: 5 residues within 4Å: Chain m: R.10 Chain u: A.75, A.76, A.77, G.78 No protein-ligand interaction detected (PLIP) MG.47: 2 residues within 4Å: Chain 9: E.27 Chain u: U.415 No protein-ligand interaction detected (PLIP) MG.48: 1 residues within 4Å: Chain u: G.470 No protein-ligand interaction detected (PLIP)

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

GTP.10: 23 residues within 4Å: Ligands: MG.11 Chain k: R.96, V.97, Q.99, T.100, G.108, F.109, L.110, R.112, T.151, G.152, C.153, G.154, K.155, S.156, A.157, T.357, T.358, R.359, D.360, F.412, P.452, Q.453 22 PLIP interactions: 22 interactions with chain k Hydrogen bonds: k:R.96, k:V.97, k:Q.99, k:T.100, k:L.110, k:L.110, k:G.152, k:K.155, k:S.156, k:S.156, k:A.157, k:T.358, k:T.358, k:R.359 Water bridges: k:G.95, k:S.156, k:S.156, k:S.156, k:D.286 Salt bridges: k:K.155, k:K.155 pi-Stacking: k:F.404

4 x SPD: SPERMIDINE(Non-covalent)

SPD.49: 10 residues within 4Å: Chain 6: M.387 Chain D: R.292 Chain u: A.452, A.453, G.454, G.466, A.467, A.468, A.469, G.470 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain 6 Hydrogen bonds: D:R.292, 6:M.387 SPD.50: 5 residues within 4Å: Chain 7: G.19 Chain D: H.267 Chain u: U.398, A.399, A.459 No protein-ligand interaction detected (PLIP) SPD.51: 10 residues within 4Å: Chain h: R.572, D.578 Chain q: Y.13, P.15 Chain u: A.218, U.259, U.261, A.262, A.263, A.264 1 PLIP interactions: 1 interactions with chain h Hydrogen bonds: h:N.581 SPD.52: 12 residues within 4Å: Chain 8: F.2, M.6, G.71, G.72 Chain q: D.10, T.12 Chain u: A.27, U.28, G.239, A.266, U.267, U.268 2 PLIP interactions: 1 interactions with chain 8, 1 interactions with chain q Hydrogen bonds: 8:F.2, q:T.12

1 x SPM: SPERMINE(Non-covalent)

SPM.53: 11 residues within 4Å: Chain a: Q.297 Chain c: T.127 Chain u: 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 a Hydrogen bonds: a: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
mS49: O
mS50: P
mS52: Q
mS53: R
mS54: S
mS55: T
mS57: U
mS58: V
mS67: W
mS69: X
mS70: Y
mS71: Z
mS72: 0
uS3m: 1
uS5m: 2
bS6m: 3
uS8m: 4
uS9m: 5
uS10m: 6
uS11m: 7
uS12m: 8
uS14m: 9
uS15m: a
bS16m: b
uS17m: c
bS18m: d
uS19m: e
bS21m: f
mt-IF-3: g
mS22: h
mS23: i
mS26: j
mS29: k
mS33: l
mS34: m
mS35: n
mS37: o
mS38: p
mS41: q
mS42: r
mS43: s
mS47: t
Unknown Protein: v
Unknown Protein: w
Unknown Protein: x

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
DB

P
DC

Q
DE

R
DF

S
DG

T
DH

U
DJ

V
DK

W
DT

X
DV

Y
DW

Z
DX

0
DY

1
CC

2
CE

3
CF

4
CH

5
CI

6
CJ

7
CK

8
CL

9
CN

a
CO

b
CP

c
CQ

d
CR

e
CS

f
CU

g
CZ

h
Ca

i
Cb

j
Cd

k
Cg

l
Ci

m
Cj

n
Ck

o
Cm

p
Cn

q
Cp

r
Cq

s
Cr

t
Cv

v
UQ

w
US

x
UT

mS48

mS51

mS56

mS59

mS60

mS61

mS62

mS63

mS64

mS65

mS66

mS68

mS73

mS74

mS49

mS50

mS52

mS53

mS54

mS55

mS57

mS58

mS67

mS69

mS70

mS71

mS72

uS3m

uS5m

bS6m

uS8m

uS9m

uS10m

uS11m

uS12m

uS14m

uS15m

bS16m

uS17m

bS18m

uS19m

bS21m

mt-IF-3

mS22

mS23

mS26

mS29

mS33

mS34

mS35

mS37

mS38

mS41

mS42

mS43

mS47

Unknown Protein

Unknown Protein

Unknown Protein

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