SMTL ID : 8pvl.1

Chaetomium thermophilum pre-60S State 7 - pre-5S rotation lacking Utp30/ITS2 - composite structure

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-2-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

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

GTP.1: 23 residues within 4Å: Chain F: F.174, P.175, N.176, V.177, G.178, K.179, S.180, S.181, V.193, E.194, P.195, T.199, T.200, D.219, T.220, N.287, K.288, D.290, I.291, S.320, C.321, A.322 Ligands: MG.2 27 PLIP interactions: 27 interactions with chain F Hydrogen bonds: F:F.174, F:N.176, F:V.177, F:G.178, F:K.179, F:S.180, F:S.180, F:S.181, F:S.181, F:P.192, F:E.194, F:E.194, F:T.200, F:T.200, F:T.200, F:T.200, F:N.287, F:K.288, F:K.288, F:S.320, F:C.321, F:A.322 Water bridges: F:G.222 Salt bridges: F:K.179, F:K.179, F:D.290 pi-Cation interactions: F:K.288 GTP.7: 26 residues within 4Å: Chain A: U.2281 Chain P: N.271, K.272, D.274, L.275, R.298, A.299, Y.334, P.335, N.336, V.337, G.338, K.339, S.340, S.341, V.354, A.355, P.356, I.357, P.358, G.359, E.360, T.361, G.380 Ligands: MG.5, MG.6 26 PLIP interactions: 26 interactions with chain P Hydrogen bonds: P:N.271, P:K.272, P:K.272, P:R.298, P:R.298, P:A.299, P:Y.334, P:N.336, P:V.337, P:G.338, P:K.339, P:S.340, P:S.341, P:S.341, P:A.355, P:P.356, P:G.359, P:E.360, P:T.361, P:T.361, P:G.380 Water bridges: P:S.340, P:K.353 Salt bridges: P:D.274, P:K.339, P:K.339

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain F: N.176, E.194, Y.196, T.199 Ligands: GTP.1 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:E.194, F:Y.196 MG.5: 4 residues within 4Å: Chain P: S.340, T.361, D.377 Ligands: GTP.7 4 PLIP interactions: 2 interactions with chain P, 2 Ligand-Water interactions Metal complexes: P:S.340, P:T.361, H2O.1, H2O.1 MG.6: 5 residues within 4Å: Chain P: N.336, A.355, I.357, E.360 Ligands: GTP.7 2 PLIP interactions: 2 interactions with chain P Metal complexes: P:A.355, P:I.357

5 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain N: C.6, C.9, C.32, R.33, C.36 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.6, N:C.9, N:C.32, N:C.36 ZN.4: 4 residues within 4Å: Chain O: C.52, C.55, H.68, H.74 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.52, O:C.55, O:H.68, O:H.74 ZN.8: 4 residues within 4Å: Chain o: C.45, C.48, C.82, C.85 4 PLIP interactions: 4 interactions with chain o Metal complexes: o:C.45, o:C.48, o:C.82, o:C.85 ZN.9: 4 residues within 4Å: Chain r: C.19, C.22, C.34, C.37 4 PLIP interactions: 4 interactions with chain r Metal complexes: r:C.19, r:C.22, r:C.34, r:C.37 ZN.10: 4 residues within 4Å: Chain u: C.39, C.42, C.57, C.60 4 PLIP interactions: 4 interactions with chain u Metal complexes: u:C.39, u:C.42, u:C.57, u:C.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thoms, M. et al., Structural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation. Embo Rep. (2023)

Release Date

2023-12-06

Peptides

Large ribosomal subunit protein uL10: E
Nucleolar GTP-binding protein 1: F
Putative RNA-binding protein: G
Pescadillo homolog: H
Ribosome biogenesis protein NSA2 homolog: I
Putative GTP binding protein: J
60S ribosomal protein l7-like protein: K0
Eukaryotic translation initiation factor 6: L
DUF2423 domain-containing protein: M
Ribosome biogenesis protein RLP24: N
Zinc finger domain-containing protein: O
Nucleolar GTP-binding protein 2: P
Ribosome biogenesis protein NOP53: Q
Ribosome production factor 2 homolog: R
Ribosome biogenesis regulatory protein: S
Ribosome assembly protein 4: T
rRNA-processing protein: U
60S ribosomal protein L2-like protein: V
60S ribosomal protein L3-like protein: W
60S ribosomal protein L4-like protein: X
60S ribosomal protein l5-like protein: Y
60S ribosomal protein L6: Z
60S ribosomal protein L8: 1
60S ribosomal protein l9-like protein: 2
Putative ribosomal protein: 3
60S ribosomal protein L12-like protein: 4
60S ribosomal protein L13: 5
60S ribosomal protein L14-like protein: 6
Ribosomal protein L15: 7
60S ribosomal protein L16-like protein: 8
60S ribosomal protein l17-like protein: 9
Ribosomal protein L18-like protein: a
Ribosomal protein L19: b
60S ribosomal protein L20: c
60S ribosomal protein l21-like protein: d
60S ribosomal protein L22-like protein: e
60S ribosomal protein l23-like protein: f
60S ribosomal protein L25-like protein: g
60S ribosomal protein L26-like protein: h
60S ribosomal protein L27: i
60S ribosomal protein L28-like protein: j
60S ribosomal protein l30-like protein: k
Putative 60S ribosomal protein: l
60S ribosomal protein L32-like protein: m
60S ribosomal protein l33-like protein: n
Ribosomal protein l34-like protein: o
dolichyl-diphosphooligosaccharide--protein glycotransferase: p
60S ribosomal protein L36: q
Ribosomal protein L37: r
60S ribosomal protein L38-like protein: s
Ribosomal protein eL39: t
60S ribosomal protein L43-like protein: u
Putative 60S ribosomal protein: v

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

E
CF

F
CH

G
CI

H
CJ

I
CK

J
CL

K
CM

0
LF

L
CN

M
CO

N
CQ

O
Cb

P
Cd

Q
Ce

R
Cf

S
Cg

T
Ch

U
Cz

V
LA

W
LB

X
LC

Y
LD

Z
LE

1
LG

2
LH

3
LJ

4
LK

5
LL

6
LM

7
LN

8
LO

9
LP

a
LQ

b
LR

c
LS

d
LT

e
LU

f
LV

g
LX

h
LY

i
LZ

j
La

k
Lc

l
Ld

m
Le

n
Lf

o
Lg

p
Lh

q
Li

r
Lj

s
Lk

t
Ll

u
Lp

v
Lq

Large ribosomal subunit protein uL10

Nucleolar GTP-binding protein 1

Putative RNA-binding protein

Pescadillo homolog

Ribosome biogenesis protein NSA2 homolog

Putative GTP binding protein

60S ribosomal protein l7-like protein

Eukaryotic translation initiation factor 6

DUF2423 domain-containing protein

Ribosome biogenesis protein RLP24

Zinc finger domain-containing protein

Nucleolar GTP-binding protein 2

Ribosome biogenesis protein NOP53

Ribosome production factor 2 homolog

Ribosome biogenesis regulatory protein

Ribosome assembly protein 4

rRNA-processing protein

60S ribosomal protein L2-like protein

60S ribosomal protein L3-like protein

60S ribosomal protein L4-like protein

60S ribosomal protein l5-like protein

60S ribosomal protein L6

60S ribosomal protein L8

60S ribosomal protein l9-like protein

Putative ribosomal protein

60S ribosomal protein L12-like protein

60S ribosomal protein L13

60S ribosomal protein L14-like protein

Ribosomal protein L15

60S ribosomal protein L16-like protein

60S ribosomal protein l17-like protein

Ribosomal protein L18-like protein

Ribosomal protein L19

60S ribosomal protein L20

60S ribosomal protein l21-like protein

60S ribosomal protein L22-like protein

60S ribosomal protein l23-like protein

60S ribosomal protein L25-like protein

60S ribosomal protein L26-like protein

60S ribosomal protein L27

60S ribosomal protein L28-like protein

60S ribosomal protein l30-like protein

Putative 60S ribosomal protein

60S ribosomal protein L32-like protein

60S ribosomal protein l33-like protein

Ribosomal protein l34-like protein

dolichyl-diphosphooligosaccharide--protein glycotransferase

60S ribosomal protein L36

Ribosomal protein L37

60S ribosomal protein L38-like protein

Ribosomal protein eL39

60S ribosomal protein L43-like protein

Putative 60S ribosomal protein

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