SMTL ID : 8pv1.1

Chaetomium thermophilum pre-60S State 6 - pre-5S rotation - L1 intermediate - composite structure

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

GTP.1: 24 residues within 4Å: Chain G: F.174, P.175, N.176, V.177, G.178, K.179, S.180, S.181, P.192, 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 23 PLIP interactions: 23 interactions with chain G Hydrogen bonds: G:F.174, G:N.176, G:V.177, G:G.178, G:K.179, G:S.180, G:S.180, G:S.181, G:S.181, G:E.194, G:E.194, G:T.200, G:T.200, G:T.200, G:N.287, G:K.288, G:K.288, G:C.321, G:A.322 Salt bridges: G:K.179, G:K.179, G:D.290 pi-Cation interactions: G:K.288 GTP.5: 26 residues within 4Å: Chain A: U.2281 Chain Q: 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.6, MG.7 26 PLIP interactions: 26 interactions with chain Q Hydrogen bonds: Q:N.271, Q:K.272, Q:K.272, Q:R.298, Q:R.298, Q:A.299, Q:Y.334, Q:N.336, Q:V.337, Q:G.338, Q:K.339, Q:S.340, Q:S.341, Q:S.341, Q:A.355, Q:A.355, Q:G.359, Q:E.360, Q:T.361, Q:T.361, Q:G.380 Water bridges: Q:S.340, Q:K.353 Salt bridges: Q:D.274, Q:K.339, Q:K.339

3 x MG: MAGNESIUM ION(Non-covalent)

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

5 x ZN: ZINC ION(Non-covalent)

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

2023-11-15

Peptides

Utp30: E
Large ribosomal subunit protein uL10: F
Nucleolar GTP-binding protein 1: G
Putative RNA-binding protein: H
Pescadillo homolog: I
Ribosome biogenesis protein NSA2 homolog: J
Putative GTP binding protein: K
60S ribosomal protein l7-like protein: L1
Eukaryotic translation initiation factor 6: M
DUF2423 domain-containing protein: N
Ribosome biogenesis protein RLP24: O
Zinc finger domain-containing protein: P
Nucleolar GTP-binding protein 2: Q
Ribosome biogenesis protein NOP53: R
Ribosome production factor 2 homolog: S
Ribosome biogenesis regulatory protein: T
Ribosome assembly protein 4: U
rRNA-processing protein: V
60S ribosomal protein L2-like protein: W
60S ribosomal protein L3-like protein: X
60S ribosomal protein L4-like protein: Y
60S ribosomal protein l5-like protein: Z
60S ribosomal protein L6: 0
60S ribosomal protein L8: 2
60S ribosomal protein l9-like protein: 3
Putative ribosomal protein: 4
60S ribosomal protein L12-like protein: 5
60S ribosomal protein L13: 6
60S ribosomal protein L14-like protein: 7
Ribosomal protein L15: 8
60S ribosomal protein L16-like protein: 9
60S ribosomal protein l17-like protein: a
Ribosomal protein L18-like protein: b
Ribosomal protein L19: c
60S ribosomal protein L20: d
60S ribosomal protein l21-like protein: e
60S ribosomal protein L22-like protein: f
60S ribosomal protein l23-like protein: g
60S ribosomal protein L25-like protein: h
60S ribosomal protein L26-like protein: i
60S ribosomal protein L27: j
60S ribosomal protein L28-like protein: k
60S ribosomal protein l30-like protein: l
Putative 60S ribosomal protein: m
60S ribosomal protein L32-like protein: n
60S ribosomal protein l33-like protein: o
Ribosomal protein l34-like protein: p
dolichyl-diphosphooligosaccharide--protein glycotransferase: q
60S ribosomal protein L36: r
Ribosomal protein L37: s
60S ribosomal protein L38-like protein: t
Ribosomal protein eL39: u
60S ribosomal protein L43-like protein: v
Putative 60S ribosomal protein: w

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

E
CB

F
CF

G
CH

H
CI

I
CJ

J
CK

K
CL

L
CM

1
LF

M
CN

N
CO

O
CQ

P
Cb

Q
Cd

R
Ce

S
Cf

T
Cg

U
Ch

V
Cz

W
LA

X
LB

Y
LC

Z
LD

0
LE

2
LG

3
LH

4
LJ

5
LK

6
LL

7
LM

8
LN

9
LO

a
LP

b
LQ

c
LR

d
LS

e
LT

f
LU

g
LV

h
LX

i
LY

j
LZ

k
La

l
Lc

m
Ld

n
Le

o
Lf

p
Lg

q
Lh

r
Li

s
Lj

t
Lk

u
Ll

v
Lp

w
Lq

Utp30

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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