SMTL ID : 8pvk.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-2-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-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 24 PLIP interactions: 24 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.180, G:S.181, G:E.194, G:E.194, G:T.200, G:T.200, G:T.200, G:T.200, G:N.287, G:K.288, G:K.288, G:C.321, G:A.322 Water bridges: G:G.222 Salt bridges: G:K.179, G:K.179, G:D.290 GTP.5: 26 residues within 4Å: Chain A: U.2281 Chain R: 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, K.353, V.354, A.355, P.356, I.357, P.358, G.359, E.360, T.361 Ligands: MG.6, MG.7 23 PLIP interactions: 23 interactions with chain R Hydrogen bonds: R:N.271, R:K.272, R:K.272, R:R.298, R:R.298, R:A.299, R:Y.334, R:N.336, R:V.337, R:G.338, R:K.339, R:S.340, R:S.341, R:A.355, R:A.355, R:G.359, R:E.360, R:T.361, R:G.380 Water bridges: R:S.340 Salt bridges: R:D.274, R:K.339, R: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 R: N.336, A.355, I.357, E.360 Ligands: GTP.5 2 PLIP interactions: 2 interactions with chain R Metal complexes: R:A.355, R:I.357 MG.7: 4 residues within 4Å: Chain R: S.340, T.361, D.377 Ligands: GTP.5 4 PLIP interactions: 2 interactions with chain R, 2 Ligand-Water interactions Metal complexes: R:S.340, R:T.361, H2O.1, H2O.1

5 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain O: C.6, C.9, C.32, 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 Q: C.52, C.55, H.68, H.74 5 PLIP interactions: 5 interactions with chain Q Metal complexes: Q:C.52, Q:C.55, Q:H.68, Q:H.68, Q:H.74 ZN.8: 4 residues within 4Å: Chain q: C.45, C.48, C.82, C.85 4 PLIP interactions: 4 interactions with chain q Metal complexes: q:C.45, q:C.48, q:C.82, q:C.85 ZN.9: 4 residues within 4Å: Chain t: C.19, C.22, C.34, C.37 4 PLIP interactions: 4 interactions with chain t Metal complexes: t:C.19, t:C.22, t:C.34, t:C.37 ZN.10: 4 residues within 4Å: Chain w: C.39, C.42, C.57, C.60 4 PLIP interactions: 4 interactions with chain w Metal complexes: w:C.39, w:C.42, w:C.57, w: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

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

E
CB

F
CF

G
CH

H
CI

I
CJ

J
CK

K
CL

L
CM

2
LF

M
CN

N
CO

O
CQ

P
Lq

Q
Cb

R
Cd

S
Ce

T
Cf

U
Cg

V
Ch

W
Cz

X
LA

Y
LB

Z
LC

0
LD

1
LE

3
LG

4
LH

5
LJ

6
LK

7
LL

8
LM

9
LN

a
LO

b
LP

c
LQ

d
LR

e
LS

f
LT

g
LU

h
LV

i
LX

j
LY

k
LZ

l
La

m
Lc

n
Ld

o
Le

p
Lf

q
Lg

r
Lh

s
Li

t
Lj

u
Lk

v
Ll

w
Lp

x
Lr

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

Putative 60S ribosomal protein

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

Ribosomal protein

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