SMTL ID : 8pv8.1

Chaetomium thermophilum pre-60S State 4 - post-5S rotation with Rix1 complex without Foot - composite structure

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

GTP.1: 24 residues within 4Å: Chain D: 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 D Hydrogen bonds: D:F.174, D:N.176, D:V.177, D:G.178, D:K.179, D:S.180, D:S.180, D:S.181, D:E.194, D:E.194, D:T.200, D:T.200, D:T.200, D:T.220, D:N.287, D:K.288, D:K.288, D:S.320, D:C.321, D:A.322 Water bridges: D:G.222 Salt bridges: D:K.179, D:K.179, D:D.290 GTP.5: 24 residues within 4Å: Chain K: 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, P.358, G.359, E.360, T.361, G.380 Ligands: MG.6, MG.7 23 PLIP interactions: 23 interactions with chain K Hydrogen bonds: K:N.271, K:K.272, K:K.272, K:A.299, K:Y.334, K:N.336, K:V.337, K:G.338, K:K.339, K:S.340, K:S.341, K:A.355, K:A.355, K:G.359, K:E.360, K:T.361, K:T.361, K:G.380 Water bridges: K:S.340, K:S.340 Salt bridges: K:D.274, K:K.339, K:K.339

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain D: N.176, E.194, Y.196, T.199 Ligands: GTP.1 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.194, D:Y.196, D:T.199 MG.6: 4 residues within 4Å: Chain K: N.336, A.355, I.357 Ligands: GTP.5 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:A.355 MG.7: 3 residues within 4Å: Chain K: S.340, T.361 Ligands: GTP.5 4 PLIP interactions: 2 interactions with chain K, 2 Ligand-Water interactions Metal complexes: K:S.340, K:T.361, H2O.1, H2O.1

5 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain I: C.6, C.9, C.32, C.36 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.6, I:C.9, I:C.32, I:C.36 ZN.4: 4 residues within 4Å: Chain J: C.52, C.55, H.68, H.74 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.52, J:C.55, J:H.68, J:H.74 ZN.8: 4 residues within 4Å: Chain c: C.45, C.48, C.82, C.85 4 PLIP interactions: 4 interactions with chain c Metal complexes: c:C.45, c:C.48, c:C.82, c:C.85 ZN.9: 4 residues within 4Å: Chain f: C.19, C.22, C.34, C.37 4 PLIP interactions: 4 interactions with chain f Metal complexes: f:C.19, f:C.22, f:C.34, f:C.37 ZN.10: 4 residues within 4Å: Chain i: C.39, C.42, C.57, C.60 4 PLIP interactions: 4 interactions with chain i Metal complexes: i:C.39, i:C.42, i:C.57, i: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

2024-01-10

Peptides

Large ribosomal subunit protein uL10: C
Nucleolar GTP-binding protein 1: D
Ribosome biogenesis protein NSA2 homolog: E
Putative GTP binding protein: F
Eukaryotic translation initiation factor 6: G
DUF2423 domain-containing protein: H
Ribosome biogenesis protein RLP24: I
Zinc finger domain-containing protein: J
Nucleolar GTP-binding protein 2: K
rRNA-processing protein: L
60S ribosomal protein L2-like protein: M
60S ribosomal protein L3-like protein: N
60S ribosomal protein L4-like protein: O
60S ribosomal protein L6: P
60S ribosomal protein l7-like protein: Q
60S ribosomal protein L8: R
60S ribosomal protein l9-like protein: S
60S ribosomal protein L12-like protein: T
60S ribosomal protein L13: U
60S ribosomal protein L14-like protein: V
Ribosomal protein L15: W
60S ribosomal protein L16-like protein: X
60S ribosomal protein l17-like protein: Y
Ribosomal protein L18-like protein: Z
Ribosomal protein L19: 0
60S ribosomal protein L20: 1
60S ribosomal protein L22-like protein: 2
60S ribosomal protein l23-like protein: 3
60S ribosomal protein L25-like protein: 4
60S ribosomal protein L26-like protein: 5
60S ribosomal protein L27: 6
60S ribosomal protein L28-like protein: 7
60S ribosomal protein l30-like protein: 8
Putative 60S ribosomal protein: 9
60S ribosomal protein L32-like protein: a
60S ribosomal protein l33-like protein: b
Ribosomal protein l34-like protein: c
dolichyl-diphosphooligosaccharide--protein glycotransferase: d
60S ribosomal protein L36: e
Ribosomal protein L37: f
60S ribosomal protein L38-like protein: g
Ribosomal protein eL39: h
60S ribosomal protein L43-like protein: i
Pre-rRNA-processing protein IPI3: jl
Pre-rRNA-processing protein RIX1: ku
Pre-rRNA-processing protein IPI1: m
Protein SDA1: n
Ribosomal protein: o
Ribosome assembly protein 4: p
Putative ribosomal protein: q
60S ribosomal protein l5-like protein: r
Putative 60S ribosomal protein: t
60S ribosomal protein l21-like protein: v
60S ribosomal protein L29: w
60S ribosomal protein L41-A: x

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
CF

D
CH

E
CK

F
CL

G
CN

H
CO

I
CQ

J
Cb

K
Cd

L
Cz

M
LA

N
LB

O
LC

P
LE

Q
LF

R
LG

S
LH

T
LK

U
LL

V
LM

W
LN

X
LO

Y
LP

Z
LQ

0
LR

1
LS

2
LU

3
LV

4
LX

5
LY

6
LZ

7
La

8
Lc

9
Ld

a
Le

b
Lf

c
Lg

d
Lh

e
Li

f
Lj

g
Lk

h
Ll

i
Lp

j
CT

l
CU

k
CW

u
CV

m
CS

n
CR

o
Lt

p
Ch

q
LJ

r
LD

t
Lq

v
LT

w
Lb

x
Lr

Large ribosomal subunit protein uL10

Nucleolar GTP-binding protein 1

Ribosome biogenesis protein NSA2 homolog

Putative GTP binding protein

Eukaryotic translation initiation factor 6

DUF2423 domain-containing protein

Ribosome biogenesis protein RLP24

Zinc finger domain-containing protein

Nucleolar GTP-binding protein 2

rRNA-processing protein

60S ribosomal protein L2-like protein

60S ribosomal protein L3-like protein

60S ribosomal protein L4-like protein

60S ribosomal protein L6

60S ribosomal protein l7-like protein

60S ribosomal protein L8

60S ribosomal protein l9-like 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 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

Pre-rRNA-processing protein IPI3

Pre-rRNA-processing protein RIX1

Pre-rRNA-processing protein IPI1

Protein SDA1

Ribosomal protein

Ribosome assembly protein 4

Putative ribosomal protein

60S ribosomal protein l5-like protein

Putative 60S ribosomal protein

60S ribosomal protein l21-like protein

60S ribosomal protein L29

60S ribosomal protein L41-A

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