SMTL ID : 8pv2.1

Chaetomium thermophilum pre-60S State 10 - pre-5S rotation with Ytm1-Erb1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

GTP.1: 24 residues within 4Å: Chain E: 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 E Hydrogen bonds: E:F.174, E:N.176, E:V.177, E:G.178, E:K.179, E:S.180, E:S.180, E:S.180, E:S.181, E:S.181, E:E.194, E:E.194, E:T.200, E:T.200, E:T.200, E:N.287, E:K.288, E:K.288, E:C.321, E:A.322 Salt bridges: E:K.179, E:K.179, E:D.290 pi-Cation interactions: E:K.288 GTP.5: 25 residues within 4Å: Chain A: U.2281 Chain L: 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 25 PLIP interactions: 25 interactions with chain L Hydrogen bonds: L:N.271, L:K.272, L:K.272, L:R.298, L:A.299, L:Y.334, L:N.336, L:V.337, L:G.338, L:K.339, L:S.340, L:S.341, L:S.341, L:A.355, L:P.356, L:G.359, L:E.360, L:T.361, L:T.361, L:G.380 Water bridges: L:S.340, L:T.361 Salt bridges: L:D.274, L:K.339, L:K.339

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain E: N.176, E.194, Y.196, T.199 Ligands: GTP.1 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:E.194, E:Y.196 MG.6: 5 residues within 4Å: Chain L: N.336, A.355, I.357, E.360 Ligands: GTP.5 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:A.355, L:I.357 MG.7: 5 residues within 4Å: Chain L: S.340, K.353, T.361, D.377 Ligands: GTP.5 4 PLIP interactions: 2 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:S.340, L:T.361, H2O.1, H2O.1

5 x ZN: ZINC ION(Non-covalent)

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

Large ribosomal subunit protein uL10: D
Nucleolar GTP-binding protein 1: E
Ribosome biogenesis protein NSA2 homolog: F
Putative GTP binding protein: G
Eukaryotic translation initiation factor 6: H
DUF2423 domain-containing protein: I
Ribosome biogenesis protein RLP24: J
Zinc finger domain-containing protein: K
Nucleolar GTP-binding protein 2: L
Ribosome production factor 2 homolog: M
Ribosome biogenesis regulatory protein: N
Ribosome assembly protein 4: O
rRNA-processing protein: P
60S ribosomal protein L2-like protein: Q
60S ribosomal protein L3-like protein: R
60S ribosomal protein L4-like protein: S
60S ribosomal protein l5-like protein: T
60S ribosomal protein L6: U
60S ribosomal protein l7-like protein: Vu
60S ribosomal protein L8: W
60S ribosomal protein l9-like protein: X
Putative ribosomal protein: Y
60S ribosomal protein L12-like protein: Z
60S ribosomal protein L13: 0
60S ribosomal protein L14-like protein: 1
Ribosomal protein L15: 2
60S ribosomal protein L16-like protein: 3
60S ribosomal protein l17-like protein: 4
Ribosomal protein L18-like protein: 5
Ribosomal protein L19: 6
60S ribosomal protein L20: 7
60S ribosomal protein l21-like protein: 8
60S ribosomal protein L22-like protein: 9
60S ribosomal protein l23-like protein: a
60S ribosomal protein L25-like protein: b
60S ribosomal protein L26-like protein: c
60S ribosomal protein L27: d
60S ribosomal protein L28-like protein: e
60S ribosomal protein l30-like protein: f
Putative 60S ribosomal protein: g
60S ribosomal protein L32-like protein: h
60S ribosomal protein l33-like protein: i
Ribosomal protein l34-like protein: j
dolichyl-diphosphooligosaccharide--protein glycotransferase: k
60S ribosomal protein L36: l
Ribosomal protein L37: m
60S ribosomal protein L38-like protein: n
Ribosomal protein eL39: o
60S ribosomal protein L43-like protein: p
Putative 60S ribosomal protein: q
Ribosome biogenesis protein ERB1: r
Ribosome biogenesis protein YTM1: s
Pescadillo homolog: t

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

D
CF

E
CH

F
CK

G
CL

H
CN

I
CO

J
CQ

K
Cb

L
Cd

M
Cf

N
Cg

O
Ch

P
Cz

Q
LA

R
LB

S
LC

T
LD

U
LE

V
LF

u
CM

W
LG

X
LH

Y
LJ

Z
LK

0
LL

1
LM

2
LN

3
LO

4
LP

5
LQ

6
LR

7
LS

8
LT

9
LU

a
LV

b
LX

c
LY

d
LZ

e
La

f
Lc

g
Ld

h
Le

i
Lf

j
Lg

k
Lh

l
Li

m
Lj

n
Lk

o
Ll

p
Lp

q
Lq

r
CC

s
CD

t
CJ

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

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 l7-like protein

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

Ribosome biogenesis protein ERB1

Ribosome biogenesis protein YTM1

Pescadillo homolog

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