SMTL ID : 8i9w.1

Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - Dbp10-3

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

GTP.1: 21 residues within 4Å: Chain I: N.176, V.177, G.178, K.179, S.180, S.181, V.193, E.194, P.195, Y.196, A.197, F.198, T.199, T.200, P.221, N.287, K.288, D.290, S.320, C.321, A.322 19 PLIP interactions: 19 interactions with chain I Hydrogen bonds: I:N.176, I:V.177, I:G.178, I:K.179, I:S.180, I:S.180, I:S.181, I:S.181, I:P.192, I:E.194, I:T.199, I:T.199, I:T.199, I:T.200, I:K.288, I:C.321 Salt bridges: I:K.179, I:D.290 pi-Cation interactions: I:K.288

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain R: C.6, C.9, C.32, R.33, C.36 2 PLIP interactions: 2 interactions with chain R Metal complexes: R:C.32, R:C.36 ZN.3: 4 residues within 4Å: Chain o: C.19, C.22, C.34, C.37 4 PLIP interactions: 4 interactions with chain o Metal complexes: o:C.19, o:C.22, o:C.34, o:C.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lau, B. et al., Mechanism of 5S RNP recruitment and helicase-surveilled rRNA maturation during pre-60S biogenesis. Embo Rep. (2023)

Release Date

2023-05-17

Peptides

Brix domain-containing protein: C
Ribosome biogenesis protein C8F11.04: D
Ribosome biogenesis protein ERB1: E
RNA helicase: F
Ribosome assembly factor mrt4: G
60S ribosome subunit biogenesis protein NIP7: H
Nucleolar GTP-binding protein 1: I
Putative RNA-binding protein: J
Pescadillo homolog: K
Ribosome biogenesis protein NSA2 homolog: L
Putative GTP binding protein: M
60S ribosomal protein l7-like protein: N4
Eukaryotic translation initiation factor 6: O
DUF2423 domain-containing protein: P
RNA methyltransferase nop2-like protein: Q
Ribosome biogenesis protein RLP24: R
Nucleolar protein 16: S
AdoMet-dependent rRNA methyltransferase SPB1: T
Nucleolar complex-associated protein 3: U
rRNA-processing protein EBP2: V
Putative 60S ribosomal protein: W
60S ribosomal subunit-like protein: X
Putative NOC2 family protein: Y
ATP-dependent RNA helicase DBP10: Z
rRNA-processing protein: 0
60S ribosomal protein L3-like protein: 1
60S ribosomal protein L4-like protein: 2
60S ribosomal protein L6: 3
60S ribosomal protein L8: 5
60S ribosomal protein l9-like protein: 6
60S ribosomal protein L12-like protein: 7
60S ribosomal protein L13: 8
60S ribosomal protein L14-like protein: 9
Ribosomal protein L15: a
60S ribosomal protein L16-like protein: b
60S ribosomal protein l17-like protein: c
Ribosomal protein L18-like protein: d
60S ribosomal protein L20: e
60S ribosomal protein l21-like protein: f
60S ribosomal protein l23-like protein: g
60S ribosomal protein L25-like protein: h
60S ribosomal protein L26-like protein: i
Putative 60S ribosomal protein: j
60S ribosomal protein L32-like protein: k
60S ribosomal protein l33-like protein: l
dolichyl-diphosphooligosaccharide--protein glycotransferase: m
60S ribosomal protein L36: n
Ribosomal protein L37: o
Ribosomal protein: p

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
CA

D
CB

E
CC

F
CE

G
CF

H
CG

I
CH

J
CI

K
CJ

L
CK

M
CL

N
CM

4
LF

O
CN

P
CO

Q
CP

R
CQ

S
CR

T
CS

U
CT

V
CU

W
CV

X
CX

Y
CY

Z
Cb

0
Cz

1
LB

2
LC

3
LE

5
LG

6
LH

7
LK

8
LL

9
LM

a
LN

b
LO

c
LP

d
LQ

e
LS

f
LT

g
LV

h
LX

i
LY

j
Ld

k
Le

l
Lf

m
Lh

n
Li

o
Lj

p
Lq

Brix domain-containing protein

Ribosome biogenesis protein C8F11.04

Ribosome biogenesis protein ERB1

RNA helicase

Ribosome assembly factor mrt4

60S ribosome subunit biogenesis protein NIP7

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

RNA methyltransferase nop2-like protein

Ribosome biogenesis protein RLP24

Nucleolar protein 16

AdoMet-dependent rRNA methyltransferase SPB1

Nucleolar complex-associated protein 3

rRNA-processing protein EBP2

Putative 60S ribosomal protein

60S ribosomal subunit-like protein

Putative NOC2 family protein

ATP-dependent RNA helicase DBP10

rRNA-processing protein

60S ribosomal protein L3-like protein

60S ribosomal protein L4-like protein

60S ribosomal protein L6

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

60S ribosomal protein L20

60S ribosomal protein l21-like protein

60S ribosomal protein l23-like protein

60S ribosomal protein L25-like protein

60S ribosomal protein L26-like protein

Putative 60S ribosomal protein

60S ribosomal protein L32-like protein

60S ribosomal protein l33-like protein

dolichyl-diphosphooligosaccharide--protein glycotransferase

60S ribosomal protein L36

Ribosomal protein L37

Ribosomal protein

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