SMTL ID : 8i9r.1

Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State 5S RNP

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-mer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: C.3041, G.3042 Chain L: K.38 No protein-ligand interaction detected (PLIP) ZN.2: 4 residues within 4Å: Chain 8: C.19, C.22, C.34, C.37 4 PLIP interactions: 4 interactions with chain 8 Metal complexes: 8:C.19, 8:C.22, 8:C.34, 8:C.37 ZN.3: 5 residues within 4Å: Chain b: I.10, C.15, C.28, C.38, C.43 1 PLIP interactions: 1 interactions with chain b Metal complexes: b:C.38

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
Nucleolar GTP-binding protein 1: G
Putative RNA-binding protein: H
Pescadillo homolog: I
60S ribosomal protein l7-like protein: JS
Eukaryotic translation initiation factor 6: K
Ribosome biogenesis protein RLP24: L
Nucleolar protein 16: M
rRNA-processing protein EBP2: N
Ribosomal RNA-processing protein 15: O
60S ribosomal protein L3-like protein: P
60S ribosomal protein L4-like protein: Q
60S ribosomal protein L6: R
60S ribosomal protein L8: 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
60S ribosomal protein L20: 0
60S ribosomal protein l21-like protein: 1
60S ribosomal protein l23-like protein: 2
60S ribosomal protein L26-like protein: 3
60S ribosomal protein L32-like protein: 4
60S ribosomal protein l33-like protein: 5
dolichyl-diphosphooligosaccharide--protein glycotransferase: 6
60S ribosomal protein L36: 7
Ribosomal protein L37: 8
Ribosomal RNA-processing protein 1: 9
Brix domain-containing protein: a
Protein MAK16: b
60S ribosome biogenesis protein Rrp14: c
Ribosome production factor 2 homolog: d
Brix domain-containing protein: e
RNA methyltransferase nop2-like protein: f
60S ribosome subunit biogenesis protein NIP7: g
Ribosomal protein: h
Ribosome biogenesis regulatory protein: i
Putative ribosomal protein: j
60S ribosomal protein l5-like protein: k
60S ribosomal subunit-like protein: m

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
CA

D
CB

E
CC

F
CE

G
CH

H
CI

I
CJ

J
CM

S
LF

K
CN

L
CQ

M
CR

N
CU

O
Ch

P
LB

Q
LC

R
LE

T
LG

U
LL

V
LM

W
LN

X
LO

Y
LP

Z
LQ

0
LS

1
LT

2
LV

3
LY

4
Le

5
Lf

6
Lh

7
Li

8
Lj

9
Cc

a
Cd

b
Ce

c
Cf

d
Cy

e
Cg

f
CP

g
CG

h
Lq

i
Cx

j
LJ

k
LD

m
CX

Brix domain-containing protein

Ribosome biogenesis protein C8F11.04

Ribosome biogenesis protein ERB1

RNA helicase

Nucleolar GTP-binding protein 1

Putative RNA-binding protein

Pescadillo homolog

60S ribosomal protein l7-like protein

Eukaryotic translation initiation factor 6

Ribosome biogenesis protein RLP24

Nucleolar protein 16

rRNA-processing protein EBP2

Ribosomal RNA-processing protein 15

60S ribosomal protein L3-like protein

60S ribosomal protein L4-like protein

60S ribosomal protein L6

60S ribosomal protein L8

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 L26-like 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 RNA-processing protein 1

Brix domain-containing protein

Protein MAK16

60S ribosome biogenesis protein Rrp14

Ribosome production factor 2 homolog

Brix domain-containing protein

RNA methyltransferase nop2-like protein

60S ribosome subunit biogenesis protein NIP7

Ribosomal protein

Ribosome biogenesis regulatory protein

Putative ribosomal protein

60S ribosomal protein l5-like protein

60S ribosomal subunit-like protein

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