SMTL ID : 8i9y.1

Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - Ytm1-2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

GTP.1: 16 residues within 4Å: Chain J: N.176, V.177, G.178, K.179, S.180, S.181, V.193, E.194, Y.196, A.197, T.199, K.288, D.290, S.320, C.321, A.322 20 PLIP interactions: 20 interactions with chain J Hydrogen bonds: J:N.176, J:N.176, J:V.177, J:G.178, J:K.179, J:S.180, J:S.180, J:S.180, J:S.181, J:S.181, J:Y.196, J:T.199, J:T.199, J:K.288, J:K.288, J:C.321, J:A.322 Salt bridges: J:K.179, J:D.290 pi-Cation interactions: J:K.288

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain S: C.6, C.9, C.32, C.36 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:C.6, S:C.9, S:C.32, S:C.36 ZN.3: 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

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
Ribosome biogenesis protein YTM1: F
RNA helicase: G
Ribosome assembly factor mrt4: H
60S ribosome subunit biogenesis protein NIP7: I
Nucleolar GTP-binding protein 1: J
Putative RNA-binding protein: K
Pescadillo homolog: L
Ribosome biogenesis protein NSA2 homolog: M
Putative GTP binding protein: N
60S ribosomal protein l7-like protein: O4
Eukaryotic translation initiation factor 6: P
DUF2423 domain-containing protein: Q
RNA methyltransferase nop2-like protein: R
Ribosome biogenesis protein RLP24: S
Nucleolar protein 16: T
AdoMet-dependent rRNA methyltransferase SPB1: U
Nucleolar complex-associated protein 3: V
rRNA-processing protein EBP2: W
Putative 60S ribosomal protein: X
60S ribosomal subunit-like protein: Y
Putative NOC2 family protein: 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
Ribosomal protein L19: e
60S ribosomal protein L20: f
60S ribosomal protein l21-like protein: g
60S ribosomal protein L22-like protein: h
60S ribosomal protein l23-like protein: i
60S ribosomal protein L25-like protein: j
60S ribosomal protein L26-like protein: k
60S ribosomal protein L27: 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
60S ribosomal protein L39: v
Ribosomal protein: w

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
CA

D
CB

E
CC

F
CD

G
CE

H
CF

I
CG

J
CH

K
CI

L
CJ

M
CK

N
CL

O
CM

4
LF

P
CN

Q
CO

R
CP

S
CQ

T
CR

U
CS

V
CT

W
CU

X
CV

Y
CX

Z
CY

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
LR

f
LS

g
LT

h
LU

i
LV

j
LX

k
LY

l
LZ

m
Lc

n
Ld

o
Le

p
Lf

q
Lg

r
Lh

s
Li

t
Lj

u
Lk

v
Ll

w
Lq

Brix domain-containing protein

Ribosome biogenesis protein C8F11.04

Ribosome biogenesis protein ERB1

Ribosome biogenesis protein YTM1

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

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

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 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

60S ribosomal protein L39

Ribosomal protein

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