SMTL ID : 6rxt.1

Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum, state A

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain P: C.103, C.132, H.134, C.142, R.146 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:C.103, P:C.132, P:H.134, P:C.142

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

GTP.2: 15 residues within 4Å: Chain Z: G.78, V.79, G.80, K.81, T.82, T.83, N.121, T.171, H.172, D.174, L.175, L.206, S.207, V.209, Y.214 19 PLIP interactions: 19 interactions with chain Z Hydrogen bonds: Z:G.78, Z:V.79, Z:G.80, Z:G.80, Z:K.81, Z:T.82, Z:T.82, Z:T.83, Z:T.83, Z:N.121, Z:T.171, Z:H.172, Z:S.207 Salt bridges: Z:K.81, Z:K.81, Z:D.174 pi-Stacking: Z:H.172, Z:H.172 pi-Cation interactions: Z:H.172

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain Z: T.82, E.118 1 PLIP interactions: 1 interactions with chain Z Metal complexes: Z:T.82

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cheng, J. et al., Thermophile 90S Pre-ribosome Structures Reveal the Reverse Order of Co-transcriptional 18S rRNA Subdomain Integration. Mol.Cell (2019)

Release Date

2019-08-14

Peptides

Periodic tryptophan protein 2-like protein: A
Utp2: B
Utp3: C
Utp4: D
Utp6: E
Utp7: F
UTP10: G
U3 small nucleolar RNA-associated protein 11: H
Utp12: I
Utp13": J
Utp14: K
Utp15: L
Utp17: M
Utp18: N
Putative U3 snoRNP protein: O
Utp24: P
Utp30: Q
Nop1: RS
Putative nucleolar protein: T
Nop58: U
snu13: VW
Rrp9: X
RNA 3'-terminal phosphate cyclase-like protein: Y
Bms1: Z
Imp3: 0
Putative U3 small nucleolar ribonucleoprotein: 1
Putative U3 small nucleolar ribonucleoprotein protein: 2
Sof1: 3
Emg1: 45
KRR1 small subunit processome component: 6
Pre-rRNA-processing protein PNO1: 7
Kre33: 89
Fcf2: a
40S ribosomal protein S1: b
40S ribosomal protein s5-like protein: c
40S ribosomal protein S7: d
40S ribosomal protein s9-like protein: e
40S ribosomal protein S13-like protein: f
40S ribosomal protein S14-like protein: g
40S ribosomal protein S16-like protein: h
40S ribosomal protein S22-like protein: i
40S ribosomal protein s23-like protein: j
40S ribosomal protein S28-like protein: k
Faf1: l
Utp8: o
Utp5": pt
Noc4: q
Putative ribosomal protein: r
Enp1: s
Utp16: u

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
UA

B
UB

C
UC

D
UD

E
UF

F
UG

G
UJ

H
UK

I
UL

J
UM

K
UN

L
UO

M
UQ

N
UR

O
UU

P
UX

Q
UZ

R
CA

S
CB

T
CC

U
CD

V
CE

W
CF

X
CG

Y
CH

Z
CI

0
CJ

1
CK

2
CL

3
CM

4
CN

5
CO

6
CP

7
CQ

8
CR

9
CS

a
CT

b
Ca

c
Cc

d
Ce

e
Cg

f
Ch

g
Ci

h
Cj

i
Cm

j
Cn

k
Cp

l
CU

o
UH

p
UE

t
UI

q
US

r
Cl

s
CX

u
UP

Periodic tryptophan protein 2-like protein

Utp2

Utp3

Utp4

Utp6

Utp7

UTP10

U3 small nucleolar RNA-associated protein 11

Utp12

Utp13"

Utp14

Utp15

Utp17

Utp18

Putative U3 snoRNP protein

Utp24

Utp30

Nop1

Putative nucleolar protein

Nop58

snu13

Rrp9

RNA 3'-terminal phosphate cyclase-like protein

Bms1

Imp3

Putative U3 small nucleolar ribonucleoprotein

Putative U3 small nucleolar ribonucleoprotein protein

Sof1

Emg1

KRR1 small subunit processome component

Pre-rRNA-processing protein PNO1

Kre33

Fcf2

40S ribosomal protein S1

40S ribosomal protein s5-like protein

40S ribosomal protein S7

40S ribosomal protein s9-like protein

40S ribosomal protein S13-like protein

40S ribosomal protein S14-like protein

40S ribosomal protein S16-like protein

40S ribosomal protein S22-like protein

40S ribosomal protein s23-like protein

40S ribosomal protein S28-like protein

Faf1

Utp8

Utp5"

Noc4

Putative ribosomal protein

Enp1

Utp16

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