SMTL ID : 6zqe.1

Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state Dis-A (Poly-Ala)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain U: T.99, D.100, C.101, C.130, C.140 No protein-ligand interaction detected (PLIP) ZN.2: 4 residues within 4Å: Chain e: C.40, C.56, S.58, C.59 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cheng, J. et al., 90 S pre-ribosome transformation into the primordial 40 S subunit. Science (2020)

Release Date

2020-09-23

Peptides

Periodic tryptophan protein 2: A
Nucleolar complex protein 14: B
Something about silencing protein 10: C
U3 small nucleolar RNA-associated protein 4: D
U3 small nucleolar RNA-associated protein 9: E
U3 small nucleolar RNA-associated protein 8: F
U3 small nucleolar RNA-associated protein 5: G
U3 small nucleolar RNA-associated protein 10: H
U3 small nucleolar RNA-associated protein 11: I
U3 small nucleolar RNA-associated protein 12: J
U3 small nucleolar RNA-associated protein 13: K
U3 small nucleolar RNA-associated protein 14: L
U3 small nucleolar RNA-associated protein 15: M
Bud site selection protein 21: N
NET1-associated nuclear protein 1: O
U3 small nucleolar RNA-associated protein 18: P
Nucleolar complex protein 4: Q
U3 small nucleolar RNA-associated protein 20: R
U3 small nucleolar RNA-associated protein 21: S
U3 small nucleolar RNA-associated protein 22: T
rRNA-processing protein FCF1: U
rRNA 2'-O-methyltransferase fibrillarin: VW
Nucleolar protein 56: X
Nucleolar protein 58: Y
13 kDa ribonucleoprotein-associated protein: Z0
Ribosomal RNA-processing protein 9: 1
U3 small nucleolar ribonucleoprotein protein IMP3: 2
U3 small nucleolar ribonucleoprotein protein IMP4: 3
U3 small nucleolar RNA-associated protein MPP10: 4
Ribosome biogenesis protein BMS1: 5
RNA 3'-terminal phosphate cyclase-like protein: 6
Ribosomal RNA-processing protein 7: 7
Probable ATP-dependent RNA helicase DHR1: 8
Ribosomal RNA small subunit methyltransferase NEP1: 9a
Essential nuclear protein 1: b
Dimethyladenosine transferase: c
rRNA-processing protein FCF2: d
40S ribosomal protein S27-A: e
Pre-rRNA-processing protein PNO1: f
40S ribosomal protein S1-A: g
40S ribosomal protein S4-A: h
40S ribosomal protein S5: i
40S ribosomal protein S6-A: j
40S ribosomal protein S7-A: k
40S ribosomal protein S8-A: l
40S ribosomal protein S9-A: m
40S ribosomal protein S11-A: n
40S ribosomal protein S13: o
40S ribosomal protein S14-A: p
40S ribosomal protein S16-A: q
40S ribosomal protein S18-A: r
40S ribosomal protein S19-A: s
40S ribosomal protein S22-A: t
40S ribosomal protein S23-A: u
40S ribosomal protein S24-A: v
40S ribosomal protein S28-A: w

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
UA

B
UB

C
UC

D
UD

E
UE

F
UH

G
UI

H
UJ

I
UK

J
UL

K
UM

L
UN

M
UO

N
UP

O
UQ

P
UR

Q
US

R
UT

S
UU

T
UV

U
UX

V
CA

W
CB

X
CD

Y
CE

Z
CF

0
CG

1
CH

2
CI

3
CJ

4
CK

5
CL

6
CM

7
CN

8
JD

9
JF

a
JG

b
JH

c
JL

d
JM

e
Db

f
JJ

g
DA

h
DE

i
DF

j
DG

k
DH

l
DI

m
DJ

n
DL

o
DN

p
DO

q
DQ

r
DS

s
DT

t
DW

u
DX

v
DY

w
Dc

Periodic tryptophan protein 2

Nucleolar complex protein 14

Something about silencing protein 10

U3 small nucleolar RNA-associated protein 4

U3 small nucleolar RNA-associated protein 9

U3 small nucleolar RNA-associated protein 8

U3 small nucleolar RNA-associated protein 5

U3 small nucleolar RNA-associated protein 10

U3 small nucleolar RNA-associated protein 11

U3 small nucleolar RNA-associated protein 12

U3 small nucleolar RNA-associated protein 13

U3 small nucleolar RNA-associated protein 14

U3 small nucleolar RNA-associated protein 15

Bud site selection protein 21

NET1-associated nuclear protein 1

U3 small nucleolar RNA-associated protein 18

Nucleolar complex protein 4

U3 small nucleolar RNA-associated protein 20

U3 small nucleolar RNA-associated protein 21

U3 small nucleolar RNA-associated protein 22

rRNA-processing protein FCF1

rRNA 2'-O-methyltransferase fibrillarin

Nucleolar protein 56

Nucleolar protein 58

13 kDa ribonucleoprotein-associated protein

Ribosomal RNA-processing protein 9

U3 small nucleolar ribonucleoprotein protein IMP3

U3 small nucleolar ribonucleoprotein protein IMP4

U3 small nucleolar RNA-associated protein MPP10

Ribosome biogenesis protein BMS1

RNA 3'-terminal phosphate cyclase-like protein

Ribosomal RNA-processing protein 7

Probable ATP-dependent RNA helicase DHR1

Ribosomal RNA small subunit methyltransferase NEP1

Essential nuclear protein 1

Dimethyladenosine transferase

rRNA-processing protein FCF2

40S ribosomal protein S27-A

Pre-rRNA-processing protein PNO1

40S ribosomal protein S1-A

40S ribosomal protein S4-A

40S ribosomal protein S5

40S ribosomal protein S6-A

40S ribosomal protein S7-A

40S ribosomal protein S8-A

40S ribosomal protein S9-A

40S ribosomal protein S11-A

40S ribosomal protein S13

40S ribosomal protein S14-A

40S ribosomal protein S16-A

40S ribosomal protein S18-A

40S ribosomal protein S19-A

40S ribosomal protein S22-A

40S ribosomal protein S23-A

40S ribosomal protein S24-A

40S ribosomal protein S28-A

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