SMTL ID : 6zqa.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain V: C.101, C.130, C.140 No protein-ligand interaction detected (PLIP) ZN.5: 4 residues within 4Å: Chain t: C.40, N.42, C.56, C.59 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain 7: T.83 Ligands: GTP.3 No protein-ligand interaction detected (PLIP)

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

GTP.3: 10 residues within 4Å: Chain 7: P.78, T.80, G.81, K.82, T.83, T.84, S.208, G.209, V.210 Ligands: MG.4 5 PLIP interactions: 5 interactions with chain 7 Hydrogen bonds: 7:T.80, 7:G.81, 7:K.82, 7:T.83, 7:T.84

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 5: E
U3 small nucleolar RNA-associated protein 6: F
U3 small nucleolar RNA-associated protein 7: G
U3 small nucleolar RNA-associated protein 8: H
U3 small nucleolar RNA-associated protein 9: I
U3 small nucleolar RNA-associated protein 10: J
U3 small nucleolar RNA-associated protein 11: K
U3 small nucleolar RNA-associated protein 12: L
U3 small nucleolar RNA-associated protein 13: M
U3 small nucleolar RNA-associated protein 14: N
U3 small nucleolar RNA-associated protein 15: O
Bud site selection protein 21: P
NET1-associated nuclear protein 1: Q
U3 small nucleolar RNA-associated protein 18: R
Nucleolar complex protein 4: S
U3 small nucleolar RNA-associated protein 21: T
U3 small nucleolar RNA-associated protein 22: U
rRNA-processing protein FCF1: V
Ribosome biogenesis protein UTP30: W
rRNA 2'-O-methyltransferase fibrillarin: XY
Nucleolar protein 56: Z
Nucleolar protein 58: 0
13 kDa ribonucleoprotein-associated protein: 12
Ribosomal RNA-processing protein 9: 3
U3 small nucleolar ribonucleoprotein protein IMP3: 4
U3 small nucleolar ribonucleoprotein protein IMP4: 5
U3 small nucleolar RNA-associated protein MPP10: 6
Ribosome biogenesis protein BMS1: 7
RNA 3'-terminal phosphate cyclase-like protein: 8
Ribosomal RNA-processing protein 7: 9
Ribosomal RNA small subunit methyltransferase NEP1: ab
Essential nuclear protein 1: c
Pre-rRNA-processing protein PNO1: d
rRNA-processing protein FCF2: e
Protein FAF1: f
KRR1 small subunit processome component: g
Protein SOF1: h
Regulator of rDNA transcription protein 14: i
40S ribosomal protein S1-A: j
Rps5p: k
40S ribosomal protein S7-A: l
40S ribosomal protein S9-A: m
40S ribosomal protein S13: n
40S ribosomal protein S14-A: o
40S ribosomal protein S16-A: p
40S ribosomal protein S18-A: q
40S ribosomal protein S22-A: r
40S ribosomal protein S23-A: s
40S ribosomal protein S27-A: t
40S ribosomal protein S28-A: u

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
UA

B
UB

C
UC

D
UD

E
UE

F
UF

G
UG

H
UH

I
UI

J
UJ

K
UK

L
UL

M
UM

N
UN

O
UO

P
UP

Q
UQ

R
UR

S
US

T
UU

U
UV

V
UX

W
UZ

X
CA

Y
CB

Z
CD

0
CE

1
CF

2
CG

3
CH

4
CI

5
CJ

6
CK

7
CL

8
CM

9
CN

a
JF

b
JG

c
JH

d
JJ

e
JM

f
JN

g
JO

h
JP

i
JQ

j
DA

k
DF

l
DH

m
DJ

n
DN

o
DO

p
DQ

q
DS

r
DW

s
DX

t
Db

u
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 5

U3 small nucleolar RNA-associated protein 6

U3 small nucleolar RNA-associated protein 7

U3 small nucleolar RNA-associated protein 8

U3 small nucleolar RNA-associated protein 9

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 21

U3 small nucleolar RNA-associated protein 22

rRNA-processing protein FCF1

Ribosome biogenesis protein UTP30

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

Ribosomal RNA small subunit methyltransferase NEP1

Essential nuclear protein 1

Pre-rRNA-processing protein PNO1

rRNA-processing protein FCF2

Protein FAF1

KRR1 small subunit processome component

Protein SOF1

Regulator of rDNA transcription protein 14

40S ribosomal protein S1-A

Rps5p

40S ribosomal protein S7-A

40S ribosomal protein S9-A

40S ribosomal protein S13

40S ribosomal protein S14-A

40S ribosomal protein S16-A

40S ribosomal protein S18-A

40S ribosomal protein S22-A

40S ribosomal protein S23-A

40S ribosomal protein S27-A

40S ribosomal protein S28-A

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