SMTL ID : 8e5t.1

Yeast co-transcriptional Noc1-Noc2 RNP assembly checkpoint intermediate

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

MG.1: 2 residues within 4Å: Chain C: V.312 Chain Z: G.1362 No protein-ligand interaction detected (PLIP) MG.2: 3 residues within 4Å: Chain C: Q.304, A.305 Chain Z: A.1352 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain F: Q.19 Chain Z: G.1349 No protein-ligand interaction detected (PLIP) MG.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain Z: U.1167, U.1168 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain Z: U.508, G.582, G.583 No protein-ligand interaction detected (PLIP) MG.14: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.15: 2 residues within 4Å: Chain Z: G.518, A.521 No protein-ligand interaction detected (PLIP) MG.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.18: 1 residues within 4Å: Chain Z: U.563 No protein-ligand interaction detected (PLIP) MG.19: 1 residues within 4Å: Chain Z: G.513 No protein-ligand interaction detected (PLIP) MG.20: 2 residues within 4Å: Chain F: K.150 Chain Z: U.508 No protein-ligand interaction detected (PLIP) MG.21: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.22: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.23: 1 residues within 4Å: Chain Z: C.1358 No protein-ligand interaction detected (PLIP) MG.24: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.25: 2 residues within 4Å: Chain Z: G.950, G.1367 No protein-ligand interaction detected (PLIP) MG.26: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.27: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.28: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.29: 2 residues within 4Å: Chain L: Q.73 Chain Z: G.742 No protein-ligand interaction detected (PLIP) MG.30: 2 residues within 4Å: Chain Z: U.724, G.726 No protein-ligand interaction detected (PLIP) MG.31: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.32: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.33: 1 residues within 4Å: Chain Z: G.1413 No protein-ligand interaction detected (PLIP) MG.34: 1 residues within 4Å: Chain Z: G.1383 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain D: I.10, C.15, C.28, C.38, C.43 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.15, D:C.28, D:C.38, D:C.43

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sanghai, Z.A. et al., A co-transcriptional ribosome assembly checkpoint controls nascent large ribosomal subunit maturation. Nat.Struct.Mol.Biol. (2023)

Release Date

2023-04-12

Peptides

Ribosome biogenesis protein MAK21: A
NOC2 isoform 1: B
60S ribosomal protein L4-A: C
Protein MAK16: D
60S ribosomal protein L6-A: E
60S ribosomal protein L7-A: F
60S ribosomal protein L8-A: G
Proteasome-interacting protein CIC1: H
60S ribosomal protein L13-A: I
60S ribosomal protein L14-A: J
60S ribosomal protein L15-A: K
60S ribosomal protein L18-A: L
60S ribosomal protein L20-A: M
Ribosome biogenesis protein BRX1: N
60S ribosomal protein L32: O
60S ribosomal protein L33-A: P
60S ribosomal protein L36-A: Q
rRNA-processing protein EBP2: R
Pescadillo homolog: S
Ribosome biogenesis protein 15: T
ATP-dependent RNA helicase HAS1: U
Ribosome biogenesis protein ERB1: V
Ribosome biogenesis protein RLP7: W
Ribosomal RNA-processing protein 1: X
60S ribosomal protein L16-A: Y

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
5

B
6

C
C

D
D

E
E

F
F

G
G

H
K

I
L

J
M

K
N

L
Q

M
S

N
b

O
e

P
f

Q
i

R
m

S
n

T
o

U
p

V
s

W
t

X
z

Y
O

Ribosome biogenesis protein MAK21

NOC2 isoform 1

60S ribosomal protein L4-A

Protein MAK16

60S ribosomal protein L6-A

60S ribosomal protein L7-A

60S ribosomal protein L8-A

Proteasome-interacting protein CIC1

60S ribosomal protein L13-A

60S ribosomal protein L14-A

60S ribosomal protein L15-A

60S ribosomal protein L18-A

60S ribosomal protein L20-A

Ribosome biogenesis protein BRX1

60S ribosomal protein L32

60S ribosomal protein L33-A

60S ribosomal protein L36-A

rRNA-processing protein EBP2

Pescadillo homolog

Ribosome biogenesis protein 15

ATP-dependent RNA helicase HAS1

Ribosome biogenesis protein ERB1

Ribosome biogenesis protein RLP7

Ribosomal RNA-processing protein 1

60S ribosomal protein L16-A

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