SMTL ID : 7naf.1

State E2 nucleolar 60S ribosomal biogenesis intermediate - Spb1-MTD local model

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x ALA- LYS- SER- LEU- ARG- ALA: UPF0642 protein YBL028C(Non-functional Binders)

ALA-LYS-SER-LEU-ARG-ALA.1: 9 residues within 4Å: Chain A: U.216, A.217, C.218, G.229, U.270, U.271, G.272, A.349, U.350 No protein-ligand interaction detected (PLIP)

1 x MET- ARG- VAL- ARG- LYS- ARG- GLN: Nuclear GTP-binding protein NUG1(Non-functional Binders)

MET-ARG-VAL-ARG-LYS-ARG-GLN.2: 9 residues within 4Å: Chain A: A.40, G.44, C.210, U.211, A.227, A.228, G.229, U.350, C.351 No protein-ligand interaction detected (PLIP)

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.3: 17 residues within 4Å: Chain A: G.239, U.240 Chain F: S.29, C.54, A.55, A.56, P.57, S.59, D.78, I.79, V.80, D.94, I.95, D.119, G.120, A.121, L.138 10 PLIP interactions: 10 interactions with chain F Hydrophobic interactions: F:D.119 Hydrogen bonds: F:S.29, F:C.54, F:S.59, F:S.59, F:I.79, F:D.94, F:D.94, F:D.119, F:D.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cruz, V.E. et al., Sequence-specific remodeling of a topologically complex RNP substrate by Spb4. Nat.Struct.Mol.Biol. (2022)

Release Date

2022-11-09

Peptides

Ribosomal RNA-processing protein 17: B
Nucleolar complex protein 2: C
60S ribosomal protein L23-A: D
Ribosome biogenesis protein RLP24: E
27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase: F
60S ribosome biogenesis factor Nog1: G
60S ribosomal protein L31-A: H
60S ribosomal protein L22-A: I
60S ribosome ribosomal protein L19A: J
60S ribosomal protein L30: K
60S ribosomal protein L3: L
Eukaryotic translation initiation factor 6: M
25S rRNA (cytosine(2870)-C(5))-methyltransferase: N

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
5

C
8

D
V

E
u

F
w

G
b

H
d

I
U

J
R

K
c

L
B

M
y

N
q

Ribosomal RNA-processing protein 17

Nucleolar complex protein 2

60S ribosomal protein L23-A

Ribosome biogenesis protein RLP24

27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase

60S ribosome biogenesis factor Nog1

60S ribosomal protein L31-A

60S ribosomal protein L22-A

60S ribosome ribosomal protein L19A

60S ribosomal protein L30

60S ribosomal protein L3

Eukaryotic translation initiation factor 6

25S rRNA (cytosine(2870)-C(5))-methyltransferase

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