SMTL ID : 8fl0.1

Human nucleolar pre-60S ribosomal subunit (State H)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

MG.1: 1 residues within 4Å: Chain B: G.2320 No protein-ligand interaction detected (PLIP) MG.2: 1 residues within 4Å: Chain B: U.1905 No protein-ligand interaction detected (PLIP) MG.3: 1 residues within 4Å: Chain B: G.1904 No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Chain B: G.2278 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Chain B: U.1348 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Chain B: G.1887 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain B: C.1915, G.1916, A.1917 Chain E: K.25 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain B: U.4752, U.4753, U.4947 Chain N: K.52 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain B: A.1908, G.1909 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain B: U.2312, G.2314 No protein-ligand interaction detected (PLIP) MG.11: 1 residues within 4Å: Chain B: G.1885 No protein-ligand interaction detected (PLIP) MG.12: 4 residues within 4Å: Chain B: U.750, G.752, G.910, U.911 No protein-ligand interaction detected (PLIP) MG.13: 1 residues within 4Å: Chain B: C.1963 No protein-ligand interaction detected (PLIP) MG.14: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.15: 1 residues within 4Å: Chain B: A.4464 No protein-ligand interaction detected (PLIP) MG.16: 1 residues within 4Å: Chain B: C.2051 No protein-ligand interaction detected (PLIP) MG.17: 4 residues within 4Å: Chain B: G.4631, U.4632, G.4666, C.4667 No protein-ligand interaction detected (PLIP) MG.18: 5 residues within 4Å: Chain B: A.5007, C.5008, G.5009, U.5039, U.5040 No protein-ligand interaction detected (PLIP) MG.19: 3 residues within 4Å: Chain B: A.4205, C.4206 Chain D: R.58 No protein-ligand interaction detected (PLIP) MG.20: 6 residues within 4Å: Chain B: C.4944 Chain N: T.57, V.58, T.59, N.65, T.67 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:T.59 MG.22: 4 residues within 4Å: Chain P: S.324, T.345, D.361 Ligands: GTP.21 1 PLIP interactions: 1 interactions with chain P Metal complexes: P:T.345 MG.26: 3 residues within 4Å: Chain 2: S.182, T.202 Ligands: GDP.24 2 PLIP interactions: 2 interactions with chain 2 Metal complexes: 2:S.182, 2:T.202

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

GTP.21: 24 residues within 4Å: Chain P: N.255, K.256, D.258, L.259, H.282, A.283, P.319, N.320, V.321, G.322, K.323, S.324, S.325, V.338, A.339, P.340, I.341, A.342, G.343, E.344, T.345, G.364 Ligands: MG.22, K.23 24 PLIP interactions: 24 interactions with chain P Hydrogen bonds: P:N.255, P:K.256, P:K.256, P:H.282, P:A.283, P:N.320, P:V.321, P:G.322, P:K.323, P:S.324, P:S.324, P:S.324, P:S.325, P:S.325, P:A.339, P:P.340, P:G.343, P:E.344, P:T.345, P:G.364 Salt bridges: P:D.258, P:K.323, P:K.323 pi-Cation interactions: P:K.256

2 x K: POTASSIUM ION(Non-covalent)

K.23: 4 residues within 4Å: Chain P: N.320, A.339, I.341 Ligands: GTP.21 2 PLIP interactions: 2 interactions with chain P Metal complexes: P:A.339, P:I.341 K.25: 5 residues within 4Å: Chain 2: N.178, Q.196, Y.198, T.201 Ligands: GDP.24 2 PLIP interactions: 2 interactions with chain 2 Metal complexes: 2:Q.196, 2:Y.198

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.24: 18 residues within 4Å: Chain 2: N.178, V.179, G.180, K.181, S.182, S.183, V.195, Q.196, P.197, N.289, K.290, D.292, V.293, S.321, T.322, L.323 Ligands: K.25, MG.26 17 PLIP interactions: 17 interactions with chain 2 Hydrogen bonds: 2:N.178, 2:V.179, 2:G.180, 2:K.181, 2:S.182, 2:S.183, 2:Q.196, 2:N.289, 2:K.290, 2:K.290, 2:S.321, 2:T.322, 2:T.322, 2:L.323 Salt bridges: 2:K.181, 2:D.292 pi-Cation interactions: 2:K.290

1 x ZN: ZINC ION(Non-covalent)

ZN.27: 4 residues within 4Å: Chain 4: C.6, C.9, C.32, C.36 4 PLIP interactions: 4 interactions with chain 4 Metal complexes: 4:C.6, 4:C.9, 4:C.32, 4:C.36

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vanden Broeck, A. et al., Principles of human pre-60 S biogenesis. Science (2023)

Release Date

2023-07-12

Peptides

60S ribosomal protein L12: A
60S ribosomal protein L11: D
60S ribosomal protein L13a: E
60S ribosomal protein L14: F
60S ribosomal protein L18: G
60S ribosomal protein L18a: H
60S ribosomal protein L21: I
60S ribosomal protein L23: J
60S ribosomal protein L28: K
60S ribosomal protein L3: L
60S ribosomal protein L32: M
60S ribosomal protein L35a: N
Guanine nucleotide-binding protein-like 3: O
Nucleolar GTP-binding protein 2: P
Ribosome production factor 2 homolog: Q
Ribosome biogenesis protein NSA2 homolog: R
Notchless protein homolog 1: S
Protein LLP homolog: T
Coiled-coil domain-containing protein 86: U
60S ribosomal protein L4: V
60S ribosomal protein L5: W
60S ribosomal protein L6: X
60S ribosomal protein L7: Y
60S ribosomal protein L9: Z
Eukaryotic translation initiation factor 6: 0
mRNA turnover protein 4 homolog: 1
GTP-binding protein 4: 2
Ribosome biogenesis regulatory protein homolog: 3
Probable ribosome biogenesis protein RLP24: 4

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
BA

D
L5

E
L7

F
L8

G
LB

H
LC

I
LE

J
LG

K
LL

L
LN

M
LQ

N
LT

O
NB

P
NC

Q
ND

R
NF

S
NJ

T
NK

U
NZ

V
SA

W
SB

X
SC

Y
SD

Z
SG

0
SK

1
SQ

2
SR

3
ST

4
SV

60S ribosomal protein L12

60S ribosomal protein L11

60S ribosomal protein L13a

60S ribosomal protein L14

60S ribosomal protein L18

60S ribosomal protein L18a

60S ribosomal protein L21

60S ribosomal protein L23

60S ribosomal protein L28

60S ribosomal protein L3

60S ribosomal protein L32

60S ribosomal protein L35a

Guanine nucleotide-binding protein-like 3

Nucleolar GTP-binding protein 2

Ribosome production factor 2 homolog

Ribosome biogenesis protein NSA2 homolog

Notchless protein homolog 1

Protein LLP homolog

Coiled-coil domain-containing protein 86

60S ribosomal protein L4

60S ribosomal protein L5

60S ribosomal protein L6

60S ribosomal protein L7

60S ribosomal protein L9

Eukaryotic translation initiation factor 6

mRNA turnover protein 4 homolog

GTP-binding protein 4

Ribosome biogenesis regulatory protein homolog

Probable ribosome biogenesis protein RLP24

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