SMTL ID : 8fl6.1

Human nuclear pre-60S ribosomal subunit (State J1)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

MG.1: 1 residues within 4Å: Chain B: A.20 No protein-ligand interaction detected (PLIP) MG.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.3: 1 residues within 4Å: Chain B: U.18 No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Chain B: G.12 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain 1: G.55, T.70, H.73 Chain D: G.2584 2 PLIP interactions: 2 interactions with chain 1 Metal complexes: 1:T.70, 1:H.73 MG.6: 1 residues within 4Å: Chain D: G.240 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain D: A.62, U.333 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Chain D: A.61 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain 0: T.17 Chain D: G.2320 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Chain D: U.1905 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain D: C.112, G.154, C.155, G.156 No protein-ligand interaction detected (PLIP) MG.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.13: 1 residues within 4Å: Chain D: G.1335 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain D: A.1337, G.2343, U.2344 No protein-ligand interaction detected (PLIP) MG.15: 1 residues within 4Å: Chain D: G.2348 No protein-ligand interaction detected (PLIP) MG.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.17: 2 residues within 4Å: Chain D: C.1898, G.2278 No protein-ligand interaction detected (PLIP) MG.18: 1 residues within 4Å: Chain D: A.235 No protein-ligand interaction detected (PLIP) MG.19: 1 residues within 4Å: Chain D: U.231 No protein-ligand interaction detected (PLIP) MG.20: 1 residues within 4Å: Chain D: U.1348 No protein-ligand interaction detected (PLIP) MG.21: 2 residues within 4Å: Chain D: A.101, G.102 No protein-ligand interaction detected (PLIP) MG.22: 1 residues within 4Å: Chain B: C.35 No protein-ligand interaction detected (PLIP) MG.23: 1 residues within 4Å: Chain D: A.56 No protein-ligand interaction detected (PLIP) MG.24: 3 residues within 4Å: Chain D: G.415, U.416, G.417 No protein-ligand interaction detected (PLIP) MG.25: 1 residues within 4Å: Chain D: A.1888 No protein-ligand interaction detected (PLIP) MG.26: 3 residues within 4Å: Chain D: G.1916, A.1917 Chain H: K.25 No protein-ligand interaction detected (PLIP) MG.27: 4 residues within 4Å: Chain D: C.83, G.85, G.1383, C.1384 No protein-ligand interaction detected (PLIP) MG.28: 2 residues within 4Å: Chain D: A.1908, G.1909 No protein-ligand interaction detected (PLIP) MG.29: 4 residues within 4Å: Chain D: U.750, G.752, G.910, U.911 No protein-ligand interaction detected (PLIP) MG.30: 2 residues within 4Å: Chain D: U.4588, G.4713 No protein-ligand interaction detected (PLIP) MG.31: 1 residues within 4Å: Chain D: A.4464 No protein-ligand interaction detected (PLIP) MG.32: 3 residues within 4Å: Chain D: G.356, C.358 Chain f: G.99 No protein-ligand interaction detected (PLIP) MG.33: 2 residues within 4Å: Chain D: A.4479 Chain l: N.169 No protein-ligand interaction detected (PLIP) MG.34: 2 residues within 4Å: Chain D: G.356, A.359 No protein-ligand interaction detected (PLIP) MG.35: 3 residues within 4Å: Chain D: A.2349, U.2350, C.2351 No protein-ligand interaction detected (PLIP) MG.36: 2 residues within 4Å: Chain D: G.1667, G.2280 No protein-ligand interaction detected (PLIP) MG.37: 3 residues within 4Å: Chain D: C.14, A.15, G.16 No protein-ligand interaction detected (PLIP) MG.38: 1 residues within 4Å: Chain D: A.51 No protein-ligand interaction detected (PLIP) MG.39: 2 residues within 4Å: Chain D: G.48, U.96 No protein-ligand interaction detected (PLIP) MG.40: 1 residues within 4Å: Chain D: U.3920 No protein-ligand interaction detected (PLIP) MG.41: 2 residues within 4Å: Chain D: G.2514, G.2516 No protein-ligand interaction detected (PLIP) MG.42: 2 residues within 4Å: Chain D: U.2362, A.2363 No protein-ligand interaction detected (PLIP) MG.43: 1 residues within 4Å: Chain D: C.2792 No protein-ligand interaction detected (PLIP) MG.44: 3 residues within 4Å: Chain D: G.1633, G.4534, A.4535 No protein-ligand interaction detected (PLIP) MG.45: 1 residues within 4Å: Chain D: G.3899 No protein-ligand interaction detected (PLIP) MG.46: 1 residues within 4Å: Chain D: A.2370 No protein-ligand interaction detected (PLIP) MG.47: 3 residues within 4Å: Chain D: C.2393, C.2817, C.2818 No protein-ligand interaction detected (PLIP) MG.48: 1 residues within 4Å: Chain D: A.4533 No protein-ligand interaction detected (PLIP) MG.49: 3 residues within 4Å: Chain D: U.3920, G.4184 Chain k: P.206 No protein-ligand interaction detected (PLIP) MG.50: 3 residues within 4Å: Chain D: A.2845, G.2848, G.3839 No protein-ligand interaction detected (PLIP) MG.51: 1 residues within 4Å: Chain D: C.3636 No protein-ligand interaction detected (PLIP) MG.52: 3 residues within 4Å: Chain D: G.2421, C.2422, A.2423 No protein-ligand interaction detected (PLIP) MG.53: 3 residues within 4Å: Chain D: U.316, U.4353, U.4354 No protein-ligand interaction detected (PLIP) MG.54: 4 residues within 4Å: Chain D: A.2870, A.2881, G.3628, A.3629 No protein-ligand interaction detected (PLIP) MG.55: 2 residues within 4Å: Chain D: U.1659, G.2348 No protein-ligand interaction detected (PLIP) MG.56: 2 residues within 4Å: Chain 6: Q.30 Chain D: A.1534 No protein-ligand interaction detected (PLIP) MG.57: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.58: 4 residues within 4Å: Chain D: C.1675, C.1676, G.4377, A.4378 No protein-ligand interaction detected (PLIP) MG.59: 2 residues within 4Å: Chain D: A.732, A.733 No protein-ligand interaction detected (PLIP) MG.60: 1 residues within 4Å: Chain D: A.4239 No protein-ligand interaction detected (PLIP) MG.61: 1 residues within 4Å: Chain D: A.4281 No protein-ligand interaction detected (PLIP) MG.62: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.63: 2 residues within 4Å: Chain D: C.1478, G.1479 No protein-ligand interaction detected (PLIP) MG.64: 2 residues within 4Å: Chain D: G.1733, G.1734 No protein-ligand interaction detected (PLIP) MG.65: 2 residues within 4Å: Chain D: G.2851, U.2852 No protein-ligand interaction detected (PLIP) MG.66: 1 residues within 4Å: Chain D: C.2430 No protein-ligand interaction detected (PLIP) MG.67: 3 residues within 4Å: Chain D: C.2410, C.2411, A.2428 No protein-ligand interaction detected (PLIP) MG.68: 3 residues within 4Å: Chain D: U.4627, A.4665 Chain X: K.373 1 PLIP interactions: 1 interactions with chain X Metal complexes: X:K.373 MG.69: 1 residues within 4Å: Chain D: G.2799 No protein-ligand interaction detected (PLIP) MG.70: 1 residues within 4Å: Chain D: G.1797 No protein-ligand interaction detected (PLIP) MG.71: 3 residues within 4Å: Chain D: U.35, G.4187, U.4188 No protein-ligand interaction detected (PLIP) MG.72: 1 residues within 4Å: Chain D: A.1737 No protein-ligand interaction detected (PLIP) MG.73: 1 residues within 4Å: Chain D: A.4339 No protein-ligand interaction detected (PLIP) MG.74: 3 residues within 4Å: Chain D: A.2438, U.2782 Chain R: T.126 No protein-ligand interaction detected (PLIP) MG.75: 1 residues within 4Å: Chain D: G.1895 No protein-ligand interaction detected (PLIP) MG.76: 2 residues within 4Å: Chain D: C.1848, U.1849 No protein-ligand interaction detected (PLIP) MG.77: 3 residues within 4Å: Chain D: A.4214, C.4215, G.4217 No protein-ligand interaction detected (PLIP) MG.78: 2 residues within 4Å: Chain D: G.4650, A.4651 No protein-ligand interaction detected (PLIP) MG.79: 1 residues within 4Å: Chain D: U.2519 No protein-ligand interaction detected (PLIP) MG.80: 5 residues within 4Å: Chain E: G.21, U.53, A.55, G.56, C.57 No protein-ligand interaction detected (PLIP) MG.81: 2 residues within 4Å: Chain D: G.1895 Chain E: A.83 No protein-ligand interaction detected (PLIP) MG.82: 1 residues within 4Å: Chain E: A.42 No protein-ligand interaction detected (PLIP) MG.83: 1 residues within 4Å: Chain Q: N.50 No protein-ligand interaction detected (PLIP) MG.84: 4 residues within 4Å: Chain 0: S.25, Y.28, V.29, I.31 3 PLIP interactions: 3 interactions with chain 0 Metal complexes: 0:S.25, 0:Y.28, 0:I.31 MG.86: 6 residues within 4Å: Chain 3: T.57, V.58, T.59, N.65, T.67 Chain D: C.4944 1 PLIP interactions: 1 interactions with chain 3 Metal complexes: 3:T.67 MG.91: 2 residues within 4Å: Chain D: A.1508 Chain f: R.110 No protein-ligand interaction detected (PLIP) MG.92: 6 residues within 4Å: Chain D: A.4544 Chain k: F.211, G.212, G.213, H.218, I.219 2 PLIP interactions: 2 interactions with chain k Metal complexes: k:F.211, k:H.218 MG.95: 3 residues within 4Å: Ligands: GDP.93 Chain s: S.182, T.202 1 PLIP interactions: 1 interactions with chain s Metal complexes: s:T.202

6 x ZN: ZINC ION(Non-covalent)

ZN.85: 5 residues within 4Å: Chain 1: S.44, C.46, C.49, C.83, C.86 4 PLIP interactions: 4 interactions with chain 1 Metal complexes: 1:C.46, 1:C.49, 1:C.83, 1:C.86 ZN.87: 4 residues within 4Å: Chain 5: C.12, C.15, C.72, C.77 4 PLIP interactions: 4 interactions with chain 5 Metal complexes: 5:C.12, 5:C.15, 5:C.72, 5:C.77 ZN.88: 4 residues within 4Å: Chain 6: C.19, C.22, C.34, C.37 4 PLIP interactions: 4 interactions with chain 6 Metal complexes: 6:C.19, 6:C.22, 6:C.34, 6:C.37 ZN.89: 4 residues within 4Å: Chain 7: C.39, C.42, C.57, C.60 4 PLIP interactions: 4 interactions with chain 7 Metal complexes: 7:C.39, 7:C.42, 7:C.57, 7:C.60 ZN.90: 4 residues within 4Å: Chain e: C.63, C.66, H.79, H.85 4 PLIP interactions: 4 interactions with chain e Metal complexes: e:C.63, e:C.66, e:H.79, e:H.85 ZN.96: 4 residues within 4Å: Chain t: C.6, C.9, C.32, C.36 4 PLIP interactions: 4 interactions with chain t Metal complexes: t:C.6, t:C.9, t:C.32, t:C.36

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

GDP.93: 18 residues within 4Å: Ligands: K.94, MG.95 Chain s: 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 16 PLIP interactions: 16 interactions with chain s Hydrogen bonds: s:N.178, s:V.179, s:G.180, s:K.181, s:S.182, s:S.183, s:S.183, s:Q.196, s:Q.196, s:K.290, s:K.290, s:T.322, s:T.322 Salt bridges: s:K.181, s:D.292 pi-Cation interactions: s:K.290

1 x K: POTASSIUM ION(Non-covalent)

K.94: 5 residues within 4Å: Ligands: GDP.93 Chain s: N.178, Q.196, Y.198, T.201 3 PLIP interactions: 3 interactions with chain s Metal complexes: s:Q.196, s:Y.198, s:T.201

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: F
60S ribosomal protein L13: G
60S ribosomal protein L13a: H
60S ribosomal protein L14: I
60S ribosomal protein L15: J
60S ribosomal protein L17: K
60S ribosomal protein L18: L
60S ribosomal protein L18a: M
60S ribosomal protein L19: N
60S ribosomal protein L21: O
60S ribosomal protein L22: P
60S ribosomal protein L23: Q
60S ribosomal protein L23a: R
60S ribosomal protein L26: S
60S ribosomal protein L27: T
60S ribosomal protein L27a: U
60S ribosomal protein L28: V
60S ribosomal protein L29: W
60S ribosomal protein L3: X
60S ribosomal protein L30: Y
60S ribosomal protein L31: Z
60S ribosomal protein L32: 0
60S ribosomal protein L34: 1
60S ribosomal protein L35: 2
60S ribosomal protein L35a: 3
60S ribosomal protein L36: 4
60S ribosomal protein L36a: 5
60S ribosomal protein L37: 6
60S ribosomal protein L37a: 7
60S ribosomal protein L38: 8
60S ribosomal protein L39: 9
Nucleolar GTP-binding protein 2: a
Ribosome biogenesis protein NSA2 homolog: b
Protein LLP homolog: c
Ribosome biogenesis protein NOP53: d
Zinc finger protein 593: e
60S ribosomal protein L4: f
60S ribosomal protein L5: g
60S ribosomal protein L6: h
60S ribosomal protein L7: i
60S ribosomal protein L7a: j
60S ribosomal protein L8: k
60S ribosomal protein L9: l
MKI67 FHA domain-interacting nucleolar phosphoprotein: m
60S ribosomal protein L7-like 1: n
Eukaryotic translation initiation factor 6: o
Ribosomal L1 domain-containing protein 1: p
Pescadillo homolog: q
mRNA turnover protein 4 homolog: r
GTP-binding protein 4: s
Probable ribosome biogenesis protein RLP24: t

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
BA

F
L5

G
L6

H
L7

I
L8

J
L9

K
LA

L
LB

M
LC

N
LD

O
LE

P
LF

Q
LG

R
LH

S
LI

T
LJ

U
LK

V
LL

W
LM

X
LN

Y
LO

Z
LP

0
LQ

1
LR

2
LS

3
LT

4
LU

5
LV

6
LW

7
LX

8
LY

9
LZ

a
NC

b
NF

c
NK

d
NL

e
NP

f
SA

g
SB

h
SC

i
SD

j
SE

k
SF

l
SG

m
SH

n
SI

o
SK

p
SL

q
SM

r
SQ

s
SR

t
SV

60S ribosomal protein L12

60S ribosomal protein L11

60S ribosomal protein L13

60S ribosomal protein L13a

60S ribosomal protein L14

60S ribosomal protein L15

60S ribosomal protein L17

60S ribosomal protein L18

60S ribosomal protein L18a

60S ribosomal protein L19

60S ribosomal protein L21

60S ribosomal protein L22

60S ribosomal protein L23

60S ribosomal protein L23a

60S ribosomal protein L26

60S ribosomal protein L27

60S ribosomal protein L27a

60S ribosomal protein L28

60S ribosomal protein L29

60S ribosomal protein L3

60S ribosomal protein L30

60S ribosomal protein L31

60S ribosomal protein L32

60S ribosomal protein L34

60S ribosomal protein L35

60S ribosomal protein L35a

60S ribosomal protein L36

60S ribosomal protein L36a

60S ribosomal protein L37

60S ribosomal protein L37a

60S ribosomal protein L38

60S ribosomal protein L39

Nucleolar GTP-binding protein 2

Ribosome biogenesis protein NSA2 homolog

Protein LLP homolog

Ribosome biogenesis protein NOP53

Zinc finger protein 593

60S ribosomal protein L4

60S ribosomal protein L5

60S ribosomal protein L6

60S ribosomal protein L7

60S ribosomal protein L7a

60S ribosomal protein L8

60S ribosomal protein L9

MKI67 FHA domain-interacting nucleolar phosphoprotein

60S ribosomal protein L7-like 1

Eukaryotic translation initiation factor 6

Ribosomal L1 domain-containing protein 1

Pescadillo homolog

mRNA turnover protein 4 homolog

GTP-binding protein 4

Probable ribosome biogenesis protein RLP24

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