SMTL ID : 8fl4.1

Human nuclear pre-60S ribosomal subunit (State I3)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

MG.1: 2 residues within 4Å: Chain D: C.19, A.20 No protein-ligand interaction detected (PLIP) MG.2: 1 residues within 4Å: Chain D: G.143 No protein-ligand interaction detected (PLIP) MG.3: 1 residues within 4Å: Chain D: G.12 No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Chain D: G.149 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain 1: G.55, T.70, H.73 Chain E: G.2584 2 PLIP interactions: 2 interactions with chain 1 Metal complexes: 1:G.55, 1:H.73 MG.6: 1 residues within 4Å: Chain E: A.198 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain E: C.332, U.333 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Chain E: A.61 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Chain 0: T.17 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Chain E: U.1905 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain E: 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 E: G.1335 No protein-ligand interaction detected (PLIP) MG.14: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.15: 3 residues within 4Å: Chain E: A.1337, G.2343, U.2344 No protein-ligand interaction detected (PLIP) MG.16: 3 residues within 4Å: Chain E: G.234, C.2303, G.2333 No protein-ligand interaction detected (PLIP) MG.17: 1 residues within 4Å: Chain E: G.2348 No protein-ligand interaction detected (PLIP) MG.18: 2 residues within 4Å: Chain E: G.114, G.116 No protein-ligand interaction detected (PLIP) MG.19: 2 residues within 4Å: Chain E: C.1369, A.1371 No protein-ligand interaction detected (PLIP) MG.20: 2 residues within 4Å: Chain E: C.1898, G.2278 No protein-ligand interaction detected (PLIP) MG.21: 1 residues within 4Å: Chain E: A.235 No protein-ligand interaction detected (PLIP) MG.22: 1 residues within 4Å: Chain E: U.231 No protein-ligand interaction detected (PLIP) MG.23: 1 residues within 4Å: Chain E: U.1348 No protein-ligand interaction detected (PLIP) MG.24: 1 residues within 4Å: Chain E: A.101 No protein-ligand interaction detected (PLIP) MG.25: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.26: 3 residues within 4Å: Chain D: C.35 Chain E: G.57, G.58 No protein-ligand interaction detected (PLIP) MG.27: 1 residues within 4Å: Chain E: A.56 No protein-ligand interaction detected (PLIP) MG.28: 4 residues within 4Å: Chain E: C.414, G.415, U.416, G.417 No protein-ligand interaction detected (PLIP) MG.29: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.30: 4 residues within 4Å: Chain E: C.1913, G.1916, A.1917 Chain I: K.25 No protein-ligand interaction detected (PLIP) MG.31: 4 residues within 4Å: Chain E: A.410, G.415, U.416, G.2331 No protein-ligand interaction detected (PLIP) MG.32: 5 residues within 4Å: Chain E: G.311, G.312, U.313, A.324, U.325 No protein-ligand interaction detected (PLIP) MG.33: 3 residues within 4Å: Chain E: G.85, G.1383, C.1384 No protein-ligand interaction detected (PLIP) MG.34: 4 residues within 4Å: Chain E: C.358, A.359, A.376, A.377 No protein-ligand interaction detected (PLIP) MG.35: 5 residues within 4Å: Chain D: A.9, G.10, C.11 Chain E: G.423, U.424 No protein-ligand interaction detected (PLIP) MG.36: 3 residues within 4Å: Chain E: U.4752, U.4753, U.4947 No protein-ligand interaction detected (PLIP) MG.37: 2 residues within 4Å: Chain E: U.416, G.417 No protein-ligand interaction detected (PLIP) MG.38: 2 residues within 4Å: Chain E: A.1908, G.1909 No protein-ligand interaction detected (PLIP) MG.39: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.40: 1 residues within 4Å: Chain E: A.335 No protein-ligand interaction detected (PLIP) MG.41: 3 residues within 4Å: Chain E: U.2312, A.2313, G.2314 No protein-ligand interaction detected (PLIP) MG.42: 1 residues within 4Å: Chain E: G.1886 No protein-ligand interaction detected (PLIP) MG.43: 3 residues within 4Å: Chain E: U.4689, G.4690 Chain m: R.244 No protein-ligand interaction detected (PLIP) MG.44: 4 residues within 4Å: Chain E: G.85, G.97 Chain H: K.11, H.13 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:H.13 MG.45: 4 residues within 4Å: Chain E: U.750, G.752, G.910, U.911 No protein-ligand interaction detected (PLIP) MG.46: 4 residues within 4Å: Chain E: A.1962, C.1963, A.1964, C.2023 No protein-ligand interaction detected (PLIP) MG.47: 3 residues within 4Å: Chain E: G.4587, G.4713 Ligands: MG.54 No protein-ligand interaction detected (PLIP) MG.48: 4 residues within 4Å: Chain 9: K.2 Chain E: A.4464, C.4486, A.4487 No protein-ligand interaction detected (PLIP) MG.49: 1 residues within 4Å: Chain E: G.356 No protein-ligand interaction detected (PLIP) MG.50: 2 residues within 4Å: Chain E: A.4479, A.4480 No protein-ligand interaction detected (PLIP) MG.51: 2 residues within 4Å: Chain 4: I.81 Chain E: G.311 No protein-ligand interaction detected (PLIP) MG.52: 2 residues within 4Å: Chain E: G.356, A.359 No protein-ligand interaction detected (PLIP) MG.53: 2 residues within 4Å: Chain E: G.4600, G.4609 No protein-ligand interaction detected (PLIP) MG.54: 4 residues within 4Å: Chain E: G.4587, U.4588, C.4712 Ligands: MG.47 No protein-ligand interaction detected (PLIP) MG.55: 3 residues within 4Å: Chain E: U.1317, C.1318, G.1658 No protein-ligand interaction detected (PLIP) MG.56: 3 residues within 4Å: Chain E: A.1330, A.2349, C.2351 No protein-ligand interaction detected (PLIP) MG.57: 2 residues within 4Å: Chain E: G.1667, G.2280 No protein-ligand interaction detected (PLIP) MG.58: 2 residues within 4Å: Chain E: C.14, A.15 No protein-ligand interaction detected (PLIP) MG.59: 1 residues within 4Å: Chain E: A.51 No protein-ligand interaction detected (PLIP) MG.60: 3 residues within 4Å: Chain E: U.46, G.48, G.292 No protein-ligand interaction detected (PLIP) MG.61: 1 residues within 4Å: Chain E: G.1880 No protein-ligand interaction detected (PLIP) MG.62: 1 residues within 4Å: Chain E: U.2048 No protein-ligand interaction detected (PLIP) MG.63: 2 residues within 4Å: Chain E: G.4187, U.4188 No protein-ligand interaction detected (PLIP) MG.64: 2 residues within 4Å: Chain E: G.2514, G.2516 No protein-ligand interaction detected (PLIP) MG.65: 1 residues within 4Å: Chain E: G.2754 No protein-ligand interaction detected (PLIP) MG.66: 3 residues within 4Å: Chain E: C.2770, G.2771, C.2772 No protein-ligand interaction detected (PLIP) MG.67: 1 residues within 4Å: Chain E: A.4281 No protein-ligand interaction detected (PLIP) MG.68: 3 residues within 4Å: Chain E: C.358, A.359, G.364 No protein-ligand interaction detected (PLIP) MG.69: 1 residues within 4Å: Chain E: A.2363 No protein-ligand interaction detected (PLIP) MG.70: 1 residues within 4Å: Chain E: C.2792 No protein-ligand interaction detected (PLIP) MG.71: 2 residues within 4Å: Chain E: G.1633, G.4534 No protein-ligand interaction detected (PLIP) MG.72: 2 residues within 4Å: Chain E: G.3897, G.3899 No protein-ligand interaction detected (PLIP) MG.73: 4 residues within 4Å: Chain E: A.2850, G.2851, U.2852, A.4496 No protein-ligand interaction detected (PLIP) MG.74: 2 residues within 4Å: Chain E: G.4647, A.4648 No protein-ligand interaction detected (PLIP) MG.75: 1 residues within 4Å: Chain E: A.2370 No protein-ligand interaction detected (PLIP) MG.76: 4 residues within 4Å: Chain E: G.4631, U.4632, G.4666, C.4667 No protein-ligand interaction detected (PLIP) MG.77: 2 residues within 4Å: Chain E: C.2393, C.2818 No protein-ligand interaction detected (PLIP) MG.78: 2 residues within 4Å: Chain E: C.4041, G.4043 No protein-ligand interaction detected (PLIP) MG.79: 1 residues within 4Å: Chain E: A.4533 No protein-ligand interaction detected (PLIP) MG.80: 3 residues within 4Å: Chain E: A.5007, C.5008, U.5039 No protein-ligand interaction detected (PLIP) MG.81: 1 residues within 4Å: Chain E: G.3958 No protein-ligand interaction detected (PLIP) MG.82: 4 residues within 4Å: Chain E: A.2403, A.2404, G.2405, C.2786 No protein-ligand interaction detected (PLIP) MG.83: 3 residues within 4Å: Chain E: U.3920, G.4184 Chain s: P.206 No protein-ligand interaction detected (PLIP) MG.84: 2 residues within 4Å: Chain E: A.2845, G.3839 No protein-ligand interaction detected (PLIP) MG.85: 1 residues within 4Å: Chain E: A.4239 No protein-ligand interaction detected (PLIP) MG.86: 1 residues within 4Å: Chain E: C.3636 No protein-ligand interaction detected (PLIP) MG.87: 3 residues within 4Å: Chain E: G.2421, C.2422, A.2423 No protein-ligand interaction detected (PLIP) MG.88: 4 residues within 4Å: Chain E: G.315, U.316, U.4353, U.4354 No protein-ligand interaction detected (PLIP) MG.89: 2 residues within 4Å: Chain E: A.2879, A.3629 No protein-ligand interaction detected (PLIP) MG.90: 2 residues within 4Å: Chain E: U.1659, G.2348 No protein-ligand interaction detected (PLIP) MG.91: 4 residues within 4Å: Chain E: C.2445, C.2446, U.2447, G.2510 No protein-ligand interaction detected (PLIP) MG.92: 1 residues within 4Å: Chain F: A.42 No protein-ligand interaction detected (PLIP) MG.93: 4 residues within 4Å: Chain K: G.175, F.180, T.183, I.184 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:G.175, K:T.183 MG.94: 3 residues within 4Å: Chain 0: S.25, Y.28, I.31 2 PLIP interactions: 2 interactions with chain 0 Metal complexes: 0:S.25, 0:Y.28 MG.96: 6 residues within 4Å: Chain 3: T.57, V.58, T.59, N.65, T.67 Chain E: C.4944 2 PLIP interactions: 2 interactions with chain 3 Metal complexes: 3:T.57, 3:T.59 MG.98: 3 residues within 4Å: Chain 5: Q.30 Chain E: A.1533, A.1534 No protein-ligand interaction detected (PLIP) MG.101: 4 residues within 4Å: Ligands: GTP.100 Chain a: S.324, T.345, D.361 2 PLIP interactions: 2 interactions with chain a Metal complexes: a:S.324, a:T.345 MG.104: 2 residues within 4Å: Chain K: R.204 Chain n: R.110 No protein-ligand interaction detected (PLIP) MG.105: 5 residues within 4Å: Chain E: A.4544 Chain s: F.211, G.212, G.213, H.218 3 PLIP interactions: 3 interactions with chain s Metal complexes: s:F.211, s:G.213, s:H.218

5 x ZN: ZINC ION(Non-covalent)

ZN.95: 4 residues within 4Å: Chain 1: 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.97: 4 residues within 4Å: Chain 5: C.19, C.22, C.34, C.37 4 PLIP interactions: 4 interactions with chain 5 Metal complexes: 5:C.19, 5:C.22, 5:C.34, 5:C.37 ZN.99: 4 residues within 4Å: Chain 6: C.39, C.42, C.57, C.60 4 PLIP interactions: 4 interactions with chain 6 Metal complexes: 6:C.39, 6:C.42, 6:C.57, 6:C.60 ZN.103: 4 residues within 4Å: Chain f: C.63, C.66, H.79, H.85 4 PLIP interactions: 4 interactions with chain f Metal complexes: f:C.63, f:C.66, f:H.79, f:H.85 ZN.108: 4 residues within 4Å: Chain z: C.6, C.9, C.32, C.36 4 PLIP interactions: 4 interactions with chain z Metal complexes: z:C.6, z:C.9, z:C.32, z:C.36

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

GTP.100: 23 residues within 4Å: Chain E: A.3821 Ligands: MG.101, K.102 Chain a: 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, G.343, E.344, T.345, G.364 22 PLIP interactions: 22 interactions with chain a Hydrogen bonds: a:N.255, a:K.256, a:K.256, a:H.282, a:A.283, a:N.320, a:V.321, a:G.322, a:K.323, a:S.324, a:S.325, a:S.325, a:A.339, a:A.339, a:G.343, a:E.344, a:T.345, a:T.345, a:G.364 Salt bridges: a:D.258, a:K.323, a:K.323

2 x K: POTASSIUM ION(Non-covalent)

K.102: 5 residues within 4Å: Ligands: GTP.100 Chain a: N.320, A.339, I.341, E.344 2 PLIP interactions: 2 interactions with chain a Metal complexes: a:A.339, a:I.341 K.107: 4 residues within 4Å: Ligands: GDP.106 Chain y: Q.196, Y.198, T.201 3 PLIP interactions: 3 interactions with chain y Metal complexes: y:Q.196, y:Y.198, y:T.201

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

GDP.106: 17 residues within 4Å: Ligands: K.107 Chain y: Y.176, N.178, V.179, G.180, K.181, S.182, S.183, V.195, Q.196, P.197, N.289, K.290, V.293, S.321, T.322, L.323 17 PLIP interactions: 17 interactions with chain y Hydrogen bonds: y:N.178, y:V.179, y:G.180, y:K.181, y:S.182, y:S.183, y:S.183, y:Q.196, y:N.289, y:K.290, y:K.290, y:S.321, y:T.322, y:T.322, y:L.323 Salt bridges: y:K.181 pi-Cation interactions: y:K.290

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 L10a: B
Ribosomal biogenesis protein LAS1L: C
60S ribosomal protein L11: G
60S ribosomal protein L13: H
60S ribosomal protein L13a: I
60S ribosomal protein L14: J
60S ribosomal protein L15: K
60S ribosomal protein L17: L
60S ribosomal protein L18: M
60S ribosomal protein L18a: N
60S ribosomal protein L19: O
60S ribosomal protein L21: P
60S ribosomal protein L22: Q
60S ribosomal protein L23: R
60S ribosomal protein L23a: S
60S ribosomal protein L26: T
60S ribosomal protein L27: U
60S ribosomal protein L27a: V
60S ribosomal protein L28: 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 L37: 5
60S ribosomal protein L37a: 6
60S ribosomal protein L38: 7
60S ribosomal protein L39: 8
Guanine nucleotide-binding protein-like 3: 9
Nucleolar GTP-binding protein 2: a
Ribosome biogenesis protein NSA2 homolog: b
Notchless protein homolog 1: c
Protein LLP homolog: d
Ribosome biogenesis protein NOP53: e
Zinc finger protein 593: f
Protein SDA1 homolog: g
Testis-expressed protein 10: h
WD repeat-containing protein 18: ij
Proline-, glutamic acid- and leucine-rich protein 1: kl
Coiled-coil domain-containing protein 86: m
60S ribosomal protein L4: n
60S ribosomal protein L5: o
60S ribosomal protein L6: p
60S ribosomal protein L7: q
60S ribosomal protein L7a: r
60S ribosomal protein L8: s
60S ribosomal protein L9: t
60S ribosomal protein L7-like 1: u
Eukaryotic translation initiation factor 6: v
Pescadillo homolog: w
mRNA turnover protein 4 homolog: x
GTP-binding protein 4: y
Probable ribosome biogenesis protein RLP24: z

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
BA

B
BB

C
BD

G
L5

H
L6

I
L7

J
L8

K
L9

L
LA

M
LB

N
LC

O
LD

P
LE

Q
LF

R
LG

S
LH

T
LI

U
LJ

V
LK

W
LL

X
LN

Y
LO

Z
LP

0
LQ

1
LR

2
LS

3
LT

4
LU

5
LW

6
LX

7
LY

8
LZ

9
NB

a
NC

b
NF

c
NJ

d
NK

e
NL

f
NP

g
NT

h
NU

i
NV

j
NW

k
NX

l
NY

m
NZ

n
SA

o
SB

p
SC

q
SD

r
SE

s
SF

t
SG

u
SI

v
SK

w
SM

x
SQ

y
SR

z
SV

60S ribosomal protein L12

60S ribosomal protein L10a

Ribosomal biogenesis protein LAS1L

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 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 L37

60S ribosomal protein L37a

60S ribosomal protein L38

60S ribosomal protein L39

Guanine nucleotide-binding protein-like 3

Nucleolar GTP-binding protein 2

Ribosome biogenesis protein NSA2 homolog

Notchless protein homolog 1

Protein LLP homolog

Ribosome biogenesis protein NOP53

Zinc finger protein 593

Protein SDA1 homolog

Testis-expressed protein 10

WD repeat-containing protein 18

Proline-, glutamic acid- and leucine-rich protein 1

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 L7a

60S ribosomal protein L8

60S ribosomal protein L9

60S ribosomal protein L7-like 1

Eukaryotic translation initiation factor 6

Pescadillo homolog

mRNA turnover protein 4 homolog

GTP-binding protein 4

Probable ribosome biogenesis protein RLP24

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