SMTL ID : 8fkv.1

Human nucleolar pre-60S ribosomal subunit (State D1)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

MG.1: 2 residues within 4Å: Chain C: C.19, A.20 No protein-ligand interaction detected (PLIP) MG.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain C: G.149, G.151 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain D: G.54, G.55 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Chain E: G.240 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain E: A.62, 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 T: R.16 No protein-ligand interaction detected (PLIP) MG.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain E: C.112, G.154, G.156 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Chain E: G.1904 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain 8: G.99 Chain E: A.355, G.356 No protein-ligand interaction detected (PLIP) MG.14: 2 residues within 4Å: Chain E: G.1335, C.2346 No protein-ligand interaction detected (PLIP) MG.15: 2 residues within 4Å: Chain E: G.356, A.359 No protein-ligand interaction detected (PLIP) MG.16: 4 residues within 4Å: Chain E: A.1337, G.2343, U.2344, G.2345 No protein-ligand interaction detected (PLIP) MG.17: 2 residues within 4Å: Chain E: G.234, C.2303 No protein-ligand interaction detected (PLIP) MG.18: 1 residues within 4Å: Chain E: G.2348 No protein-ligand interaction detected (PLIP) MG.19: 3 residues within 4Å: Chain E: A.113, G.114, G.116 No protein-ligand interaction detected (PLIP) MG.20: 2 residues within 4Å: Chain E: C.1369, A.1371 No protein-ligand interaction detected (PLIP) MG.21: 2 residues within 4Å: Chain E: C.1898, G.2278 No protein-ligand interaction detected (PLIP) MG.22: 3 residues within 4Å: Chain E: C.1665, A.2279, G.2280 No protein-ligand interaction detected (PLIP) MG.23: 3 residues within 4Å: Chain E: G.229, G.230, A.235 No protein-ligand interaction detected (PLIP) MG.24: 1 residues within 4Å: Chain E: U.231 No protein-ligand interaction detected (PLIP) MG.25: 1 residues within 4Å: Chain E: U.1348 No protein-ligand interaction detected (PLIP) MG.26: 2 residues within 4Å: Chain E: A.101, G.102 No protein-ligand interaction detected (PLIP) MG.27: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.28: 1 residues within 4Å: Chain C: C.35 No protein-ligand interaction detected (PLIP) MG.29: 1 residues within 4Å: Chain E: A.56 No protein-ligand interaction detected (PLIP) MG.30: 4 residues within 4Å: Chain E: C.414, G.415, U.416, G.417 No protein-ligand interaction detected (PLIP) MG.31: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.32: 2 residues within 4Å: Chain E: G.1667, G.2280 No protein-ligand interaction detected (PLIP) MG.33: 4 residues within 4Å: Chain E: C.1915, G.1916, A.1917 Chain G: K.25 No protein-ligand interaction detected (PLIP) MG.34: 4 residues within 4Å: Chain E: A.410, G.415, U.416, G.2331 No protein-ligand interaction detected (PLIP) MG.35: 3 residues within 4Å: Chain E: A.410, G.2330, G.2331 No protein-ligand interaction detected (PLIP) MG.36: 4 residues within 4Å: Chain E: G.311, G.312, A.324, U.325 No protein-ligand interaction detected (PLIP) MG.37: 3 residues within 4Å: Chain E: G.85, G.1383, C.1384 No protein-ligand interaction detected (PLIP) MG.38: 3 residues within 4Å: Chain E: A.2285, G.2286 Chain Q: K.10 No protein-ligand interaction detected (PLIP) MG.39: 5 residues within 4Å: Chain E: G.2309, C.2310, G.2328, U.2329, G.2330 No protein-ligand interaction detected (PLIP) MG.40: 4 residues within 4Å: Chain E: C.358, A.359, A.376, A.377 No protein-ligand interaction detected (PLIP) MG.41: 5 residues within 4Å: Chain C: A.9, G.10, C.11 Chain E: G.423, U.424 No protein-ligand interaction detected (PLIP) MG.42: 3 residues within 4Å: Chain E: U.4752, U.4753, U.4947 No protein-ligand interaction detected (PLIP) MG.43: 2 residues within 4Å: Chain E: U.416, G.417 No protein-ligand interaction detected (PLIP) MG.44: 2 residues within 4Å: Chain E: A.1908, G.1909 No protein-ligand interaction detected (PLIP) MG.45: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.46: 4 residues within 4Å: Chain E: A.59, G.60, A.335, U.337 No protein-ligand interaction detected (PLIP) MG.47: 2 residues within 4Å: Chain E: U.2312, G.2314 No protein-ligand interaction detected (PLIP) MG.48: 1 residues within 4Å: Chain E: G.1886 No protein-ligand interaction detected (PLIP) MG.49: 3 residues within 4Å: Chain E: G.4690, U.4697, C.4698 No protein-ligand interaction detected (PLIP) MG.50: 2 residues within 4Å: Chain E: U.96, G.97 No protein-ligand interaction detected (PLIP) MG.51: 4 residues within 4Å: Chain E: G.752, C.753, G.910, U.911 No protein-ligand interaction detected (PLIP) MG.52: 1 residues within 4Å: Chain E: C.1963 No protein-ligand interaction detected (PLIP) MG.53: 1 residues within 4Å: Chain E: A.4464 No protein-ligand interaction detected (PLIP) MG.54: 0 residues within 4Å: (No contacts) 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: 1 residues within 4Å: Chain E: U.1882 No protein-ligand interaction detected (PLIP) MG.57: 4 residues within 4Å: Chain I: G.175, F.180, T.183, I.184 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:G.175 MG.58: 3 residues within 4Å: Chain E: U.4627, A.4665 Chain R: K.373 1 PLIP interactions: 1 interactions with chain R Metal complexes: R:K.373 MG.59: 4 residues within 4Å: Chain T: S.25, Y.28, V.29, I.31 3 PLIP interactions: 3 interactions with chain T Metal complexes: T:S.25, T:Y.28, T:I.31 MG.60: 6 residues within 4Å: Chain E: C.4944 Chain V: T.57, V.58, T.59, N.65, T.67 2 PLIP interactions: 2 interactions with chain V Metal complexes: V:T.57, V:T.67 MG.63: 2 residues within 4Å: Chain 2: T.147 Ligands: ADP.62 No protein-ligand interaction detected (PLIP) MG.65: 2 residues within 4Å: Chain 8: R.110 Chain E: A.1508 No protein-ligand interaction detected (PLIP) MG.66: 2 residues within 4Å: Chain E: G.190 Chain k: R.335 No protein-ligand interaction detected (PLIP) MG.69: 3 residues within 4Å: Ligands: GDP.67 Chain m: S.182, T.202 2 PLIP interactions: 2 interactions with chain m Metal complexes: m:S.182, m:T.202 MG.70: 6 residues within 4Å: Chain p: L.661, D.664, E.666, Q.686, N.687, T.688 3 PLIP interactions: 3 interactions with chain p Metal complexes: p:L.661, p:D.664, p:Q.686

2 x ZN: ZINC ION(Non-covalent)

ZN.61: 4 residues within 4Å: Chain X: C.19, C.22, C.34, C.37 4 PLIP interactions: 4 interactions with chain X Metal complexes: X:C.19, X:C.22, X:C.34, X:C.37 ZN.71: 4 residues within 4Å: Chain q: C.6, C.9, C.32, C.36 4 PLIP interactions: 4 interactions with chain q Metal complexes: q:C.6, q:C.9, q:C.32, q:C.36

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.62: 13 residues within 4Å: Chain 2: F.98, Y.116, V.118, T.120, Q.123, T.142, G.143, S.144, G.145, K.146, T.147, F.185 Ligands: MG.63 13 PLIP interactions: 13 interactions with chain 2 Hydrogen bonds: 2:T.120, 2:Q.123, 2:Q.123, 2:G.143, 2:S.144, 2:G.145, 2:K.146, 2:T.147, 2:T.147, 2:T.147 Salt bridges: 2:K.146 pi-Stacking: 2:Y.116, 2:Y.116

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.64: 9 residues within 4Å: Chain 4: W.8, L.11, C.17, F.19, K.20, C.29, C.39, C.44, L.46 4 PLIP interactions: 4 interactions with chain 4, Metal complexes: 4:C.17, 4:C.29, 4:C.39, 4:C.44

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

GDP.67: 19 residues within 4Å: Ligands: K.68, MG.69 Chain m: Y.176, 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 18 PLIP interactions: 18 interactions with chain m Hydrogen bonds: m:N.178, m:V.179, m:G.180, m:K.181, m:S.182, m:S.183, m:S.183, m:Q.196, m:P.197, m:N.289, m:K.290, m:K.290, m:S.321, m:T.322, m:T.322 Salt bridges: m:K.181, m:D.292 pi-Cation interactions: m:K.290

1 x K: POTASSIUM ION(Non-covalent)

K.68: 5 residues within 4Å: Ligands: GDP.67 Chain m: N.178, Q.196, Y.198, T.201 1 PLIP interactions: 1 interactions with chain m Metal complexes: m:Q.196

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
60S ribosomal protein L13: F
60S ribosomal protein L13a: G
60S ribosomal protein L14: H
60S ribosomal protein L15: I
60S ribosomal protein L17: J
60S ribosomal protein L18: K
60S ribosomal protein L18a: L
60S ribosomal protein L21: M
60S ribosomal protein L23: N
60S ribosomal protein L23a: O
60S ribosomal protein L26: P
60S ribosomal protein L27a: Q
60S ribosomal protein L3: R
60S ribosomal protein L31: S
60S ribosomal protein L32: T
60S ribosomal protein L35: U
60S ribosomal protein L35a: V
60S ribosomal protein L36: W
60S ribosomal protein L37: X
Nucleolar complex protein 2 homolog: Y
Guanine nucleotide-binding protein-like 3: Z
Ribosome biogenesis protein NSA2 homolog: 0
60S ribosome subunit biogenesis protein NIP7 homolog: 1
ATP-dependent RNA helicase DDX54: 2
Protein LLP homolog: 3
Protein MAK16 homolog: 4
Ribosomal RNA processing protein 1 homolog A: 5
WD repeat-containing protein 74: 6
Ribosome production factor 1: 7
60S ribosomal protein L4: 8
60S ribosomal protein L6: 9
60S ribosomal protein L7: a
60S ribosomal protein L7a: b
60S ribosomal protein L9: c
MKI67 FHA domain-interacting nucleolar phosphoprotein: d
60S ribosomal protein L7-like 1: e
pre-rRNA 2'-O-ribose RNA methyltransferase FTSJ3: f
Eukaryotic translation initiation factor 6: g
Ribosomal L1 domain-containing protein 1: h
Pescadillo homolog: i
Probable rRNA-processing protein EBP2: j
Ribosome biogenesis protein BRX1 homolog: k
mRNA turnover protein 4 homolog: l
GTP-binding protein 4: m
Ribosome biogenesis protein BOP1: n
Ribosome biogenesis regulatory protein homolog: o
Nucleolar complex protein 3 homolog: p
Probable ribosome biogenesis protein RLP24: q
ATP-dependent RNA helicase DDX18: r
Probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase: s
Nucleolar protein 16: t

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
BA

B
BB

F
L6

G
L7

H
L8

I
L9

J
LA

K
LB

L
LC

M
LE

N
LG

O
LH

P
LI

Q
LK

R
LN

S
LP

T
LQ

U
LS

V
LT

W
LU

X
LW

Y
NA

Z
NB

0
NF

1
NH

2
NI

3
NK

4
NM

5
NO

6
NQ

7
NS

8
SA

9
SC

a
SD

b
SE

c
SG

d
SH

e
SI

f
SJ

g
SK

h
SL

i
SM

j
SN

k
SO

l
SQ

m
SR

n
SS

o
ST

p
SU

q
SV

r
SW

s
SY

t
SZ

60S ribosomal protein L12

60S ribosomal protein L10a

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 L21

60S ribosomal protein L23

60S ribosomal protein L23a

60S ribosomal protein L26

60S ribosomal protein L27a

60S ribosomal protein L3

60S ribosomal protein L31

60S ribosomal protein L32

60S ribosomal protein L35

60S ribosomal protein L35a

60S ribosomal protein L36

60S ribosomal protein L37

Nucleolar complex protein 2 homolog

Guanine nucleotide-binding protein-like 3

Ribosome biogenesis protein NSA2 homolog

60S ribosome subunit biogenesis protein NIP7 homolog

ATP-dependent RNA helicase DDX54

Protein LLP homolog

Protein MAK16 homolog

Ribosomal RNA processing protein 1 homolog A

WD repeat-containing protein 74

Ribosome production factor 1

60S ribosomal protein L4

60S ribosomal protein L6

60S ribosomal protein L7

60S ribosomal protein L7a

60S ribosomal protein L9

MKI67 FHA domain-interacting nucleolar phosphoprotein

60S ribosomal protein L7-like 1

pre-rRNA 2'-O-ribose RNA methyltransferase FTSJ3

Eukaryotic translation initiation factor 6

Ribosomal L1 domain-containing protein 1

Pescadillo homolog

Probable rRNA-processing protein EBP2

Ribosome biogenesis protein BRX1 homolog

mRNA turnover protein 4 homolog

GTP-binding protein 4

Ribosome biogenesis protein BOP1

Ribosome biogenesis regulatory protein homolog

Nucleolar complex protein 3 homolog

Probable ribosome biogenesis protein RLP24

ATP-dependent RNA helicase DDX18

Probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase

Nucleolar protein 16

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