SMTL ID : 8fkr.1

Human nucleolar pre-60S ribosomal subunit (State B1)

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-mer

Ligands

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

MG.1: 2 residues within 4Å: Chain B: A.20 Chain D: U.2293 No protein-ligand interaction detected (PLIP) MG.2: 1 residues within 4Å: Chain B: U.142 No protein-ligand interaction detected (PLIP) MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Chain C: G.54 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Chain D: G.240 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain D: A.62, U.333 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Chain D: A.61 No protein-ligand interaction detected (PLIP) MG.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Chain D: U.1905 No protein-ligand interaction detected (PLIP) MG.10: 4 residues within 4Å: Chain D: C.112, G.154, C.155, G.156 No protein-ligand interaction detected (PLIP) MG.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain D: G.356, C.358 No protein-ligand interaction detected (PLIP) MG.13: 1 residues within 4Å: Chain D: G.1335 No protein-ligand interaction detected (PLIP) MG.14: 2 residues within 4Å: Chain D: G.356, A.359 No protein-ligand interaction detected (PLIP) MG.15: 2 residues within 4Å: Chain D: A.1337, U.2344 No protein-ligand interaction detected (PLIP) MG.16: 2 residues within 4Å: Chain D: G.234, C.2303 No protein-ligand interaction detected (PLIP) MG.17: 1 residues within 4Å: Chain D: G.2348 No protein-ligand interaction detected (PLIP) MG.18: 2 residues within 4Å: Chain D: G.114, G.116 No protein-ligand interaction detected (PLIP) MG.19: 2 residues within 4Å: Chain D: C.1369, A.1371 No protein-ligand interaction detected (PLIP) MG.20: 2 residues within 4Å: Chain D: C.1898, G.2278 No protein-ligand interaction detected (PLIP) MG.21: 3 residues within 4Å: Chain D: C.1665, A.2279, G.2280 No protein-ligand interaction detected (PLIP) MG.22: 2 residues within 4Å: Chain D: G.229, A.235 No protein-ligand interaction detected (PLIP) MG.23: 1 residues within 4Å: Chain D: U.231 No protein-ligand interaction detected (PLIP) MG.24: 1 residues within 4Å: Chain D: U.1348 No protein-ligand interaction detected (PLIP) MG.25: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.26: 1 residues within 4Å: Chain D: A.101 No protein-ligand interaction detected (PLIP) MG.27: 1 residues within 4Å: Chain D: A.353 No protein-ligand interaction detected (PLIP) MG.28: 1 residues within 4Å: Chain D: C.2365 No protein-ligand interaction detected (PLIP) MG.29: 2 residues within 4Å: Chain D: G.57, G.58 No protein-ligand interaction detected (PLIP) MG.30: 1 residues within 4Å: Chain D: A.56 No protein-ligand interaction detected (PLIP) MG.31: 4 residues within 4Å: Chain D: C.414, G.415, U.416, G.417 No protein-ligand interaction detected (PLIP) MG.32: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.33: 2 residues within 4Å: Chain D: G.1667, G.2280 No protein-ligand interaction detected (PLIP) MG.34: 3 residues within 4Å: Chain D: G.1916, A.1917 Chain F: K.25 No protein-ligand interaction detected (PLIP) MG.35: 4 residues within 4Å: Chain D: A.410, G.415, U.416, G.2331 No protein-ligand interaction detected (PLIP) MG.36: 3 residues within 4Å: Chain D: A.410, G.2330, G.2331 No protein-ligand interaction detected (PLIP) MG.37: 5 residues within 4Å: Chain D: G.311, G.312, A.324, U.325 Chain h: K.97 No protein-ligand interaction detected (PLIP) MG.38: 3 residues within 4Å: Chain D: G.85, G.1383, C.1384 No protein-ligand interaction detected (PLIP) MG.39: 2 residues within 4Å: Chain D: G.2286 Chain P: K.10 No protein-ligand interaction detected (PLIP) MG.40: 2 residues within 4Å: Chain D: G.2309, U.2329 No protein-ligand interaction detected (PLIP) MG.41: 4 residues within 4Å: Chain D: C.358, A.359, A.376, A.377 No protein-ligand interaction detected (PLIP) MG.42: 3 residues within 4Å: Chain D: U.4628, A.4672, U.4673 No protein-ligand interaction detected (PLIP) MG.43: 4 residues within 4Å: Chain B: G.10, C.11 Chain D: G.423, U.424 No protein-ligand interaction detected (PLIP) MG.44: 4 residues within 4Å: Chain D: U.4752, U.4753, G.4945, U.4947 No protein-ligand interaction detected (PLIP) MG.45: 1 residues within 4Å: Chain D: U.416 No protein-ligand interaction detected (PLIP) MG.46: 3 residues within 4Å: Chain 7: K.221 Chain D: A.1907, A.1908 No protein-ligand interaction detected (PLIP) MG.47: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.48: 1 residues within 4Å: Chain D: A.335 No protein-ligand interaction detected (PLIP) MG.49: 2 residues within 4Å: Chain D: G.4400 Chain j: Y.124 No protein-ligand interaction detected (PLIP) MG.50: 4 residues within 4Å: Chain H: G.175, F.180, T.183, I.184 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:G.175 MG.51: 2 residues within 4Å: Chain Q: K.373, F.374 No protein-ligand interaction detected (PLIP) MG.52: 3 residues within 4Å: Chain R: S.25, Y.28, I.31 3 PLIP interactions: 3 interactions with chain R Metal complexes: R:S.25, R:Y.28, R:I.31 MG.53: 6 residues within 4Å: Chain D: C.4944 Chain T: T.57, V.58, T.59, N.65, T.67 3 PLIP interactions: 3 interactions with chain T Metal complexes: T:T.57, T:V.58, T:T.59 MG.56: 2 residues within 4Å: Chain 5: R.110 Chain D: A.1508 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.54: 4 residues within 4Å: Chain V: C.19, C.22, C.34, C.37 4 PLIP interactions: 4 interactions with chain V Metal complexes: V:C.19, V:C.22, V:C.34, V:C.37 ZN.59: 4 residues within 4Å: Chain m: C.6, C.9, C.32, C.36 4 PLIP interactions: 4 interactions with chain m Metal complexes: m:C.6, m:C.9, m:C.32, m:C.36

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

SF4.55: 10 residues within 4Å: Chain 0: W.8, L.11, C.17, F.19, K.20, C.29, L.38, C.39, C.44, L.46 4 PLIP interactions: 4 interactions with chain 0, Metal complexes: 0:C.17, 0:C.29, 0:C.39, 0:C.44

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

GDP.57: 18 residues within 4Å: Ligands: K.58 Chain j: P.177, N.178, V.179, G.180, K.181, S.182, S.183, V.195, Q.196, P.197, T.202, N.289, K.290, D.292, S.321, T.322, L.323 16 PLIP interactions: 16 interactions with chain j Hydrogen bonds: j:N.178, j:G.180, j:K.181, j:S.182, j:S.183, j:S.183, j:Q.196, j:T.202, j:K.290, j:K.290, j:T.322, j:T.322, j:L.323 Salt bridges: j:K.181, j:D.292 pi-Cation interactions: j:K.290

1 x K: POTASSIUM ION(Non-covalent)

K.58: 5 residues within 4Å: Ligands: GDP.57 Chain j: N.178, Q.196, Y.198, T.201 2 PLIP interactions: 2 interactions with chain j Metal complexes: j:Q.196, j: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 L13: E
60S ribosomal protein L13a: F
60S ribosomal protein L14: G
60S ribosomal protein L15: H
60S ribosomal protein L17: I
60S ribosomal protein L18: J
60S ribosomal protein L18a: K
60S ribosomal protein L21: L
60S ribosomal protein L23: M
60S ribosomal protein L23a: N
60S ribosomal protein L26: O
60S ribosomal protein L27a: P
60S ribosomal protein L3: Q
60S ribosomal protein L32: R
60S ribosomal protein L35: S
60S ribosomal protein L35a: T
60S ribosomal protein L36: U
60S ribosomal protein L37: V
Guanine nucleotide-binding protein-like 3: W
Surfeit locus protein 6: X
Ribosome biogenesis protein NSA2 homolog: Y
RRP15-like protein: Z
Protein MAK16 homolog: 0
Suppressor of SWI4 1 homolog: 1
Ribosomal RNA processing protein 1 homolog A: 2
WD repeat-containing protein 74: 3
Ribosome production factor 1: 4
60S ribosomal protein L4: 5
60S ribosomal protein L6: 6
60S ribosomal protein L7: 7
60S ribosomal protein L7a: 8
60S ribosomal protein L9: 9
MKI67 FHA domain-interacting nucleolar phosphoprotein: a
60S ribosomal protein L7-like 1: b
pre-rRNA 2'-O-ribose RNA methyltransferase FTSJ3: c
Eukaryotic translation initiation factor 6: d
Ribosomal L1 domain-containing protein 1: e
Pescadillo homolog: f
Probable rRNA-processing protein EBP2: g
Ribosome biogenesis protein BRX1 homolog: h
mRNA turnover protein 4 homolog: i
GTP-binding protein 4: j
Ribosome biogenesis protein BOP1: k
Ribosome biogenesis regulatory protein homolog: l
Probable ribosome biogenesis protein RLP24: m
ATP-dependent RNA helicase DDX18: n
Nucleolar protein 16: o

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
BA

E
L6

F
L7

G
L8

H
L9

I
LA

J
LB

K
LC

L
LE

M
LG

N
LH

O
LI

P
LK

Q
LN

R
LQ

S
LS

T
LT

U
LU

V
LW

W
NB

X
NE

Y
NF

Z
NG

0
NM

1
NN

2
NO

3
NQ

4
NS

5
SA

6
SC

7
SD

8
SE

9
SG

a
SH

b
SI

c
SJ

d
SK

e
SL

f
SM

g
SN

h
SO

i
SQ

j
SR

k
SS

l
ST

m
SV

n
SW

o
SZ

60S ribosomal protein L12

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 L32

60S ribosomal protein L35

60S ribosomal protein L35a

60S ribosomal protein L36

60S ribosomal protein L37

Guanine nucleotide-binding protein-like 3

Surfeit locus protein 6

Ribosome biogenesis protein NSA2 homolog

RRP15-like protein

Protein MAK16 homolog

Suppressor of SWI4 1 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

Probable ribosome biogenesis protein RLP24

ATP-dependent RNA helicase DDX18

Nucleolar protein 16

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