SMTL ID : 8xxn.1

Cryo-EM structure of the human 43S ribosome with PDCD4

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-mer

Ligands

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

MG.1: 4 residues within 4Å: Chain B: U.667, A.668, A.669, A.670 No protein-ligand interaction detected (PLIP) MG.2: 4 residues within 4Å: Chain B: G.999, A.1082, G.1858 Chain T: G.16 No protein-ligand interaction detected (PLIP) MG.3: 2 residues within 4Å: Chain B: G.16, G.659 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain B: G.90, G.446 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Chain B: G.432 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain B: G.434, A.435, C.450 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain B: A.449, C.450 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain B: G.410, A.426, U.427 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Chain B: C.632 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain B: U.652, A.653 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain B: A.679, G.680, C.1026 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain B: G.684, A.685, A.864 No protein-ligand interaction detected (PLIP) MG.13: 1 residues within 4Å: Chain B: A.1035 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain B: G.1165, G.1166, G.1167 No protein-ligand interaction detected (PLIP) MG.15: 3 residues within 4Å: Chain B: A.1386, G.1387, C.1482 No protein-ligand interaction detected (PLIP) MG.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.17: 5 residues within 4Å: Chain B: A.1832, G.1836, G.1837, U.1839, U.1840 No protein-ligand interaction detected (PLIP) MG.18: 4 residues within 4Å: Chain B: U.1830, A.1831, A.1832, G.1837 No protein-ligand interaction detected (PLIP) MG.19: 1 residues within 4Å: Chain B: U.1839 No protein-ligand interaction detected (PLIP) MG.20: 1 residues within 4Å: Chain B: U.1072 No protein-ligand interaction detected (PLIP) MG.21: 4 residues within 4Å: Chain B: A.1831, A.1832, U.1840, C.1853 No protein-ligand interaction detected (PLIP) MG.22: 3 residues within 4Å: Chain B: C.1047, G.1048, G.1068 No protein-ligand interaction detected (PLIP) MG.25: 3 residues within 4Å: Chain B: U.63, C.315 Chain Y: Q.177 No protein-ligand interaction detected (PLIP)

3 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.23: 5 residues within 4Å: Chain T: C.23, N.25, C.26, C.74, C.77 4 PLIP interactions: 4 interactions with chain T Metal complexes: T:C.23, T:C.26, T:C.74, T:C.77 ZN.24: 4 residues within 4Å: Chain V: C.21, C.24, C.39, C.42 4 PLIP interactions: 4 interactions with chain V Metal complexes: V:C.21, V:C.24, V:C.39, V:C.42 ZN.26: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ye, X. et al., Human tumor suppressor PDCD4 directly interacts with ribosomes to repress translation. Cell Res. (2024)

Release Date

2024-05-01

Peptides

60S ribosomal protein L41: A
40S ribosomal protein SA: C
40S ribosomal protein S3a: D
40S ribosomal protein S3: E
40S ribosomal protein S4, X isoform: F
40S ribosomal protein S5: G
40S ribosomal protein S7: H
40S ribosomal protein S8: I
40S ribosomal protein S10: J
40S ribosomal protein S11: K
40S ribosomal protein S15: L
40S ribosomal protein S16: M
40S ribosomal protein S17: N
40S ribosomal protein S18: O
40S ribosomal protein S19: P
40S ribosomal protein S20: Q
40S ribosomal protein S21: R
40S ribosomal protein S23: S
40S ribosomal protein S26: T
40S ribosomal protein S28: U
40S ribosomal protein S29: V
Receptor of activated protein C kinase 1: W
40S ribosomal protein S2: X
40S ribosomal protein S6: Y
40S ribosomal protein S9: Z
40S ribosomal protein S12: 0
40S ribosomal protein S13: 1
40S ribosomal protein S14: 2
40S ribosomal protein S15a: 3
40S ribosomal protein S24: 4
40S ribosomal protein S25: 5
40S ribosomal protein S27: 6
40S ribosomal protein S30: 7
Ubiquitin-40S ribosomal protein S27a: 8
Eukaryotic translation initiation factor 1: 9
Eukaryotic initiation factor 4A-I: a
Programmed cell death protein 4: b
Eukaryotic translation initiation factor 3 subunit A: c
Eukaryotic translation initiation factor 3 subunit B: d
Eukaryotic translation initiation factor 3 subunit C: e
Eukaryotic translation initiation factor 3 subunit E: f
Eukaryotic translation initiation factor 3 subunit F: g
Eukaryotic translation initiation factor 3 subunit G: h
Eukaryotic translation initiation factor 3 subunit H: i
Eukaryotic translation initiation factor 3 subunit I: j
Eukaryotic translation initiation factor 3 subunit K: k
Eukaryotic translation initiation factor 3 subunit L: l
Eukaryotic translation initiation factor 3 subunit M: m
Eukaryotic translation initiation factor 3 subunit D: n

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
Ln

C
SA

D
SB

E
SD

F
SE

G
SF

H
SH

I
SI

J
SK

K
SL

L
SP

M
SQ

N
SR

O
SS

P
ST

Q
SU

R
SV

S
SX

T
Sa

U
Sc

V
Sd

W
Sg

X
SC

Y
SG

Z
SJ

0
SM

1
SN

2
SO

3
SW

4
SY

5
SZ

6
Sb

7
Se

8
Sf

9
C1

a
4A

b
CD

c
3A

d
3B

e
3C

f
3E

g
3F

h
3G

i
3H

j
3I

k
3K

l
3L

m
3M

n
3N

60S ribosomal protein L41

40S ribosomal protein SA

40S ribosomal protein S3a

40S ribosomal protein S3

40S ribosomal protein S4, X isoform

40S ribosomal protein S5

40S ribosomal protein S7

40S ribosomal protein S8

40S ribosomal protein S10

40S ribosomal protein S11

40S ribosomal protein S15

40S ribosomal protein S16

40S ribosomal protein S17

40S ribosomal protein S18

40S ribosomal protein S19

40S ribosomal protein S20

40S ribosomal protein S21

40S ribosomal protein S23

40S ribosomal protein S26

40S ribosomal protein S28

40S ribosomal protein S29

Receptor of activated protein C kinase 1

40S ribosomal protein S2

40S ribosomal protein S6

40S ribosomal protein S9

40S ribosomal protein S12

40S ribosomal protein S13

40S ribosomal protein S14

40S ribosomal protein S15a

40S ribosomal protein S24

40S ribosomal protein S25

40S ribosomal protein S27

40S ribosomal protein S30

Ubiquitin-40S ribosomal protein S27a

Eukaryotic translation initiation factor 1

Eukaryotic initiation factor 4A-I

Programmed cell death protein 4

Eukaryotic translation initiation factor 3 subunit A

Eukaryotic translation initiation factor 3 subunit B

Eukaryotic translation initiation factor 3 subunit C

Eukaryotic translation initiation factor 3 subunit E

Eukaryotic translation initiation factor 3 subunit F

Eukaryotic translation initiation factor 3 subunit G

Eukaryotic translation initiation factor 3 subunit H

Eukaryotic translation initiation factor 3 subunit I

Eukaryotic translation initiation factor 3 subunit K

Eukaryotic translation initiation factor 3 subunit L

Eukaryotic translation initiation factor 3 subunit M

Eukaryotic translation initiation factor 3 subunit D

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