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Cryo-EM structure of the plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine, small subunit

Analyse Cryo-EM structure of the plasmodium falciparum 80S ribosome bound to the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3J7A
Type: protein + RNA
Length: 5,788 residues
Chains: 33
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 18S ribosomal RNA; 40S ribosomal protein ES1; 40S ribosomal protein US2; 40S ribosomal…
UniProt: O97313, Q8IJD4, Q8IKH8, Q8I3R0, Q8IIU8, Q8IL02, Q8IDR9, Q8IBN5, Q8IET7, O77395, Q8IM10, Q8IAX5, Q8IK02, Q8IBQ5, Q8I3U6, O97248, O97249, Q8IIA2, C0H4K8, Q8IDB0, O77381, Q8I502, C0H5C2, Q8IFP2, Q8IHS5, Q8I3R6, Q8ILN8, O96258, Q8IEN2, Q8IKL9, O96269
Ligands: 34G, MG, ZN
Pockets: 20 · best druggability 0.90

Structure

electron microscopy · 33 distinct chains · 33% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	18S ribosomal RNA	rna	1608	—	—
B	40S ribosomal protein ES1	protein	210	32% helix, 22% strand	O97313
C	40S ribosomal protein US2	protein	195	36% helix, 11% strand	Q8IJD4
D	40S ribosomal protein US3	protein	157	42% helix, 20% strand	Q8IKH8
E	40S ribosomal protein US4	protein	185	51% helix, 4% strand	Q8I3R0
F	40S ribosomal protein ES4	protein	257	14% helix, 30% strand	Q8IIU8
G	40S ribosomal protein US5	protein	224	32% helix, 23% strand	Q8IL02
H	40S ribosomal protein ES6	protein	204	25% helix, 21% strand	Q8IDR9
I	40S ribosomal protein US7	protein	180	55% helix, 4% strand	Q8IBN5
J	40S ribosomal protein ES7	protein	188	32% helix, 20% strand	Q8IET7
K	40S ribosomal protein US8	protein	129	33% helix, 29% strand	O77395
L	40S ribosomal protein ES8	protein	172	23% helix, 28% strand	Q8IM10
M	40S ribosomal protein US9	protein	138	34% helix, 21% strand	Q8IAX5
N	40S ribosomal protein US10	protein	98	24% helix, 29% strand	Q8IK02
O	40S ribosomal protein ES10	protein	79	46% helix, 10% strand	Q8IBQ5
P	40S ribosomal protein US11	protein	127	24% helix, 19% strand	Q8I3U6
Q	40S ribosomal protein US12	protein	144	20% helix, 28% strand	O97248
R	40S ribosomal protein ES12	protein	98	44% helix, 9% strand	O97249
S	40S ribosomal protein US13	protein	128	41% helix, 2% strand	Q8IIA2
T	40S ribosomal protein US14	protein	48	29% helix, 13% strand	C0H4K8
U	40S ribosomal protein US15	protein	149	54% helix, 0% strand	Q8IDB0
V	40S ribosomal protein US17	protein	146	5% helix, 27% strand	O77381
W	40S ribosomal protein ES17	protein	95	63% helix, 0% strand	Q8I502
X	40S ribosomal protein US19	protein	96	44% helix, 4% strand	C0H5C2
Y	40S ribosomal protein ES19	protein	154	52% helix, 11% strand	Q8IFP2
Z	40S ribosomal protein ES21	protein	72	28% helix, 28% strand	Q8IHS5
1	40S ribosomal protein ES24	protein	120	28% helix, 28% strand	Q8I3R6
2	40S ribosomal protein ES25	protein	41	49% helix, 10% strand	Q8ILN8
3	40S ribosomal protein ES26	protein	95	21% helix, 19% strand	O96258
4	40S ribosomal protein ES27	protein	76	0% helix, 17% strand	Q8IEN2
5	40S ribosomal protein ES28	protein	58	0% helix, 43% strand	Q8IKL9
6	40S ribosomal protein ES30	protein	43	42% helix, 0% strand	O96269
7	TRNA	rna	74	—	—

Ligands and binding sites

34G · emetine · ligand · chains A, P
MG · Magnesium ion · metal · 67 copies · chains A, U, 3, M, D
ZN · Zinc ion · metal · chains A, T

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	996	0.90	0.94	117	MG
2	973	0.90	0.93	119	empty
3	1112	0.89	0.92	113	MG
4	980	0.89	0.91	134	empty
5	1122	0.88	0.91	94	MG

Interfaces

86 interfaces between chains.

A–H · 4433 Å² buried · 100 hydrogen bonds · protein-nucleic
A–F · 4316 Å² buried · 78 hydrogen bonds · protein-nucleic
A–Q · 3756 Å² buried · 77 hydrogen bonds · protein-nucleic
A–E · 3746 Å² buried · 76 hydrogen bonds · protein-nucleic
A–L · 3433 Å² buried · 79 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

3J7A · Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan… · the same entry in another collection · chain N against N, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt O97313
Every structure of UniProt Q8IJD4
Every structure of UniProt Q8IKH8
Every structure of UniProt Q8I3R0
Every structure of UniProt Q8IIU8
Every structure of UniProt Q8IL02
Every structure of UniProt Q8IDR9
Every structure of UniProt Q8IBN5
Every structure of UniProt Q8IET7
Every structure of UniProt O77395
Every structure of UniProt Q8IM10
Every structure of UniProt Q8IAX5
Every structure of UniProt Q8IK02
Every structure of UniProt Q8IBQ5
Every structure of UniProt Q8I3U6
Every structure of UniProt O97248
Every structure of UniProt O97249
Every structure of UniProt Q8IIA2
Every structure of UniProt C0H4K8
Every structure of UniProt Q8IDB0
Every structure of UniProt O77381
Every structure of UniProt Q8I502
Every structure of UniProt C0H5C2
Every structure of UniProt Q8IFP2
Every structure of UniProt Q8IHS5
Every structure of UniProt Q8I3R6
Every structure of UniProt Q8ILN8
Every structure of UniProt O96258
Every structure of UniProt Q8IEN2
Every structure of UniProt Q8IKL9
Every structure of UniProt O96269
Elsewhere: RCSB PDB 3J7A · PDBe 3J7A · UniProt O97313 · UniProt Q8IJD4 · UniProt Q8IKH8 · UniProt Q8I3R0 · UniProt Q8IIU8 · UniProt Q8IL02 · UniProt Q8IDR9 · UniProt Q8IBN5 · UniProt Q8IET7 · UniProt O77395 · UniProt Q8IM10 · UniProt Q8IAX5 · UniProt Q8IK02 · UniProt Q8IBQ5 · UniProt Q8I3U6 · UniProt O97248 · UniProt O97249 · UniProt Q8IIA2 · UniProt C0H4K8 · UniProt Q8IDB0 · UniProt O77381 · UniProt Q8I502 · UniProt C0H5C2 · UniProt Q8IFP2 · UniProt Q8IHS5 · UniProt Q8I3R6 · UniProt Q8ILN8 · UniProt O96258 · UniProt Q8IEN2 · UniProt Q8IKL9 · UniProt O96269

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