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Cryoem structure of the human 40S small ribosomal subunit in complex with translation initiation factors EIF1A and EIF5B.

Analyse Cryoem structure of the human 40S small ribosomal subunit in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7TQL
Type: protein + RNA
Length: 7,239 residues
Chains: 38
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Eukaryotic translation initiation factor 5B; 18S ribosomal RNA; Human met-trnaimet…
EC: 3.6.5.3, 4.2.99.18
UniProt: O60841, P15880, P62701, P23396, P62753, P62081, P62241, P46781, P46782, P62280, A0A2R8Y7H1, P62841, P62249, P39019, P62244, P62266, P62847, P63220, P42677, P62854, P62979, P63244
Ligands: GNP, 5GP, ZN
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 38 distinct chains · 30% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	Eukaryotic translation initiation factor 5B (EC 3.6.5.3)	protein	619	26% helix, 23% strand	O60841
2	18S ribosomal RNA	rna	1656	—	—
3	Human met-trnaimet	rna	75	—	—
4	Translation initiation factor EIF1A	protein	90	14% helix, 28% strand	—
B	Ribosomal protein US2	protein	206	36% helix, 15% strand	—
C	Ribosomal protein US2	protein	213	30% helix, 34% strand	—
D	40S ribosomal protein S2	protein	218	33% helix, 27% strand	P15880
E	40S ribosomal protein S4, X isoform	protein	258	14% helix, 31% strand	P62701
F	40S ribosomal protein S3 (EC 4.2.99.18)	protein	225	32% helix, 25% strand	P23396
G	40S ribosomal protein S6	protein	226	27% helix, 25% strand	P62753
H	40S ribosomal protein S7	protein	185	40% helix, 23% strand	P62081
I	40S ribosomal protein S8	protein	205	28% helix, 26% strand	P62241
J	40S ribosomal protein S9	protein	180	47% helix, 5% strand	P46781
K	40S ribosomal protein S5	protein	189	52% helix, 7% strand	P46782
L	40S ribosomal protein S11	protein	147	6% helix, 31% strand	P62280
M	40S ribosomal protein S10	protein	97	43% helix, 14% strand	A0A2R8Y7H1
N	Ribosomal protein US15	protein	141	54% helix, 0% strand	—
O	Ribosomal protein ES12	protein	120	38% helix, 18% strand	—
P	Ribosomal protein US11	protein	134	26% helix, 25% strand	—
Q	40S ribosomal protein S15	protein	115	34% helix, 15% strand	P62841
R	40S ribosomal protein S16	protein	139	43% helix, 19% strand	P62249
S	Ribosomal protein ES17	protein	132	46% helix, 6% strand	—
T	Ribosomal protein US13	protein	140	44% helix, 9% strand	—
U	40S ribosomal protein S19	protein	139	50% helix, 14% strand	P39019
V	Ribosomal protein US10	protein	101	25% helix, 40% strand	—
W	40S ribosomal protein S15A	protein	129	34% helix, 26% strand	P62244
X	40S ribosomal protein S23	protein	141	24% helix, 29% strand	P62266
Y	Isoform 3 of 40S ribosomal protein S24	protein	123	36% helix, 27% strand	P62847
Z	40S ribosomal protein S21	protein	82	22% helix, 27% strand	P63220
a	Ribosomal protein ES25	protein	72	44% helix, 17% strand	—
b	40S ribosomal protein S27	protein	82	7% helix, 26% strand	P42677
c	40S ribosomal protein S26	protein	99	16% helix, 23% strand	P62854
d	Ribosomal protein ES28	protein	58	0% helix, 50% strand	—
e	Ribosomal protein ES30	protein	51	31% helix, 0% strand	—
f	Ribosomal protein US14	protein	54	26% helix, 11% strand	—
g	40S ribosomal protein S27A	protein	65	6% helix, 22% strand	P62979
h	Ribosomal protein EL41	protein	19	84% helix, 0% strand	—
j	Receptor of activated protein C kinase 1	protein	314	0% helix, 50% strand	P63244

Ligands and binding sites

GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains 1
5GP · Guanosine-5'-monophosphate · ligand · chains 2, 3
ZN · Zinc ion · metal · 3 copies · chains c, f, g

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	1009	0.88	0.90	87	empty
2	907	0.87	0.90	86	empty
3	733	0.86	0.90	67	empty
4	514	0.86	0.93	65	empty
5	1198	0.85	0.87	79	empty

Interfaces

98 interfaces between chains.

2–G · 5205 Å² buried · 110 hydrogen bonds · protein-nucleic
2–I · 4389 Å² buried · 99 hydrogen bonds · protein-nucleic
2–E · 3893 Å² buried · 70 hydrogen bonds · protein-nucleic
2–X · 3713 Å² buried · 70 hydrogen bonds · protein-nucleic
2–J · 3638 Å² buried · 77 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

7TQL · CryoEM structure of the human 40S small ribosomal subunit in complex with translation… · the same entry in another collection · chain 3 against 3, 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 O60841
Every structure of UniProt P15880
Every structure of UniProt P62701
Every structure of UniProt P23396
Every structure of UniProt P62753
Every structure of UniProt P62081
Every structure of UniProt P62241
Every structure of UniProt P46781
Every structure of UniProt P46782
Every structure of UniProt P62280
Every structure of UniProt A0A2R8Y7H1
Every structure of UniProt P62841
Every structure of UniProt P62249
Every structure of UniProt P39019
Every structure of UniProt P62244
Every structure of UniProt P62266
Every structure of UniProt P62847
Every structure of UniProt P63220
Every structure of UniProt P42677
Every structure of UniProt P62854
Every structure of UniProt P62979
Every structure of UniProt P63244
Elsewhere: RCSB PDB 7TQL · PDBe 7TQL · UniProt O60841 · UniProt P15880 · UniProt P62701 · UniProt P23396 · UniProt P62753 · UniProt P62081 · UniProt P62241 · UniProt P46781 · UniProt P46782 · UniProt P62280 · UniProt A0A2R8Y7H1 · UniProt P62841 · UniProt P62249 · UniProt P39019 · UniProt P62244 · UniProt P62266 · UniProt P62847 · UniProt P63220 · UniProt P42677 · UniProt P62854 · UniProt P62979 · UniProt P63244

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