Research workbench

Cryo-EM structure of a late human pre-40S ribosomal subunit - state H2

Analyse Cryo-EM structure of a late human pre-40S ribosomal subunit - state H2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6ZXH
Type: protein + RNA
Length: 6,845 residues
Chains: 36
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pre-18S ribosomal RNA; 40S ribosomal protein sa; 40S ribosomal protein S3A; 40S ribosomal…
EC: 4.2.99.18, 2.7.11.1, 3.6.3.-
UniProt: P08865, P61247, P15880, P62854, P62701, P23396, P62753, P62081, P62241, P46781, P46782, P62280, P46783, P62277, P62263, P25398, P62841, P08708, P62249, P62269, P39019, P63220, P62244, P62266, P62847, P60866, P62851, P42677, P62857, P62273, P62861, P62979, P63244, Q8N9N8, Q9BRS2
Ligands: ASP, ATP, MG, ZN
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 36 distinct chains · 31% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
2	Pre-18S ribosomal RNA	rna	1651	—	—
A	40S ribosomal protein sa	protein	216	37% helix, 14% strand	P08865
B	40S ribosomal protein S3A	protein	211	27% helix, 37% strand	P61247
C	40S ribosomal protein S2	protein	216	33% helix, 28% strand	P15880
h	40S ribosomal protein S26	protein	99	16% helix, 23% strand	P62854
E	40S ribosomal protein S4, X isoform	protein	255	15% helix, 32% strand	P62701
D	40S ribosomal protein S3 (EC 4.2.99.18)	protein	224	33% helix, 27% strand	P23396
G	40S ribosomal protein S6	protein	223	22% helix, 25% strand	P62753
H	40S ribosomal protein S7	protein	179	35% helix, 23% strand	P62081
I	40S ribosomal protein S8	protein	199	29% helix, 28% strand	P62241
J	40S ribosomal protein S9	protein	176	52% helix, 6% strand	P46781
F	40S ribosomal protein S5	protein	184	51% helix, 7% strand	P46782
L	40S ribosomal protein S11	protein	136	3% helix, 35% strand	P62280
K	40S ribosomal protein S10	protein	95	40% helix, 15% strand	P46783
N	40S ribosomal protein S13	protein	149	57% helix, 0% strand	P62277
O	40S ribosomal protein S14	protein	126	24% helix, 27% strand	P62263
M	40S ribosomal protein S12	protein	108	40% helix, 15% strand	P25398
P	40S ribosomal protein S15	protein	132	36% helix, 13% strand	P62841
R	40S ribosomal protein S17	protein	132	48% helix, 6% strand	P08708
Q	40S ribosomal protein S16	protein	140	39% helix, 20% strand	P62249
S	40S ribosomal protein S18	protein	141	40% helix, 9% strand	P62269
T	40S ribosomal protein S19	protein	141	48% helix, 13% strand	P39019
V	40S ribosomal protein S21	protein	83	19% helix, 24% strand	P63220
W	40S ribosomal protein S15A	protein	129	32% helix, 28% strand	P62244
X	40S ribosomal protein S23	protein	139	25% helix, 29% strand	P62266
Y	40S ribosomal protein S24	protein	122	34% helix, 30% strand	P62847
U	40S ribosomal protein S20	protein	98	26% helix, 44% strand	P60866
Z	40S ribosomal protein S25	protein	82	40% helix, 16% strand	P62851
b	40S ribosomal protein S27	protein	77	8% helix, 25% strand	P42677
c	40S ribosomal protein S28	protein	61	0% helix, 48% strand	P62857
d	40S ribosomal protein S29	protein	54	26% helix, 9% strand	P62273
e	40S ribosomal protein S30	protein	50	34% helix, 0% strand	P62861
f	Ubiquitin-40S ribosomal protein S27A	protein	57	0% helix, 26% strand	P62979
g	Receptor of activated protein C kinase 1	protein	295	0% helix, 52% strand	P63244
j	Probable RNA-binding protein EIF1AD	protein	116	17% helix, 30% strand	Q8N9N8
z	SERINE/THREONINE-protein kinase RIO1 (EC 2.7.11.1, 3.6.3.-)	protein	349	47% helix, 14% strand	Q9BRS2

Ligands and binding sites

ASP · Aspartic acid · ligand · chains 2, U, d
ATP · Adenosine-5'-triphosphate · ligand · chains 2, z
MG · Magnesium ion · metal · 131 copies · chains 2, T, h, I, C, z, O, N, U, Q, X, G, F, d
ZN · Zinc ion · metal · 3 copies · chains h, 2, d, f

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	1020	0.89	0.91	105	MG
2	1102	0.88	0.90	97	MG
3	977	0.88	0.90	82	empty
4	799	0.87	0.91	94	ASP, MG
5	818	0.87	0.90	74	MG

Interfaces

103 interfaces between chains.

2–G · 5187 Å² buried · 114 hydrogen bonds · protein-nucleic
2–z · 4314 Å² buried · 86 hydrogen bonds · protein-nucleic
2–I · 4229 Å² buried · 101 hydrogen bonds · protein-nucleic
2–E · 3798 Å² buried · 67 hydrogen bonds · protein-nucleic
2–J · 3652 Å² buried · 80 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 74 modified, 1 disulfide (nucleotide modification, disulfide).

Compared structures

6ZXH · Cryo-EM structure of a late human pre-40S ribosomal subunit - State H2 · the same entry in another collection · chain J against J, 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 P08865
Every structure of UniProt P61247
Every structure of UniProt P15880
Every structure of UniProt P62854
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 P46783
Every structure of UniProt P62277
Every structure of UniProt P62263
Every structure of UniProt P25398
Every structure of UniProt P62841
Every structure of UniProt P08708
Every structure of UniProt P62249
Every structure of UniProt P62269
Every structure of UniProt P39019
Every structure of UniProt P63220
Every structure of UniProt P62244
Every structure of UniProt P62266
Every structure of UniProt P62847
Every structure of UniProt P60866
Every structure of UniProt P62851
Every structure of UniProt P42677
Every structure of UniProt P62857
Every structure of UniProt P62273
Every structure of UniProt P62861
Every structure of UniProt P62979
Every structure of UniProt P63244
Every structure of UniProt Q8N9N8
Every structure of UniProt Q9BRS2
Elsewhere: RCSB PDB 6ZXH · PDBe 6ZXH · UniProt P08865 · UniProt P61247 · UniProt P15880 · UniProt P62854 · UniProt P62701 · UniProt P23396 · UniProt P62753 · UniProt P62081 · UniProt P62241 · UniProt P46781 · UniProt P46782 · UniProt P62280 · UniProt P46783 · UniProt P62277 · UniProt P62263 · UniProt P25398 · UniProt P62841 · UniProt P08708 · UniProt P62249 · UniProt P62269 · UniProt P39019 · UniProt P63220 · UniProt P62244 · UniProt P62266 · UniProt P62847 · UniProt P60866 · UniProt P62851 · UniProt P42677 · UniProt P62857 · UniProt P62273 · UniProt P62861 · UniProt P62979 · UniProt P63244 · UniProt Q8N9N8 · UniProt Q9BRS2

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