Research workbench

Subunit joining exposes nascent pre-40S rRNA for processing and quality control

Analyse Subunit joining exposes nascent pre-40S rRNA for processing and quality control in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6WDR
Type: protein + RNA
Length: 6,631 residues
Chains: 32
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 40S ribosomal protein S0-a; 40S ribosomal protein S2; 40S ribosomal protein S3; 40S…
UniProt: P32905, P25443, P05750, P0CX35, P26783, P0CX37, P26786, P0CX39, O13516, Q08745, P0CX47, P48589, P05756, Q01855, P0CX51, P02407, P0CX55, P07280, P38701, P0C0V8, P0C0W1, P0CX29, P0CX31, Q3E792, P35997, Q3E7X9, P41057, P0CX33, P05759, P38011, Q07381
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 32 distinct chains · 23% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	40S ribosomal protein S0-a	protein	206	31% helix, 12% strand	P32905
C	40S ribosomal protein S2	protein	217	28% helix, 28% strand	P25443
D	40S ribosomal protein S3	protein	223	19% helix, 9% strand	P05750
E	40S ribosomal protein S4-a	protein	260	13% helix, 30% strand	P0CX35
F	40S ribosomal protein S5	protein	206	38% helix, 1% strand	P26783
G	40S ribosomal protein S6-a	protein	232	28% helix, 20% strand	P0CX37
H	40S ribosomal protein S7-a	protein	184	36% helix, 19% strand	P26786
I	40S ribosomal protein S8-a	protein	188	19% helix, 23% strand	P0CX39
J	40S ribosomal protein S9-a	protein	185	45% helix, 3% strand	O13516
K	40S ribosomal protein S10-a	protein	96	26% helix, 2% strand	Q08745
L	40S ribosomal protein S11-a	protein	140	3% helix, 32% strand	P0CX47
M	40S ribosomal protein S12	protein	125	11% helix, 6% strand	P48589
N	40S ribosomal protein S13	protein	150	49% helix, 0% strand	P05756
P	40S ribosomal protein S15	protein	127	10% helix, 4% strand	Q01855
Q	40S ribosomal protein S16-a	protein	127	37% helix, 19% strand	P0CX51
R	40S ribosomal protein S17-a	protein	125	46% helix, 7% strand	P02407
S	40S ribosomal protein S18-a	protein	135	34% helix, 2% strand	P0CX55
T	40S ribosomal protein S19-a	protein	143	46% helix, 9% strand	P07280
U	40S ribosomal protein S20	protein	103	20% helix, 35% strand	P38701
V	40S ribosomal protein S21-a	protein	87	17% helix, 24% strand	P0C0V8
W	40S ribosomal protein S22-a	protein	129	17% helix, 29% strand	P0C0W1
X	40S ribosomal protein S23-a	protein	144	17% helix, 26% strand	P0CX29
Y	40S ribosomal protein S24-a	protein	134	29% helix, 26% strand	P0CX31
Z	40S ribosomal protein S25-a	protein	63	29% helix, 17% strand	Q3E792
b	40S ribosomal protein S27-a	protein	81	5% helix, 21% strand	P35997
c	40S ribosomal protein S28-a	protein	63	0% helix, 41% strand	Q3E7X9
d	40S ribosomal protein S29-a	protein	37	27% helix, 8% strand	P41057
e	40S ribosomal protein S30-a	protein	48	25% helix, 4% strand	P0CX33
f	Ubiquitin-40S ribosomal protein S31	protein	71	0% helix, 0% strand	P05759
g	Guanine nucleotide-binding protein subunit beta-like protein	protein	317	0% helix, 44% strand	P38011
k	Ribosome biogenesis protein TSR1	protein	638	14% helix, 24% strand	Q07381
2	20S ribosomal RNA	rna	1647	—	—

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	936	0.87	0.89	110	empty
2	687	0.87	0.92	73	empty
3	847	0.87	0.90	66	empty
4	1095	0.86	0.88	84	empty
5	1078	0.85	0.86	90	empty

Interfaces

83 interfaces between chains.

G–2 · 4928 Å² buried · 80 hydrogen bonds · protein-nucleic
E–2 · 3743 Å² buried · 36 hydrogen bonds · protein-nucleic
I–2 · 3698 Å² buried · 57 hydrogen bonds · protein-nucleic
X–2 · 3393 Å² buried · 47 hydrogen bonds · protein-nucleic
J–2 · 3143 Å² buried · 46 hydrogen bonds · protein-nucleic

Compared structures

6WDR · Subunit joining exposes nascent pre-40S rRNA for processing and quality control · the same entry in another collection · chain L against L, 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 P32905
Every structure of UniProt P25443
Every structure of UniProt P05750
Every structure of UniProt P0CX35
Every structure of UniProt P26783
Every structure of UniProt P0CX37
Every structure of UniProt P26786
Every structure of UniProt P0CX39
Every structure of UniProt O13516
Every structure of UniProt Q08745
Every structure of UniProt P0CX47
Every structure of UniProt P48589
Every structure of UniProt P05756
Every structure of UniProt Q01855
Every structure of UniProt P0CX51
Every structure of UniProt P02407
Every structure of UniProt P0CX55
Every structure of UniProt P07280
Every structure of UniProt P38701
Every structure of UniProt P0C0V8
Every structure of UniProt P0C0W1
Every structure of UniProt P0CX29
Every structure of UniProt P0CX31
Every structure of UniProt Q3E792
Every structure of UniProt P35997
Every structure of UniProt Q3E7X9
Every structure of UniProt P41057
Every structure of UniProt P0CX33
Every structure of UniProt P05759
Every structure of UniProt P38011
Every structure of UniProt Q07381
Elsewhere: RCSB PDB 6WDR · PDBe 6WDR · UniProt P32905 · UniProt P25443 · UniProt P05750 · UniProt P0CX35 · UniProt P26783 · UniProt P0CX37 · UniProt P26786 · UniProt P0CX39 · UniProt O13516 · UniProt Q08745 · UniProt P0CX47 · UniProt P48589 · UniProt P05756 · UniProt Q01855 · UniProt P0CX51 · UniProt P02407 · UniProt P0CX55 · UniProt P07280 · UniProt P38701 · UniProt P0C0V8 · UniProt P0C0W1 · UniProt P0CX29 · UniProt P0CX31 · UniProt Q3E792 · UniProt P35997 · UniProt Q3E7X9 · UniProt P41057 · UniProt P0CX33 · UniProt P05759 · UniProt P38011 · UniProt Q07381

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