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Structure of a yeast ABCE1-bound 48S initiation complex

Analyse Structure of a yeast ABCE1-bound 48S initiation complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6ZU9
Type: protein + RNA
Length: 9,699 residues
Chains: 44
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 18S ribosomal RNA; 40S ribosomal protein S0-a; 40S ribosomal protein S1-a; 40S ribosomal…
UniProt: P32905, P33442, P25443, P0CX35, P0CX37, P26786, P0CX39, O13516, P0CX47, P05756, P06367, P0C0V8, P0C0W1, P0CX29, P0CX31, P39938, P35997, P0CX33, Q01855, P05750, A0A1L4AA68, Q08745, P48589, P0CX51, P02407, P0CX55, P07280, P38701, Q3E792, P41057, P05759, P38011, P0C0X0, P40217, Q04067, P38431, P38249, P06103, P32497, P38912, Q03195
Ligands: SF4, ADP, ATP, MG, ZN
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 44 distinct chains · 33% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
2	18S ribosomal RNA	rna	1771	—	—
P	40S ribosomal protein S0-a	protein	206	34% helix, 13% strand	P32905
Q	40S ribosomal protein S1-a	protein	226	26% helix, 29% strand	P33442
R	40S ribosomal protein S2	protein	216	31% helix, 29% strand	P25443
S	40S ribosomal protein S4-a	protein	258	17% helix, 31% strand	P0CX35
T	40S ribosomal protein S6-a	protein	228	30% helix, 24% strand	P0CX37
U	40S ribosomal protein S7-a	protein	184	35% helix, 21% strand	P26786
V	40S ribosomal protein S8-a	protein	187	26% helix, 28% strand	P0CX39
W	40S ribosomal protein S9-a	protein	184	49% helix, 1% strand	O13516
X	40S ribosomal protein S11-a	protein	142	4% helix, 35% strand	P0CX47
Y	40S ribosomal protein S13	protein	150	57% helix, 0% strand	P05756
Z	40S ribosomal protein S14-a	protein	127	27% helix, 26% strand	P06367
a	40S ribosomal protein S21-a	protein	87	18% helix, 29% strand	P0C0V8
b	40S ribosomal protein S22-a	protein	129	35% helix, 27% strand	P0C0W1
c	40S ribosomal protein S23-a	protein	144	23% helix, 26% strand	P0CX29
d	40S ribosomal protein S24-a	protein	134	37% helix, 25% strand	P0CX31
e	40S ribosomal protein S26-a	protein	97	16% helix, 21% strand	P39938
f	40S ribosomal protein S27-a	protein	81	11% helix, 22% strand	P35997
g	40S ribosomal protein S30-a	protein	53	34% helix, 0% strand	P0CX33
E	40S ribosomal protein S15	protein	117	33% helix, 15% strand	Q01855
B	40S ribosomal protein S3	protein	222	38% helix, 30% strand	P05750
C	RPS5P	protein	206	49% helix, 6% strand	A0A1L4AA68
D	40S ribosomal protein S10-a	protein	92	41% helix, 10% strand	Q08745
F	40S ribosomal protein S12	protein	121	37% helix, 8% strand	P48589
H	40S ribosomal protein S16-a	protein	141	41% helix, 20% strand	P0CX51
I	40S ribosomal protein S17-a	protein	121	53% helix, 5% strand	P02407
J	40S ribosomal protein S18-a	protein	145	37% helix, 9% strand	P0CX55
K	40S ribosomal protein S19-a	protein	143	48% helix, 10% strand	P07280
L	40S ribosomal protein S20	protein	100	26% helix, 39% strand	P38701
M	40S ribosomal protein S25-a	protein	82	39% helix, 21% strand	Q3E792
N	40S ribosomal protein S29-a	protein	53	26% helix, 9% strand	P41057
O	Ubiquitin-40S ribosomal protein S31	protein	73	0% helix, 3% strand	P05759
h	Guanine nucleotide-binding protein subunit beta-like protein	protein	312	0% helix, 52% strand	P38011
i	40S ribosomal protein S28-B	protein	63	0% helix, 48% strand	P0C0X0
l	Eukaryotic translation initiation factor 3 subunit I	protein	330	6% helix, 52% strand	P40217
r	Eukaryotic translation initiation factor 3 subunit G	protein	53	36% helix, 6% strand	Q04067
1	TRNA	rna	75	—	—
m	Eukaryotic translation initiation factor 5	protein	147	29% helix, 18% strand	P38431
o	Eukaryotic translation initiation factor 3 subunit a	protein	529	71% helix, 2% strand	P38249
p	Eukaryotic translation initiation factor 3 subunit B	protein	646	13% helix, 37% strand	P06103
q	Eukaryotic translation initiation factor 3 subunit C	protein	636	64% helix, 0% strand	P32497
3	MRNA	rna	8	—	—
A	Eukaryotic translation initiation factor 1A	protein	101	10% helix, 34% strand	P38912
k	Translation initiation factor RLI1	protein	579	30% helix, 18% strand	Q03195

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · 2 copies · chains k
ADP · Adenosine-5'-diphosphate · ligand · chains k
ATP · Adenosine-5'-triphosphate · ligand · chains k
MG · Magnesium ion · metal · 4 copies · chains 2, S, C, k
ZN · Zinc ion · metal · 3 copies · chains N, O, m

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	924	0.88	0.91	87	empty
2	1143	0.85	0.87	126	empty
3	1015	0.85	0.86	150	empty
4	728	0.85	0.89	110	empty
5	634	0.85	0.90	66	empty

Interfaces

102 interfaces between chains.

2–T · 2420 Å² buried · 27 hydrogen bonds · protein-nucleic
2–V · 2226 Å² buried · 21 hydrogen bonds · protein-nucleic
2–S · 1992 Å² buried · 26 hydrogen bonds · protein-nucleic
2–c · 1853 Å² buried · 22 hydrogen bonds · protein-nucleic
2–K · 1694 Å² buried · 21 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 11 modified (nucleotide modification).

Compared structures

6ZU9 · Structure of a yeast ABCE1-bound 48S initiation complex · the same entry in another collection · chain Y against Y, 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 P33442
Every structure of UniProt P25443
Every structure of UniProt P0CX35
Every structure of UniProt P0CX37
Every structure of UniProt P26786
Every structure of UniProt P0CX39
Every structure of UniProt O13516
Every structure of UniProt P0CX47
Every structure of UniProt P05756
Every structure of UniProt P06367
Every structure of UniProt P0C0V8
Every structure of UniProt P0C0W1
Every structure of UniProt P0CX29
Every structure of UniProt P0CX31
Every structure of UniProt P39938
Every structure of UniProt P35997
Every structure of UniProt P0CX33
Every structure of UniProt Q01855
Every structure of UniProt P05750
Every structure of UniProt A0A1L4AA68
Every structure of UniProt Q08745
Every structure of UniProt P48589
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 Q3E792
Every structure of UniProt P41057
Every structure of UniProt P05759
Every structure of UniProt P38011
Every structure of UniProt P0C0X0
Every structure of UniProt P40217
Every structure of UniProt Q04067
Every structure of UniProt P38431
Every structure of UniProt P38249
Every structure of UniProt P06103
Every structure of UniProt P32497
Every structure of UniProt P38912
Every structure of UniProt Q03195
Elsewhere: RCSB PDB 6ZU9 · PDBe 6ZU9 · UniProt P32905 · UniProt P33442 · UniProt P25443 · UniProt P0CX35 · UniProt P0CX37 · UniProt P26786 · UniProt P0CX39 · UniProt O13516 · UniProt P0CX47 · UniProt P05756 · UniProt P06367 · UniProt P0C0V8 · UniProt P0C0W1 · UniProt P0CX29 · UniProt P0CX31 · UniProt P39938 · UniProt P35997 · UniProt P0CX33 · UniProt Q01855 · UniProt P05750 · UniProt A0A1L4AA68 · UniProt Q08745 · UniProt P48589 · UniProt P0CX51 · UniProt P02407 · UniProt P0CX55 · UniProt P07280 · UniProt P38701 · UniProt Q3E792 · UniProt P41057 · UniProt P05759 · UniProt P38011 · UniProt P0C0X0 · UniProt P40217 · UniProt Q04067 · UniProt P38431 · UniProt P38249 · UniProt P06103 · UniProt P32497 · UniProt P38912 · UniProt Q03195

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