Research workbench

Structure of a partial yeast 48S preinitiation complex in open conformation

Analyse Structure of a partial yeast 48S preinitiation complex in open conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3JAQ
Type: protein + RNA
Length: 8,269 residues
Chains: 47
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Met-trnai; 18S rRNA; MRNA; US2; ES1; US5; US3; ES4; US7; ES6; ES7; ES8; US4; ES10; US17…
UniProt: Q6CN12, Q6CWD0, Q6CKL3, Q6CRK7, Q6CWJ2, Q6CRA3, Q6CM04, Q6CTD6, Q6CMG3, Q6CM18, Q6CVZ5, Q6CX80, Q6CLU4, Q6CJK0, P27069, Q6CKV4, Q875N2, Q6CWU3, Q6CWT9, Q6CXM0, Q6CIM1, Q6CXT6, Q6CW21, F2Z602, Q6CU44, Q6CW78, Q6CS01, Q6CNL2, P33285, Q6CPG3, Q6CUH5, P69061, Q6CNI7, P0CX86, P38912, P20459, P32481, P09064, P32911, P40217, P06103, A6ZZ25
Ligands: MET, GCP, MG, ZN
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 47 distinct chains · 27% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	Met-trnai	rna	75	—	—
2	18S rRNA	rna	1780	—	—
3	MRNA	rna	2	—	—
A	US2	protein	208	32% helix, 13% strand	Q6CN12
B	ES1	protein	222	29% helix, 31% strand	Q6CWD0
C	US5	protein	217	29% helix, 24% strand	Q6CKL3
D	US3	protein	223	32% helix, 25% strand	Q6CRK7
E	ES4	protein	260	12% helix, 28% strand	Q6CWJ2
F	US7	protein	206	45% helix, 6% strand	Q6CRA3
G	ES6	protein	226	22% helix, 27% strand	Q6CM04
H	ES7	protein	184	34% helix, 20% strand	Q6CTD6
I	ES8	protein	188	26% helix, 22% strand	Q6CMG3
J	US4	protein	182	50% helix, 2% strand	Q6CM18
K	ES10	protein	96	42% helix, 9% strand	Q6CVZ5
L	US17	protein	155	3% helix, 26% strand	Q6CX80
M	ES12	protein	117	36% helix, 12% strand	Q6CLU4
N	US15	protein	150	57% helix, 0% strand	Q6CJK0
O	US11	protein	127	24% helix, 19% strand	P27069
P	US19	protein	119	28% helix, 13% strand	Q6CKV4
Q	US9	protein	141	33% helix, 19% strand	Q875N2
R	ES17	protein	111	54% helix, 4% strand	Q6CWU3
S	US13	protein	145	32% helix, 4% strand	Q6CWT9
T	ES19	protein	143	45% helix, 10% strand	Q6CXM0
U	US10	protein	106	25% helix, 34% strand	Q6CIM1
V	ES21	protein	87	20% helix, 26% strand	Q6CXT6
W	US8	protein	129	34% helix, 24% strand	Q6CW21
X	US12	protein	144	23% helix, 24% strand	F2Z602
Y	ES24	protein	134	34% helix, 26% strand	Q6CU44
Z	ES25	protein	70	31% helix, 11% strand	Q6CW78
a	ES26	protein	98	7% helix, 21% strand	Q6CS01
b	ES27	protein	81	7% helix, 21% strand	Q6CNL2
c	ES28	protein	62	0% helix, 48% strand	P33285
d	US14	protein	53	21% helix, 9% strand	Q6CPG3
e	ES30	protein	54	24% helix, 0% strand	Q6CUH5
f	ES31	protein	69	0% helix, 17% strand	P69061
g	RACK1	protein	318	1% helix, 51% strand	Q6CNI7
h	EL41	protein	25	88% helix, 0% strand	P0CX86
i	EIF1A	protein	95	11% helix, 35% strand	P38912
j	EIF2 alpha	protein	249	35% helix, 19% strand	P20459
k	EIF2 gamma	protein	396	12% helix, 36% strand	P32481
l	EIF2 beta	protein	128	34% helix, 15% strand	P09064
m	EIF1	protein	86	26% helix, 31% strand	P32911
o	EIF3A	protein	92	85% helix, 0% strand	—
p	EIF3C	protein	88	82% helix, 0% strand	—
q	EIF3I	protein	342	4% helix, 49% strand	P40217
r	EIF3B	protein	34	65% helix, 0% strand	P06103
s	EIF3G	protein	52	27% helix, 4% strand	A6ZZ25

Ligands and binding sites

MET · Methionine · ligand · chains 1, k
GCP · Phosphomethylphosphonic acid guanylate ester · ligand · chains k, l
MG · Magnesium ion · metal · 82 copies · chains 2, O, a, B, C, D, T, d, S, Q, U, k
ZN · Zinc ion · metal · 4 copies · chains a, b, f, l

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	1146	0.89	0.92	111	MG
2	789	0.89	0.93	100	MG
3	930	0.88	0.91	123	MG
4	901	0.88	0.91	69	MG
5	966	0.88	0.90	74	empty

Interfaces

124 interfaces between chains.

2–G · 5351 Å² buried · 118 hydrogen bonds · protein-nucleic
2–E · 4575 Å² buried · 79 hydrogen bonds · protein-nucleic
2–I · 4226 Å² buried · 118 hydrogen bonds · protein-nucleic
2–X · 4088 Å² buried · 76 hydrogen bonds · protein-nucleic
2–J · 3997 Å² buried · 84 hydrogen bonds · protein-nucleic

Modifications

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

Compared structures

Q6CW21 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S22 (Q6CW21) · a predicted model of the same protein · chain W against A, TM-score 0.98
Q6CN12 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S0 (Q6CN12) · a predicted model of the same protein · chain A against A, TM-score 0.98
P27069 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S14 (P27069) · a predicted model of the same protein · chain O against A, TM-score 0.97
P40217 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 3 subunit… · a predicted model of the same protein · chain q against A, TM-score 0.97
P32481 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 2 subunit… · a predicted model of the same protein · chain k against A, TM-score 0.96
Q6CM04 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S6 (Q6CM04) · a predicted model of the same protein · chain G against A, TM-score 0.96
Q6CWD0 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S1 (Q6CWD0) · a predicted model of the same protein · chain B against A, TM-score 0.95
Q875N2 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S16 (Q875N2) · a predicted model of the same protein · chain Q against A, TM-score 0.95
Q6CXT6 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S21 (Q6CXT6) · a predicted model of the same protein · chain V against A, TM-score 0.95
P38912 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 1A (P38912) · a predicted model of the same protein · chain i against A, TM-score 0.92
P09064 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 2 subunit… · a predicted model of the same protein · chain l against A, TM-score 0.91
P32911 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor eif-1… · a predicted model of the same protein · chain m against A, TM-score 0.90

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 Q6CN12
Every structure of UniProt Q6CWD0
Every structure of UniProt Q6CKL3
Every structure of UniProt Q6CRK7
Every structure of UniProt Q6CWJ2
Every structure of UniProt Q6CRA3
Every structure of UniProt Q6CM04
Every structure of UniProt Q6CTD6
Every structure of UniProt Q6CMG3
Every structure of UniProt Q6CM18
Every structure of UniProt Q6CVZ5
Every structure of UniProt Q6CX80
Every structure of UniProt Q6CLU4
Every structure of UniProt Q6CJK0
Every structure of UniProt P27069
Every structure of UniProt Q6CKV4
Every structure of UniProt Q875N2
Every structure of UniProt Q6CWU3
Every structure of UniProt Q6CWT9
Every structure of UniProt Q6CXM0
Every structure of UniProt Q6CIM1
Every structure of UniProt Q6CXT6
Every structure of UniProt Q6CW21
Every structure of UniProt F2Z602
Every structure of UniProt Q6CU44
Every structure of UniProt Q6CW78
Every structure of UniProt Q6CS01
Every structure of UniProt Q6CNL2
Every structure of UniProt P33285
Every structure of UniProt Q6CPG3
Every structure of UniProt Q6CUH5
Every structure of UniProt P69061
Every structure of UniProt Q6CNI7
Every structure of UniProt P0CX86
Every structure of UniProt P38912
Every structure of UniProt P20459
Every structure of UniProt P32481
Every structure of UniProt P09064
Every structure of UniProt P32911
Every structure of UniProt P40217
Every structure of UniProt P06103
Every structure of UniProt A6ZZ25
Elsewhere: RCSB PDB 3JAQ · PDBe 3JAQ · UniProt Q6CN12 · UniProt Q6CWD0 · UniProt Q6CKL3 · UniProt Q6CRK7 · UniProt Q6CWJ2 · UniProt Q6CRA3 · UniProt Q6CM04 · UniProt Q6CTD6 · UniProt Q6CMG3 · UniProt Q6CM18 · UniProt Q6CVZ5 · UniProt Q6CX80 · UniProt Q6CLU4 · UniProt Q6CJK0 · UniProt P27069 · UniProt Q6CKV4 · UniProt Q875N2 · UniProt Q6CWU3 · UniProt Q6CWT9 · UniProt Q6CXM0 · UniProt Q6CIM1 · UniProt Q6CXT6 · UniProt Q6CW21 · UniProt F2Z602 · UniProt Q6CU44 · UniProt Q6CW78 · UniProt Q6CS01 · UniProt Q6CNL2 · UniProt P33285 · UniProt Q6CPG3 · UniProt Q6CUH5 · UniProt P69061 · UniProt Q6CNI7 · UniProt P0CX86 · UniProt P38912 · UniProt P20459 · UniProt P32481 · UniProt P09064 · UniProt P32911 · UniProt P40217 · UniProt P06103 · UniProt A6ZZ25

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