Research workbench

Cryoem structure of 40S-EIF1-EIF1A preinitiation complex

Analyse Cryoem structure of 40S-EIF1-EIF1A preinitiation complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3J80
Type: protein + RNA
Length: 6,818 residues
Chains: 37
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 18S rRNA; US2; ES1; US5; ES4; ES6; ES7; ES8; US4; US17; US15; US11; ES21; US8; US12…
UniProt: Q6CN12, Q6CWD0, Q6CKL3, Q6CWJ2, Q6CM04, Q6CTD6, Q6CMG3, Q6CM18, Q6CX80, Q6CJK0, P27069, Q6CXT6, Q6CW21, F2Z602, Q6CU44, Q6CS01, Q6CNL2, Q6CUH5, Q6CRK7, Q6CRA3, Q6CVZ5, Q6CLU4, Q6CKV4, Q875N2, Q6CWU3, Q6CWT9, Q6CXM0, Q6CIM1, Q6CW78, P33285, Q6CPG3, P69061, Q6CNI7, P0CX86, P38912, P32911
Ligands: MG, ZN
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 37 distinct chains · 28% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
2	18S rRNA	rna	1779	—	—
A	US2	protein	206	33% helix, 16% strand	Q6CN12
B	ES1	protein	214	28% helix, 28% strand	Q6CWD0
C	US5	protein	217	30% helix, 27% strand	Q6CKL3
E	ES4	protein	260	15% helix, 27% strand	Q6CWJ2
G	ES6	protein	226	27% helix, 26% strand	Q6CM04
H	ES7	protein	184	30% helix, 22% strand	Q6CTD6
I	ES8	protein	188	26% helix, 23% strand	Q6CMG3
J	US4	protein	182	51% helix, 2% strand	Q6CM18
L	US17	protein	155	3% helix, 29% strand	Q6CX80
N	US15	protein	150	56% helix, 0% strand	Q6CJK0
O	US11	protein	127	27% helix, 18% strand	P27069
V	ES21	protein	87	18% helix, 18% strand	Q6CXT6
W	US8	protein	129	33% helix, 26% strand	Q6CW21
X	US12	protein	144	24% helix, 23% strand	F2Z602
Y	ES24	protein	134	36% helix, 23% strand	Q6CU44
a	ES26	protein	97	13% helix, 21% strand	Q6CS01
b	ES27	protein	81	7% helix, 19% strand	Q6CNL2
e	ES30	protein	53	26% helix, 0% strand	Q6CUH5
D	US3	protein	223	31% helix, 26% strand	Q6CRK7
F	US7	protein	206	47% helix, 6% strand	Q6CRA3
K	ES10	protein	96	40% helix, 16% strand	Q6CVZ5
M	ES12	protein	122	37% helix, 9% strand	Q6CLU4
P	US19	protein	123	29% helix, 11% strand	Q6CKV4
Q	US9	protein	141	33% helix, 21% strand	Q875N2
R	ES17	protein	120	46% helix, 8% strand	Q6CWU3
S	US13	protein	145	36% helix, 6% strand	Q6CWT9
T	ES19	protein	143	47% helix, 10% strand	Q6CXM0
U	US10	protein	106	23% helix, 38% strand	Q6CIM1
Z	ES25	protein	70	36% helix, 16% strand	Q6CW78
c	ES28	protein	63	0% helix, 40% strand	P33285
d	US14	protein	53	26% helix, 9% strand	Q6CPG3
f	ES31	protein	69	0% helix, 20% strand	P69061
g	RACK1	protein	318	0% helix, 51% strand	Q6CNI7
h	EL41	protein	25	88% helix, 0% strand	P0CX86
i	EIF1A	protein	96	10% helix, 39% strand	P38912
j	EIF1	protein	86	26% helix, 37% strand	P32911

Ligands and binding sites

MG · Magnesium ion · metal · 67 copies · chains 2, E, I, D, X, G, a, T, U
ZN · Zinc ion · metal · 3 copies · chains a, b, 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	808	0.89	0.93	94	MG
2	719	0.88	0.92	85	MG
3	880	0.87	0.90	75	MG
4	809	0.87	0.91	63	MG
5	649	0.86	0.92	96	empty

Interfaces

98 interfaces between chains.

2–G · 5457 Å² buried · 105 hydrogen bonds · protein-nucleic
2–E · 4592 Å² buried · 80 hydrogen bonds · protein-nucleic
2–I · 3970 Å² buried · 117 hydrogen bonds · protein-nucleic
2–X · 3957 Å² buried · 94 hydrogen bonds · protein-nucleic
2–J · 3914 Å² buried · 73 hydrogen bonds · protein-nucleic

Compared structures

3J80 · CryoEM structure of 40S-eIF1-eIF1A preinitiation complex · 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 Q6CN12
Every structure of UniProt Q6CWD0
Every structure of UniProt Q6CKL3
Every structure of UniProt Q6CWJ2
Every structure of UniProt Q6CM04
Every structure of UniProt Q6CTD6
Every structure of UniProt Q6CMG3
Every structure of UniProt Q6CM18
Every structure of UniProt Q6CX80
Every structure of UniProt Q6CJK0
Every structure of UniProt P27069
Every structure of UniProt Q6CXT6
Every structure of UniProt Q6CW21
Every structure of UniProt F2Z602
Every structure of UniProt Q6CU44
Every structure of UniProt Q6CS01
Every structure of UniProt Q6CNL2
Every structure of UniProt Q6CUH5
Every structure of UniProt Q6CRK7
Every structure of UniProt Q6CRA3
Every structure of UniProt Q6CVZ5
Every structure of UniProt Q6CLU4
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 Q6CW78
Every structure of UniProt P33285
Every structure of UniProt Q6CPG3
Every structure of UniProt P69061
Every structure of UniProt Q6CNI7
Every structure of UniProt P0CX86
Every structure of UniProt P38912
Every structure of UniProt P32911
Elsewhere: RCSB PDB 3J80 · PDBe 3J80 · UniProt Q6CN12 · UniProt Q6CWD0 · UniProt Q6CKL3 · UniProt Q6CWJ2 · UniProt Q6CM04 · UniProt Q6CTD6 · UniProt Q6CMG3 · UniProt Q6CM18 · UniProt Q6CX80 · UniProt Q6CJK0 · UniProt P27069 · UniProt Q6CXT6 · UniProt Q6CW21 · UniProt F2Z602 · UniProt Q6CU44 · UniProt Q6CS01 · UniProt Q6CNL2 · UniProt Q6CUH5 · UniProt Q6CRK7 · UniProt Q6CRA3 · UniProt Q6CVZ5 · UniProt Q6CLU4 · UniProt Q6CKV4 · UniProt Q875N2 · UniProt Q6CWU3 · UniProt Q6CWT9 · UniProt Q6CXM0 · UniProt Q6CIM1 · UniProt Q6CW78 · UniProt P33285 · UniProt Q6CPG3 · UniProt P69061 · UniProt Q6CNI7 · UniProt P0CX86 · UniProt P38912 · UniProt P32911

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