MolNFT v1 · #68104 · protein + RNA

Cryoem structure of a partial yeast 48S preinitiation complex

3J81 · 18S rRNA: “Cryoem structure of a partial yeast 48S preinitiation complex”. Electron microscopy, 3 ligands (MET, MG, ZN), 20 pockets (best druggability 0.90). MolNFT v1 #68104 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 3J81
Type: protein + RNA
Length: 7,561 residues
Chains: 42
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 18S rRNA; US2; ES1; US5; US3; ES4; US7; ES6; ES7; ES8; US4; ES10; US17; ES12; US15; US11…
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, P69061, Q6CNI7, Q6CPG3, Q6CUH5, P0CX86, P38912, P20459, P32911, P32481, P09064
Ligands: MET, MG, ZN
Pockets: 20 · best druggability 0.90

Structure

electron microscopy · 42 distinct chains · 27% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
2	18S rRNA	rna	1780	—	—
A	US2	protein	207	29% helix, 11% strand	Q6CN12
B	ES1	protein	215	24% helix, 29% strand	Q6CWD0
C	US5	protein	217	32% helix, 23% strand	Q6CKL3
D	US3	protein	223	33% helix, 25% strand	Q6CRK7
E	ES4	protein	260	10% helix, 27% strand	Q6CWJ2
F	US7	protein	206	47% helix, 5% strand	Q6CRA3
G	ES6	protein	226	24% helix, 27% strand	Q6CM04
H	ES7	protein	184	29% helix, 19% strand	Q6CTD6
I	ES8	protein	188	25% helix, 28% strand	Q6CMG3
J	US4	protein	182	48% helix, 2% strand	Q6CM18
K	ES10	protein	96	38% helix, 4% strand	Q6CVZ5
L	US17	protein	155	3% helix, 22% strand	Q6CX80
M	ES12	protein	117	38% helix, 8% strand	Q6CLU4
N	US15	protein	150	54% helix, 0% strand	Q6CJK0
O	US11	protein	127	21% helix, 18% strand	P27069
P	US19	protein	119	27% helix, 11% strand	Q6CKV4
Q	US9	protein	141	34% helix, 21% strand	Q875N2
R	ES17	protein	120	51% helix, 4% strand	Q6CWU3
S	US13	protein	145	36% helix, 4% strand	Q6CWT9
T	ES19	protein	143	47% helix, 9% strand	Q6CXM0
U	US10	protein	106	23% helix, 37% strand	Q6CIM1
V	ES21	protein	87	20% helix, 30% strand	Q6CXT6
W	US8	protein	129	33% helix, 21% strand	Q6CW21
X	US12	protein	144	19% helix, 19% strand	F2Z602
Y	ES24	protein	134	34% helix, 25% strand	Q6CU44
Z	ES25	protein	70	37% helix, 11% strand	Q6CW78
a	ES26	protein	97	9% helix, 14% strand	Q6CS01
b	ES27	protein	81	7% helix, 22% strand	Q6CNL2
c	ES28	protein	62	0% helix, 47% strand	P33285
f	ES31	protein	69	0% helix, 13% strand	P69061
g	RACK1	protein	318	1% helix, 49% strand	Q6CNI7
d	US14	protein	53	23% helix, 9% strand	Q6CPG3
e	ES30	protein	54	26% helix, 0% strand	Q6CUH5
h	EL41	protein	25	88% helix, 0% strand	P0CX86
1	Met-trnai	rna	74	—	—
3	MRNA	rna	22	—	—
i	EIF1A	protein	111	13% helix, 28% strand	P38912
j	EIF2 alpha	protein	252	36% helix, 21% strand	P20459
m	EIF1	protein	90	22% helix, 31% strand	P32911
k	EIF2 gamma	protein	365	15% helix, 35% strand	P32481
l	EIF2 beta	protein	17	65% helix, 0% strand	P09064

Ligands and binding sites

MET · Methionine · ligand · chains 1, k
MG · Magnesium ion · metal · 81 copies · chains 2, E, D, a, B, S, T, 3, O, i, G
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	1011	0.90	0.93	98	MG
2	1108	0.88	0.91	109	MG
3	981	0.88	0.90	122	MG
4	658	0.87	0.93	65	MG
5	657	0.87	0.93	65	MG

Interfaces

125 interfaces between chains.

2–G · 5646 Å² buried · 120 hydrogen bonds · protein-nucleic
2–E · 4714 Å² buried · 87 hydrogen bonds · protein-nucleic
2–I · 4169 Å² buried · 104 hydrogen bonds · protein-nucleic
2–X · 4160 Å² buried · 105 hydrogen bonds · protein-nucleic
2–J · 4024 Å² buried · 82 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

3J81 · CryoEM structure of a partial yeast 48S preinitiation complex · the same entry in another collection · chain K against K, 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 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 P69061
Every structure of UniProt Q6CNI7
Every structure of UniProt Q6CPG3
Every structure of UniProt Q6CUH5
Every structure of UniProt P0CX86
Every structure of UniProt P38912
Every structure of UniProt P20459
Every structure of UniProt P32911
Every structure of UniProt P32481
Every structure of UniProt P09064
Elsewhere: RCSB PDB 3J81 · PDBe 3J81 · 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 P69061 · UniProt Q6CNI7 · UniProt Q6CPG3 · UniProt Q6CUH5 · UniProt P0CX86 · UniProt P38912 · UniProt P20459 · UniProt P32911 · UniProt P32481 · UniProt P09064

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