Research workbench

Cryo-EM structure of the 90S pre-ribosome

Analyse Cryo-EM structure of the 90S pre-ribosome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5JPQ
Type: protein + RNA
Length: 15,066 residues
Chains: 56
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: WD40 domain proteins; UTP10; UTP-a oligomerization domain; U3 small nucleolar…
UniProt: G0S5L1, Q06078, G0SDL4, G0SE90, G0SE30, G0S3V7, G0S273, G0S7X0
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 38 distinct chains · 36% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, J, K, L, N, P, l, n	WD40 domain proteins	protein	300	1% helix, 53% strand	—
G	UTP10	protein	283	80% helix, 0% strand	G0S5L1
H	UTP-a oligomerization domain	protein	343	92% helix, 0% strand	—
I	U3 small nucleolar RNA-associated protein 21	protein	634	0% helix, 52% strand	Q06078
M, O, m	WD40 domain proteins	protein	309	0% helix, 54% strand	—
Q	UTP6	protein	375	83% helix, 0% strand	—
R	UTP-B oligomerisation domain	protein	332	90% helix, 0% strand	—
S, T	Pre mRNA splicing protein	protein	367	65% helix, 7% strand	—
U, V	SNU13	protein	122	47% helix, 16% strand	—
W, X	NOP1	protein	227	27% helix, 33% strand	—
Y	RRP9	protein	365	4% helix, 50% strand	—
Z	RCL1	protein	355	31% helix, 28% strand	—
a	BMS1	protein	54	48% helix, 2% strand	—
b	IMP3	protein	153	50% helix, 5% strand	G0SDL4
c	Putative U3 small nucleolar ribonucleoprotein	protein	192	15% helix, 32% strand	G0SE90
d	UTP24	protein	124	43% helix, 15% strand	G0SE30
e	EMG1	protein	211	31% helix, 24% strand	—
f	EMG1	protein	218	28% helix, 23% strand	—
g, h	KRR1 small subunit processome component	protein	174	53% helix, 18% strand	G0S3V7
i	KRE33	protein	659	39% helix, 17% strand	G0S273
j	KRE33	protein	677	40% helix, 16% strand	G0S273
k	UTP30	protein	182	39% helix, 25% strand	G0S7X0
o	ES1	protein	215	22% helix, 33% strand	—
p	ES4	protein	259	15% helix, 32% strand	—
q	US7	protein	169	34% helix, 1% strand	—
r	ES6	protein	235	29% helix, 24% strand	—
s	ES7	protein	186	43% helix, 20% strand	—
t	ES8	protein	207	29% helix, 26% strand	—
u	US4	protein	157	34% helix, 2% strand	—
v	US15	protein	117	42% helix, 2% strand	—
w	US11	protein	128	11% helix, 5% strand	—
x	US9	protein	134	15% helix, 5% strand	—
y	US17	protein	157	6% helix, 27% strand	—
z	US8	protein	127	26% helix, 3% strand	—
0	ES24	protein	148	42% helix, 23% strand	—
1	ES28	protein	47	0% helix, 0% strand	—
2	18S ribosomal RNA	rna	852	—	—
3	U3 RNA	rna	164	—	—

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	1065	0.86	0.87	188	empty
2	1149	0.86	0.87	179	empty
3	920	0.85	0.87	152	empty
4	901	0.85	0.87	151	empty
5	1078	0.84	0.85	137	empty

Interfaces

103 interfaces between chains.

r–2 · 4499 Å² buried · 221 hydrogen bonds · protein-nucleic
t–2 · 2857 Å² buried · 112 hydrogen bonds · protein-nucleic
y–2 · 2301 Å² buried · 105 hydrogen bonds · protein-nucleic
p–2 · 1926 Å² buried · 46 hydrogen bonds · protein-nucleic
o–2 · 1362 Å² buried · 116 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 isopeptide (isopeptide).

Compared structures

5JPQ · Cryo-EM structure of the 90S pre-ribosome · the same entry in another collection · chain 3 against 3, 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 G0S5L1
Every structure of UniProt Q06078
Every structure of UniProt G0SDL4
Every structure of UniProt G0SE90
Every structure of UniProt G0SE30
Every structure of UniProt G0S3V7
Every structure of UniProt G0S273
Every structure of UniProt G0S7X0
Elsewhere: RCSB PDB 5JPQ · PDBe 5JPQ · UniProt G0S5L1 · UniProt Q06078 · UniProt G0SDL4 · UniProt G0SE90 · UniProt G0SE30 · UniProt G0S3V7 · UniProt G0S273 · UniProt G0S7X0

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