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Cryo-EM structure of 90S small subunit preribosomes in transition states (State A1)

Analyse Cryo-EM structure of 90S small subunit preribosomes in transition states (State… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6LQU
Type: protein + RNA
Length: 27,233 residues
Chains: 72
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.7
Source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c); Saccharomyces cerevisiae…
Molecule: U3 snoRNA; 5' ets; 18S pre-rRNA; 40S ribosomal protein S4-A; 40S ribosomal protein S5…
EC: 2.1.1.-, 2.1.1.260, 2.3.1.-
UniProt: P0CX35, P26783, P0CX37, P26786, P0CX39, O13516, P0CX47, P48589, P05756, P06367, P0CX51, P0CX55, Q3E7Y3, P0CX29, P0CX31, Q3E7X9, P15646, Q12460, Q12499, Q06506, P39990, Q06679, Q04177, P53276, P38882, P42945, Q04305, Q02931, P25635, Q12220, Q05946, P40362, Q06078, Q02354, Q08492, P40055, P34247, P47083, P32899, P53941, Q12136, P33750, Q12035, Q05498, P48234, P40079, P25586, Q05022, P53254, P25368, Q06287, P36144, Q08965, Q08096, P53914, Q99207, Q06512, P35194, Q04500, P38333, P40546, P40470, Q06631
Ligands: GTP, ZN, MG
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · resolution 3.7 · 71 distinct chains · 36% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
3A	U3 snoRNA	rna	175	—	—
5A	5' ets	rna	523	—	—
SA	18S pre-rRNA	rna	1242	—	—
SF	40S ribosomal protein S4-A	protein	229	14% helix, 23% strand	P0CX35
SG	40S ribosomal protein S5	protein	213	45% helix, 10% strand	P26783
SH	40S ribosomal protein S6-A	protein	167	26% helix, 24% strand	P0CX37
SI	40S ribosomal protein S7-A	protein	165	35% helix, 19% strand	P26786
SJ	40S ribosomal protein S8-A	protein	166	20% helix, 23% strand	P0CX39
SK	40S ribosomal protein S9-A	protein	171	53% helix, 5% strand	O13516
SM	40S ribosomal protein S11-A	protein	123	3% helix, 20% strand	P0CX47
SN	40S ribosomal protein S12	protein	119	38% helix, 5% strand	P48589
SO	40S ribosomal protein S13	protein	134	54% helix, 0% strand	P05756
SP	40S ribosomal protein S14-A	protein	118	30% helix, 25% strand	P06367
SR	40S ribosomal protein S16-A	protein	125	41% helix, 22% strand	P0CX51
ST	40S ribosomal protein S18-A	protein	117	39% helix, 5% strand	P0CX55
SX	40S ribosomal protein S22-B	protein	127	31% helix, 29% strand	Q3E7Y3
SY	40S ribosomal protein S23-A	protein	103	10% helix, 32% strand	P0CX29
SZ	40S ribosomal protein S24-A	protein	102	25% helix, 34% strand	P0CX31
Sd	40S ribosomal protein S28-A	protein	63	0% helix, 40% strand	Q3E7X9
3B	rRNA 2'-O-methyltransferase fibrillarin (EC 2.1.1.-)	protein	240	28% helix, 32% strand	P15646
3C	rRNA 2'-O-methyltransferase fibrillarin (EC 2.1.1.-)	protein	225	26% helix, 28% strand	P15646
3D	Nucleolar protein 56	protein	369	59% helix, 8% strand	Q12460
3E	Nucleolar protein 58	protein	431	57% helix, 6% strand	Q12499
3F	Ribosomal RNA-processing protein 9	protein	454	11% helix, 38% strand	Q06506
3G, 3H	13 kDa ribonucleoprotein-associated protein	protein	121	48% helix, 17% strand	P39990
A4	U3 small nucleolar RNA-associated protein 4	protein	662	5% helix, 43% strand	Q06679
A5	U3 small nucleolar RNA-associated protein 5	protein	514	21% helix, 34% strand	Q04177
A8	U3 small nucleolar RNA-associated protein 8	protein	548	24% helix, 14% strand	P53276
A9	U3 small nucleolar RNA-associated protein 9	protein	128	75% helix, 0% strand	P38882
AE	U3 small nucleolar RNA-associated protein 10	protein	1534	66% helix, 0% strand	P42945
AF	U3 small nucleolar RNA-associated protein 15	protein	493	22% helix, 33% strand	Q04305
AG	NET1-associated nuclear protein 1	protein	826	9% helix, 39% strand	Q02931
B1	Periodic tryptophan protein 2	protein	834	14% helix, 37% strand	P25635
B2	U3 small nucleolar RNA-associated protein 12	protein	851	20% helix, 39% strand	Q12220
B3	U3 small nucleolar RNA-associated protein 13	protein	752	17% helix, 28% strand	Q05946
B8	U3 small nucleolar RNA-associated protein 18	protein	477	12% helix, 36% strand	P40362
BE	U3 small nucleolar RNA-associated protein 21	protein	865	14% helix, 39% strand	Q06078
B6	U3 small nucleolar RNA-associated protein 6	protein	374	74% helix, 0% strand	Q02354
5B	Bud site selection protein 21	protein	60	43% helix, 15% strand	Q08492
5C	U3 small nucleolar RNA-associated protein 7	protein	516	20% helix, 28% strand	P40055
5D	U3 small nucleolar RNA-associated protein 11	protein	235	41% helix, 7% strand	P34247
5E	U3 small nucleolar RNA-associated protein MPP10	protein	204	40% helix, 8% strand	P47083
5F	U3 small nucleolar ribonucleoprotein protein IMP3	protein	182	53% helix, 5% strand	P32899
5G	U3 small nucleolar ribonucleoprotein protein IMP4	protein	282	32% helix, 25% strand	P53941
5H	Something about silencing protein 10	protein	136	48% helix, 2% strand	Q12136
5I	Protein SOF1	protein	461	15% helix, 37% strand	P33750
5J	rRNA-processing protein FCF2	protein	151	44% helix, 4% strand	Q12035
5K	rRNA-processing protein FCF1	protein	175	33% helix, 14% strand	Q05498
RA	Ribosome biogenesis protein ENP2	protein	338	2% helix, 36% strand	P48234
RB	U3 small nucleolar ribonucleoprotein protein LCP5	protein	134	44% helix, 4% strand	P40079
RC	KRR1 small subunit processome component	protein	175	54% helix, 20% strand	P25586
RD	rRNA biogenesis protein RRP5	protein	265	78% helix, 0% strand	Q05022
RE	U3 small nucleolar RNA-associated protein 22	protein	1079	38% helix, 12% strand	P53254
RF	Ribosomal RNA-processing protein 7	protein	174	32% helix, 14% strand	P25368
RG	Ribosomal RNA small subunit methyltransferase NEP1 (EC 2.1.1.260)	protein	216	24% helix, 23% strand	Q06287
RH	Ribosomal RNA small subunit methyltransferase NEP1 (EC 2.1.1.260)	protein	230	28% helix, 27% strand	Q06287
RI	Ribosome biogenesis protein UTP30	protein	252	27% helix, 16% strand	P36144
RJ	Ribosome biogenesis protein BMS1	protein	796	30% helix, 24% strand	Q08965
RK	RNA 3'-terminal phosphate cyclase-like protein	protein	360	29% helix, 28% strand	Q08096
RL	RNA cytidine acetyltransferase (EC 2.3.1.-)	protein	805	45% helix, 12% strand	P53914
RM	RNA cytidine acetyltransferase (EC 2.3.1.-)	protein	766	39% helix, 10% strand	P53914
RN	Nucleolar complex protein 14	protein	607	64% helix, 2% strand	Q99207
RO	Nucleolar complex protein 4	protein	525	55% helix, 1% strand	Q06512
RP	U3 small nucleolar RNA-associated protein 20	protein	2109	67% helix, 0% strand	P35194
RQ	U3 small nucleolar RNA-associated protein 14	protein	226	40% helix, 4% strand	Q04500
RS	Essential nuclear protein 1	protein	251	61% helix, 0% strand	P38333
RT	Pno1	protein	171	53% helix, 19% strand	—
RV	Protein FAF1	protein	190	48% helix, 5% strand	P40546
RW	Regulator of rDNA transcription protein 14	protein	63	54% helix, 0% strand	P40470
RY	Protein BFR2	protein	37	14% helix, 3% strand	Q06631
X1	Unassigned helices	protein	61	34% helix, 2% strand	—

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · chains RJ
ZN · Zinc ion · metal · chains 5K
MG · Magnesium ion · metal · chains RJ

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	1779	0.89	0.91	158	empty
2	1082	0.88	0.90	91	empty
3	1955	0.88	0.89	159	empty
4	621	0.88	0.92	84	empty
5	1066	0.87	0.89	112	empty

Interfaces

327 interfaces between chains.

SA–RJ · 5727 Å² buried · 96 hydrogen bonds · protein-nucleic
B1–BE · 5345 Å² buried · 48 hydrogen bonds · protein-protein
RJ–RK · 3533 Å² buried · 36 hydrogen bonds · protein-protein
A5–AF · 3081 Å² buried · 32 hydrogen bonds · protein-protein
SA–SJ · 3078 Å² buried · 87 hydrogen bonds · protein-nucleic

Compared structures

P25635 · AlphaFold monomer V2.0 prediction for periodic tryptophan protein 2 (P25635) · a predicted model of the same protein · chain B1 against A, TM-score 1.00
Q08096 · AlphaFold monomer V2.0 prediction for RNA 3'-terminal phosphate cyclase-like protein… · a predicted model of the same protein · chain RK against A, TM-score 0.99
Q06679 · AlphaFold monomer V2.0 prediction for U3 small nucleolar RNA- associated protein 4… · a predicted model of the same protein · chain A4 against A, TM-score 0.98
P15646 · AlphaFold monomer V2.0 prediction for rRNA 2'-O-methyltransferase fibrillarin (P15646) · a predicted model of the same protein · chain 3B against A, TM-score 0.98
P53254 · AlphaFold monomer V2.0 prediction for U3 small nucleolar RNA- associated protein 22… · a predicted model of the same protein · chain RE against A, TM-score 0.98
P39990 · AlphaFold monomer V2.0 prediction for 13 kda ribonucleoprotein- associated protein… · a predicted model of the same protein · chain 3G against A, TM-score 0.98
P36144 · AlphaFold monomer V2.0 prediction for ribosome biogenesis protein UTP30 (P36144) · a predicted model of the same protein · chain RI against A, TM-score 0.98
Q08965 · AlphaFold monomer V2.0 prediction for ribosome biogenesis protein BMS1 (Q08965) · a predicted model of the same protein · chain RJ against A, TM-score 0.97
P06367 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S14-a (P06367) · a predicted model of the same protein · chain SP against A, TM-score 0.97
P48234 · AlphaFold monomer V2.0 prediction for ribosome biogenesis protein ENP2 (P48234) · a predicted model of the same protein · chain RA against A, TM-score 0.97
P05756 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S13 (P05756) · a predicted model of the same protein · chain SO against A, TM-score 0.97

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