Research workbench

Ytm1 associated nascent 60S ribosome State 2

Analyse Ytm1 associated nascent 60S ribosome State 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 8ESQ
Type: protein + RNA
Length: 12,724 residues
Chains: 58
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.8
Source: Schizosaccharomyces pombe
Molecule: Noc2; RNA (2231-mer); RNA (150-mer); Protein mak16; RNA (81-mer); 60S ribosomal protein…
EC: 3.6.4.13, 2.1.1.-
UniProt: Q9P7G0, Q9UTE6, P05767, Q9HGL6, P40372, Q9P784, Q09916, P79071, P25457, O13672, Q10232, O94288, O13802, Q9UT32, O74175, O94238, O74895, O42991, O14339, Q10192, P05734, P0CT68, Q09668, P0CT60, Q9USZ6, Q10330, P78946, O14388, P36585, O94659, Q9UTP0, Q9URX6, P79015, Q9USG6, O42846, O74904, O94658, P05733, Q9USR7, Q1MTQ9, O74399, O60164, O74978, Q9URY0, O94268, Q9UU79, O74791, P17937, Q10353, Q9Y7Z1, O42832, O14180, O94476, Q96WW3, Q9UUC1
Ligands: ZN
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · resolution 2.8 · 58 distinct chains · 39% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
7	Noc2	protein	245	81% helix, 0% strand	Q9P7G0
1	RNA (2231-mer)	rna	2230	—	—
2	RNA (150-mer)	rna	150	—	—
3	Protein mak16	protein	160	47% helix, 13% strand	Q9UTE6
6	RNA (81-mer)	rna	81	—	—
8	60S ribosomal protein L39	protein	35	51% helix, 0% strand	P05767
A	Ribosome biogenesis protein brx1	protein	211	19% helix, 36% strand	Q9HGL6
B	60S ribosomal protein L3-A	protein	339	17% helix, 31% strand	P40372
C	60S ribosomal protein L4-B	protein	359	32% helix, 11% strand	Q9P784
D	ATP-dependent RNA helicase has1 (EC 3.6.4.13)	protein	427	48% helix, 15% strand	Q09916
E	60S ribosomal protein L6	protein	165	23% helix, 15% strand	P79071
F	60S ribosomal protein L7-B	protein	237	53% helix, 14% strand	P25457
G	60S ribosomal protein L8	protein	206	57% helix, 9% strand	O13672
H	60S ribosomal protein L9-A	protein	183	25% helix, 40% strand	Q10232
I	Nucleolar complex-associated protein 3	protein	460	68% helix, 0% strand	O94288
J	Probable rRNA-processing protein ebp2	protein	118	60% helix, 3% strand	O13802
K	Putative ribosome biogenesis protein C8F11.04	protein	251	35% helix, 22% strand	Q9UT32
L	60S ribosomal protein L13	protein	116	40% helix, 11% strand	O74175
M	60S ribosomal protein L14	protein	125	33% helix, 23% strand	O94238
N	60S ribosomal protein L15-A	protein	166	37% helix, 20% strand	O74895
O	60S ribosomal protein L16-B	protein	196	55% helix, 12% strand	O42991
P	60S ribosomal protein L17-A	protein	159	42% helix, 22% strand	O14339
Q	60S ribosomal protein L18-A	protein	133	38% helix, 18% strand	Q10192
R	60S ribosomal protein L19-A	protein	114	62% helix, 5% strand	P05734
S	60S ribosomal protein L20-A	protein	168	22% helix, 30% strand	P0CT68
U	60S ribosomal protein L22	protein	98	35% helix, 29% strand	Q09668
V	60S ribosomal protein L23-A	protein	132	8% helix, 34% strand	P0CT60
W	Ribosome assembly factor mrt4	protein	215	27% helix, 7% strand	Q9USZ6
X	60S ribosomal protein L25-A	protein	132	30% helix, 19% strand	Q10330
Y	60S ribosomal protein L26	protein	125	28% helix, 32% strand	P78946
Z	60S ribosomal protein L27-A	protein	134	31% helix, 28% strand	O14388
a	60S ribosomal protein L28-A	protein	80	28% helix, 24% strand	P36585
b	Probable nucleolar GTP-binding protein 1	protein	403	52% helix, 8% strand	O94659
c	60S ribosomal protein L30-2	protein	96	45% helix, 18% strand	Q9UTP0
d	60S ribosomal protein L31	protein	97	32% helix, 29% strand	Q9URX6
e	60S ribosomal protein L32-A	protein	121	18% helix, 10% strand	P79015
f	60S ribosomal protein L33-B	protein	106	9% helix, 53% strand	Q9USG6
g	60S ribosomal protein L34-A	protein	106	28% helix, 11% strand	O42846
h	60S ribosomal protein L35	protein	121	69% helix, 4% strand	O74904
i	60S ribosomal protein L36-B	protein	85	73% helix, 1% strand	O94658
j	60S ribosomal protein L37-B	protein	71	21% helix, 8% strand	P05733
k	60S ribosomal protein L38-1	protein	70	27% helix, 33% strand	Q9USR7
l	60S ribosome subunit biogenesis protein nip7	protein	174	31% helix, 26% strand	Q1MTQ9
m	Ribosome biogenesis protein erb1	protein	572	12% helix, 28% strand	O74399
n	Pescadillo homolog	protein	433	47% helix, 11% strand	O60164
o	Uncharacterized RNA-binding protein C1827.05c	protein	137	39% helix, 25% strand	O74978
p	Ribosome biogenesis protein ytm1	protein	290	0% helix, 54% strand	Q9URY0
q	25S rRNA (cytosine-C(5))-methyltransferase nop2 (EC 2.1.1.-)	protein	341	44% helix, 20% strand	O94268
r	Ribosome biogenesis protein nsa2	protein	166	40% helix, 20% strand	Q9UU79
s	GTPase grn1	protein	32	63% helix, 0% strand	O74791
t	60S ribosomal protein L7-A	protein	235	49% helix, 15% strand	P17937
u	Ribosome biogenesis protein rlp24	protein	114	43% helix, 11% strand	Q10353
v	Nucleolar protein 16	protein	161	45% helix, 1% strand	Q9Y7Z1
w	AdoMet-dependent rRNA methyltransferase spb1 (EC 2.1.1.-)	protein	504	47% helix, 12% strand	O42832
x	Brix domain-containing protein C4F8.04	protein	45	58% helix, 0% strand	O14180
y	Eukaryotic translation initiation factor 6	protein	225	32% helix, 25% strand	O94476
z	UPF0642 protein C32H8.05	protein	35	74% helix, 0% strand	Q96WW3
T	60S ribosomal protein L21-A	protein	34	26% helix, 12% strand	Q9UUC1

Ligands and binding sites

ZN · Zinc ion · metal · chains j

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	1193	0.88	0.90	117	empty
2	896	0.88	0.91	93	empty
3	998	0.88	0.90	99	empty
4	1023	0.87	0.89	93	empty
5	1185	0.87	0.89	106	empty

Interfaces

201 interfaces between chains.

1–C · 8387 Å² buried · 194 hydrogen bonds · protein-nucleic
1–B · 6211 Å² buried · 139 hydrogen bonds · protein-nucleic
1–2 · 5273 Å² buried · 334 hydrogen bonds · nucleic-nucleic
1–N · 4661 Å² buried · 102 hydrogen bonds · protein-nucleic
1–O · 4201 Å² buried · 83 hydrogen bonds · protein-nucleic

Compared structures

O94268 · AlphaFold monomer V2.0 prediction for 25S rRNA (cytosine-C(5))-methyltransferase NOP2… · a predicted model of the same protein · chain q against A, TM-score 0.99
P40372 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L3-a (P40372) · a predicted model of the same protein · chain B against A, TM-score 0.99
P78946 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L26 (P78946) · a predicted model of the same protein · chain Y against A, TM-score 0.99
Q9URX6 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L31 (Q9URX6) · a predicted model of the same protein · chain d against A, TM-score 0.98
O94476 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 6 (O94476) · a predicted model of the same protein · chain y against A, TM-score 0.98
P79015 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L32-a (P79015) · a predicted model of the same protein · chain e against A, TM-score 0.98
P36585 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L28-a (P36585) · a predicted model of the same protein · chain a against A, TM-score 0.98
O74895 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L15-a (O74895) · a predicted model of the same protein · chain N against A, TM-score 0.98
O42991 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L16-B (O42991) · a predicted model of the same protein · chain O against A, TM-score 0.98
Q10232 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L9-a (Q10232) · a predicted model of the same protein · chain H against A, TM-score 0.97
Q9URY0 · AlphaFold monomer V2.0 prediction for ribosome biogenesis protein YTM1 (Q9URY0) · a predicted model of the same protein · chain p against A, TM-score 0.97
Q9USG6 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L33-B (Q9USG6) · a predicted model of the same protein · chain f against A, TM-score 0.97

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