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State D architectural model (NSA1-tap flag-YTM1) - visualizing the assembly pathway of nucleolar pre-60S ribosomes

Analyse State D architectural model (NSA1-tap flag-YTM1) - visualizing the assembly… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6EM5
Type: protein + RNA
Length: 13,250 residues
Chains: 57
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5.8S ribosomal RNA; Internal transcribed spacer 2; 60S ribosomal protein L13-a; 60S…
EC: 3.6.4.13, 2.1.1.310, 2.1.1.167
UniProt: Q12690, P36105, P05748, P0CX49, P0CX82, P0CX23, Q02753, P05749, P0C2H6, P14120, P0C2H8, P38061, P05744, P87262, O14455, P49166, P49167, Q02326, P17076, P26784, P0CX41, P04456, P05743, P0CX84, P14126, P10664, P05738, Q08235, P38779, Q04660, Q03532, P33201, Q08962, Q02892, P53927, P53261, P40078, P40010, P40693, Q12522, P38202, Q12024, P40991, Q07915, P40007, P25582, Q07896, P36049, P38805, P10962, P35178, P53136, P05737, P05740
Pockets: 20 · best druggability 0.80

Structure

electron microscopy · 57 distinct chains · 33% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
2	5.8S ribosomal RNA	rna	158	—	—
6	Internal transcribed spacer 2	rna	65	—	—
L	60S ribosomal protein L13-a	protein	122	41% helix, 12% strand	Q12690
M	60S ribosomal protein L14-a	protein	136	38% helix, 26% strand	P36105
N	60S ribosomal protein L15-a	protein	186	37% helix, 19% strand	P05748
Q	60S ribosomal protein L18-a	protein	134	38% helix, 14% strand	P0CX49
R	60S ribosomal protein L19-a	protein	120	63% helix, 3% strand	P0CX82
S	60S ribosomal protein L20-a	protein	170	21% helix, 29% strand	P0CX23
T	60S ribosomal protein L21-a	protein	22	82% helix, 0% strand	Q02753
U	60S ribosomal protein L22-a	protein	98	30% helix, 30% strand	P05749
Z	60S ribosomal protein L27-a	protein	135	21% helix, 27% strand	P0C2H6
c	60S ribosomal protein L30	protein	97	44% helix, 15% strand	P14120
d	60S ribosomal protein L31-a	protein	107	32% helix, 23% strand	P0C2H8
e	60S ribosomal protein L32	protein	125	22% helix, 10% strand	P38061
f	60S ribosomal protein L33-a	protein	106	4% helix, 49% strand	P05744
g	60S ribosomal protein L34-a	protein	112	34% helix, 11% strand	P87262
i	60S ribosomal protein L36-B	protein	72	78% helix, 0% strand	O14455
j	60S ribosomal protein L37-a	protein	73	16% helix, 8% strand	P49166
k	60S ribosomal protein L38	protein	77	22% helix, 42% strand	P49167
E	60S ribosomal protein L6-a	protein	156	20% helix, 19% strand	Q02326
G	60S ribosomal protein L8-a	protein	184	47% helix, 8% strand	P17076
O	60S ribosomal protein L16-a	protein	197	48% helix, 7% strand	P26784
V	60S ribosomal protein L23-a	protein	134	8% helix, 36% strand	P0CX41
X	60S ribosomal protein L25	protein	141	30% helix, 18% strand	P04456
Y	60S ribosomal protein L26-a	protein	126	27% helix, 32% strand	P05743
h	60S ribosomal protein L35-a	protein	119	59% helix, 3% strand	P0CX84
B	60S ribosomal protein L3	protein	341	13% helix, 29% strand	P14126
C	60S ribosomal protein L4-a	protein	359	28% helix, 9% strand	P10664
H	60S ribosomal protein L9-a	protein	190	18% helix, 36% strand	P05738
A	Ribosome biogenesis protein BRX1	protein	198	18% helix, 39% strand	Q08235
K	Proteasome-interacting protein CIC1	protein	257	35% helix, 21% strand	P38779
m	Ribosome biogenesis protein ERB1	protein	645	14% helix, 27% strand	Q04660
D	ATP-dependent RNA helicase HAS1 (EC 3.6.4.13)	protein	194	37% helix, 11% strand	Q03532
W	Ribosome assembly factor MRT4	protein	232	30% helix, 19% strand	P33201
l	60S ribosome subunit biogenesis protein NIP7	protein	174	24% helix, 21% strand	Q08962
b	Nucleolar GTP-binding protein 1	protein	421	48% helix, 8% strand	Q02892
o	Ribosome biogenesis protein 15	protein	133	28% helix, 26% strand	P53927
n	Pescadillo homolog	protein	411	47% helix, 9% strand	P53261
r	Ribosome biogenesis protein NSA2	protein	176	34% helix, 19% strand	P40078
s	Nuclear GTP-binding protein NUG1	protein	36	58% helix, 0% strand	P40010
t	Ribosome biogenesis protein RLP7	protein	290	43% helix, 12% strand	P40693
y	Eukaryotic translation initiation factor 6	protein	225	26% helix, 25% strand	Q12522
z	UPF0642 protein YBL028C	protein	55	82% helix, 0% strand	P38202
p	Ribosome biogenesis protein YTM1	protein	298	0% helix, 50% strand	Q12024
q	25S rRNA (CYTOSINE(2870)-C(5))-methyltransferase (EC 2.1.1.310)	protein	317	28% helix, 16% strand	P40991
u	Ribosome biogenesis protein RLP24	protein	116	42% helix, 9% strand	Q07915
v	Nucleolar protein 16	protein	130	48% helix, 0% strand	P40007
w	27S pre-rRNA (GUANOSINE(2922)-2'-O)-methyltransferase (EC 2.1.1.167)	protein	436	41% helix, 13% strand	P25582
I	Nucleolar complex-associated protein 3	protein	451	62% helix, 0% strand	Q07896
J	RRNA-processing protein EBP2	protein	132	60% helix, 1% strand	P36049
x	Ribosome production factor 1	protein	267	31% helix, 22% strand	P38805
3	Protein MAK16	protein	173	40% helix, 14% strand	P10962
4	Ribosomal RNA-processing protein 1	protein	220	58% helix, 0% strand	P35178
5	Ribosome biogenesis protein NSA1	protein	385	3% helix, 46% strand	P53136
1	25S ribosomal RNA	rna	2438	—	—
F	60S ribosomal protein L7-a	protein	241	54% helix, 13% strand	P05737
P	60S ribosomal protein L17-a	protein	137	36% helix, 26% strand	P05740

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	829	0.80	0.84	111	empty
2	855	0.79	0.83	171	empty
3	982	0.76	0.80	116	empty
4	1143	0.76	0.79	156	empty
5	592	0.75	0.83	103	empty

Interfaces

155 interfaces between chains.

C–1 · 2936 Å² buried · 38 hydrogen bonds · protein-nucleic
B–1 · 2505 Å² buried · 41 hydrogen bonds · protein-nucleic
N–1 · 1773 Å² buried · 18 hydrogen bonds · protein-nucleic
2–1 · 1706 Å² buried · 34 hydrogen bonds · nucleic-nucleic
g–1 · 1567 Å² buried · 30 hydrogen bonds · protein-nucleic

Compared structures

6EM5 · State D architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of… · the same entry in another collection · chain U against U, TM-score 1.00

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