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Structure of the mammalian rescue complex with Pelota and Hbs1l assembled on a polyadenylated mRNA.

Analyse Structure of the mammalian rescue complex with Pelota and Hbs1l assembled on a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5LZY
Type: protein + RNA
Length: 18,160 residues
Chains: 86
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.99
Source: Homo sapiens; Oryctolagus cuniculus
Molecule: uL2; uL3; uL4; 60S ribosomal protein L5; 60S ribosomal protein L6; uL30; eL8; uL6…
EC: 3.1.-.-
UniProt: G1TT27, G1TL06, G1SYJ6, G1SKF7, G1TUB1, G1STW0, G1TX33, B7NZQ2, G1TUB8, G1SZ12, G1T0C1, G1TVT6, G1SHQ2, G1T6D1, G1SE28, G1SE76, G1SQH0, G1TXF6, G1SNY0, G1SGR6, G1TDL2, G1SHG0, G1U437, G1SF08, G1SIT5, G1TTQ5, G1TTN1, G1U344, G1SY53, G1U7L1, G1SMR7, G1SS70, G1TNM3, G1TFM5, G1TM55, G1SVB0, B7NZS8, G1TPV3, G1TRM4, G1SFR8, G1SP51, G1T1F0, G1U0Q2, G1SGX4, G1TU13, G1TPG3, G1TN62, G1SIZ2, G1TG89, G1TDB3, G1TZ76, G1TIB4, G1U7M4, G1T8A2, G1SK22, G1SJB4, Q9BRX2, Q9Y450
Ligands: GCP, MG, ZN
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · resolution 3.99 · 85 distinct chains · 32% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	uL2	protein	248	11% helix, 25% strand	G1TT27
B	uL3	protein	394	14% helix, 24% strand	G1TL06
C	uL4	protein	362	36% helix, 10% strand	—
D	60S ribosomal protein L5	protein	293	42% helix, 9% strand	G1SYJ6
E	60S ribosomal protein L6	protein	216	20% helix, 19% strand	G1SKF7
F	uL30	protein	225	53% helix, 15% strand	G1TUB1
G	eL8	protein	233	50% helix, 9% strand	G1STW0
H	uL6	protein	190	21% helix, 32% strand	G1TX33
I	Ribosomal protein L10 (Predicted)	protein	205	24% helix, 25% strand	B7NZQ2
J	uL5	protein	170	32% helix, 24% strand	G1TUB8
L	eL13	protein	210	45% helix, 10% strand	—
M	eL14	protein	138	47% helix, 23% strand	G1SZ12
N	Ribosomal protein L15	protein	203	33% helix, 17% strand	G1T0C1
O	uL13	protein	199	55% helix, 11% strand	—
P	uL22	protein	153	33% helix, 28% strand	G1TVT6
Q	eL18	protein	187	29% helix, 10% strand	—
R	eL19	protein	180	69% helix, 3% strand	—
S	eL20	protein	176	23% helix, 30% strand	—
T	eL21	protein	159	17% helix, 25% strand	G1SHQ2
U	eL22	protein	99	35% helix, 20% strand	—
V	eL14	protein	131	9% helix, 33% strand	G1T6D1
W	eL24	protein	106	44% helix, 11% strand	G1SE28
X	eL23	protein	118	28% helix, 22% strand	G1SE76
Y	uL24	protein	134	35% helix, 25% strand	G1SQH0
Z	60S ribosomal protein L27	protein	135	24% helix, 28% strand	G1TXF6
a	uL15	protein	147	31% helix, 15% strand	G1SNY0
b	eL29	protein	104	63% helix, 0% strand	G1SGR6
c	eL30	protein	98	45% helix, 18% strand	G1TDL2
d	eL31	protein	107	24% helix, 25% strand	G1SHG0
e	eL32	protein	128	18% helix, 6% strand	G1U437
f	eL33	protein	109	6% helix, 43% strand	G1SF08
g	eL34	protein	114	32% helix, 7% strand	—
h	uL29	protein	122	65% helix, 2% strand	G1SIT5
i	60S ribosomal protein L36	protein	102	63% helix, 1% strand	G1TTQ5
j	eL37	protein	86	20% helix, 7% strand	—
k	eL38	protein	69	28% helix, 33% strand	—
l	eL39	protein	50	38% helix, 0% strand	G1TTN1
m	eL40	protein	52	27% helix, 15% strand	—
n	eL41	protein	25	80% helix, 0% strand	—
o	eL42	protein	104	10% helix, 27% strand	G1U344
p	eL43	protein	91	42% helix, 11% strand	G1SY53
r	eL28	protein	124	33% helix, 19% strand	G1U7L1
s	uL10	protein	196	35% helix, 17% strand	—
t	uL11	protein	153	39% helix, 12% strand	G1SMR7
2, 3	tRNA	rna	75	—	—
5	28S ribosomal RNA	rna	3543	—	—
7	5S ribosomal RNA	rna	120	—	—
8	5.8S ribosomal RNA	rna	151	—	—
9	18S ribosomal RNA	rna	1698	—	—
AA	uS2	protein	217	39% helix, 14% strand	—
BB	40S ribosomal protein S3a	protein	213	28% helix, 33% strand	G1SS70
CC	uS5	protein	221	33% helix, 23% strand	—
DD	uS3	protein	228	34% helix, 22% strand	G1TNM3
EE	eS4	protein	262	16% helix, 30% strand	—
FF	uS7	protein	185	51% helix, 8% strand	G1TFM5
GG	40S ribosomal protein S6	protein	237	32% helix, 19% strand	G1TM55
HH	eS7	protein	185	35% helix, 19% strand	G1SVB0
II	eS8	protein	206	30% helix, 22% strand	—
JJ	Ribosomal protein S9 (Predicted)	protein	185	51% helix, 5% strand	B7NZS8
KK	eS10	protein	96	38% helix, 15% strand	G1TPV3
LL	uS17	protein	143	3% helix, 27% strand	G1TRM4
MM	40S ribosomal protein S12	protein	117	44% helix, 9% strand	G1SFR8
NN	uS15	protein	149	54% helix, 1% strand	G1SP51
OO	uS11	protein	136	24% helix, 24% strand	G1T1F0
PP	uS19	protein	120	34% helix, 16% strand	G1U0Q2
QQ	uS9	protein	142	42% helix, 20% strand	G1SGX4
RR	eS17	protein	132	48% helix, 6% strand	G1TU13
SS	uS13	protein	144	40% helix, 9% strand	G1TPG3
TT	eS19	protein	141	53% helix, 11% strand	G1TN62
UU	uS10	protein	100	26% helix, 29% strand	G1SIZ2
VV	eS21	protein	83	22% helix, 27% strand	—
WW	uS8	protein	129	33% helix, 25% strand	G1TG89
XX	uS12	protein	141	25% helix, 28% strand	—
YY	eS24	protein	124	28% helix, 28% strand	—
ZZ	eS25	protein	75	47% helix, 19% strand	G1TDB3
aa	eS26	protein	101	18% helix, 23% strand	—
bb	40S ribosomal protein S27	protein	83	10% helix, 23% strand	G1TZ76
cc	eS28	protein	62	0% helix, 47% strand	G1TIB4
dd	uS14	protein	55	38% helix, 9% strand	G1U7M4
ee	eS30	protein	55	33% helix, 0% strand	G1T8A2
ff	eS31	protein	68	0% helix, 21% strand	G1SK22
gg	RACK1	protein	313	0% helix, 50% strand	G1SJB4
hh	mRNA (polyadenylated)	rna	8	—	—
ii	Protein pelota homolog (EC 3.1.-.-)	protein	372	34% helix, 30% strand	Q9BRX2
jj	HBS1-like protein	protein	425	22% helix, 30% strand	Q9Y450

Ligands and binding sites

GCP · Phosphomethylphosphonic acid guanylate ester · ligand · chains jj
MG · Magnesium ion · metal · 236 copies · chains B, 5, I, L, P, Q, V, a, e, j, C, g, h, N, l, A, H, b, X, Y, 8, f, 7, 9, EE, NN, OO, aa, DD, QQ, TT, hh, jj
ZN · Zinc ion · metal · 8 copies · chains g, j, m, o, p, aa, dd, ff

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	1142	0.89	0.91	121	MG
2	1174	0.89	0.91	113	MG
3	1083	0.89	0.91	95	MG
4	735	0.88	0.92	81	MG
5	671	0.88	0.93	64	MG

Interfaces

281 interfaces between chains.

C–5 · 9626 Å² buried · 203 hydrogen bonds · protein-nucleic
B–5 · 9359 Å² buried · 211 hydrogen bonds · protein-nucleic
A–5 · 7667 Å² buried · 196 hydrogen bonds · protein-nucleic
N–5 · 7230 Å² buried · 149 hydrogen bonds · protein-nucleic
E–5 · 6083 Å² buried · 108 hydrogen bonds · protein-nucleic

Compared structures

Q9Y450 · AlphaFold monomer V2.0 prediction for HBS1-like protein (Q9Y450) · a predicted model of the same protein · chain jj against A, TM-score 0.98
Q9BRX2 · AlphaFold monomer V2.0 prediction for protein pelota homolog (Q9BRX2) · a predicted model of the same protein · chain ii against A, TM-score 0.97

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