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MolNFT v2 · #126717 · protein + RNA

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

5LZY: “Structure of the mammalian rescue complex with Pelota and Hbs1l assembled on a polyadenylated mRNA.”. Electron microscopy at 3.99, 3 ligands (GCP, MG, ZN). MolNFT v2 #126717 on GenesisL1: 3D structure, binding sites and pockets in…

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
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

Structure

electron microscopy · resolution 3.99 · 85 distinct chains.

ChainMoleculeTypeResiduesSecondary structureUniProt
A—protein248—G1TT27
B—protein394—G1TL06
C—protein362——
D—protein293—G1SYJ6
E—protein216—G1SKF7
F—protein225—G1TUB1
G—protein233—G1STW0
H—protein190—G1TX33
I—protein205—B7NZQ2
J—protein170—G1TUB8
L—protein210——
M—protein138—G1SZ12
N—protein203—G1T0C1
O—protein199——
P—protein153—G1TVT6
Q—protein187——
R—protein180——
S—protein176——
T—protein159—G1SHQ2
U—protein99——
V—protein131—G1T6D1
W—protein106—G1SE28
X—protein118—G1SE76
Y—protein134—G1SQH0
Z—protein135—G1TXF6
a—protein147—G1SNY0
b—protein104—G1SGR6
c—protein98—G1TDL2
d—protein107—G1SHG0
e—protein128—G1U437
f—protein109—G1SF08
g—protein114——
h—protein122—G1SIT5
i—protein102—G1TTQ5
j—protein86——
k—protein69——
l—protein50—G1TTN1
m—protein52——
n—protein25——
o—protein104—G1U344
p—protein91—G1SY53
r—protein124—G1U7L1
s—protein196——
t—protein153—G1SMR7
2, 3—rna75——
5—rna3543——
7—rna120——
8—rna151——
9—rna1698——
AA—protein217——
BB—protein213—G1SS70
CC—protein221——
DD—protein228—G1TNM3
EE—protein262——
FF—protein185—G1TFM5
GG—protein237—G1TM55
HH—protein185—G1SVB0
II—protein206——
JJ—protein185—B7NZS8
KK—protein96—G1TPV3
LL—protein143—G1TRM4
MM—protein117—G1SFR8
NN—protein149—G1SP51
OO—protein136—G1T1F0
PP—protein120—G1U0Q2
QQ—protein142—G1SGX4
RR—protein132—G1TU13
SS—protein144—G1TPG3
TT—protein141—G1TN62
UU—protein100—G1SIZ2
VV—protein83——
WW—protein129—G1TG89
XX—protein141——
YY—protein124——
ZZ—protein75—G1TDB3
aa—protein101——
bb—protein83—G1TZ76
cc—protein62—G1TIB4
dd—protein55—G1U7M4
ee—protein55—G1T8A2
ff—protein68—G1SK22
gg—protein313—G1SJB4
hh—rna8——
ii—protein372—Q9BRX2
jj—protein425—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, b, X, 8, 7, 9, aa, EE, DD, QQ, TT, OO, 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.

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

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