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MolNFT v1 · #140355 · protein + RNA

Cryo-EM structure of the intron-lariat spliceosome ready for disassembly from S.CEREVISIAE at 3.5 ångström

5Y88: “Cryo-EM structure of the intron-lariat spliceosome ready for disassembly from S.CEREVISIAE at 3.5 ångström”. Electron microscopy, 4 ligands (IHP, GTP, MG). MolNFT v1 #140355 on GenesisL1: 3D structure, binding sites and pockets in…

PDB
5Y88
Type
protein + RNA
Length
9,450 residues
Chains
44
Method
electron microscopy
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
UniProt
P33334, P36048, Q06091, Q04048, Q12309, Q03654, P53277, P25337, P38241, Q12046, Q12417, Q03772, P28004, P28320, P40968, P52868, Q06411, P36118, P53131, P40018, Q12330, P54999, P40204, P43321, Q02260, Q06217, Q08963, P40567, P32523
Ligands
IHP, GTP, MG, ZN

Structure

electron microscopy · 39 distinct chains.

ChainMoleculeTypeResiduesSecondary structureUniProt
A—protein1903—P33334
B—rna117——
C—protein913—P36048
D—rna101——
E—rna28——
F—rna82——
G—protein155—Q06091
H—protein601—Q04048
I—protein541—Q12309
J—protein431—Q03654
K—protein102—P53277
L—protein157—P25337
M—protein182—P38241
N—protein261—Q12046
O—protein337—Q12417
P—protein68—Q03772
Q—protein201—P28004
R—protein46—P28320
S—protein23—P40968
T—protein107—P52868
U—protein488—Q06411
V—protein91—P36118
W—protein708—P53131
a—protein80—P40018
b, i—protein75—Q12330
c, j—protein70—P54999
d, k—protein69—P40204
e, l—protein82—P43321
f, m—protein82—Q02260
g—protein94—Q06217
o—protein135—Q08963
p—protein81—P40567
h—protein78—P40018
n—protein65—Q06217
q—protein126—P32523
r—protein129—P32523
s—protein129—P32523
t—protein125—P32523
x—rna9——

Ligands and binding sites

  • IHP · Inositol hexakisphosphate · ligand · chains A
  • GTP · Guanosine-5'-triphosphate · ligand · chains C
  • MG · Magnesium ion · metal · 6 copies · chains C, D
  • ZN · Zinc ion · metal · 6 copies · chains L, M, N

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Compared structures

  • 5Y88 · Cryo-EM structure of the intron-lariat spliceosome ready for disassembly from… · the same entry in another collection · chain K against K, TM-score 1.00

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