GL1X · GenesisL1 explorer

MolNFT v2 · #157065 · protein + RNA

Cryo-EM structure of 90S small subunit preribosomes in transition states (State A1)

6LQU: “Cryo-EM structure of 90S small subunit preribosomes in transition states (State A1)”. Electron microscopy at 3.7, 3 ligands (GTP, ZN, MG). MolNFT v2 #157065 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
6LQU
Type
protein + RNA
Length
27,233 residues
Chains
72
Method
electron microscopy
Collection
MolNFT v2 / PDB Bank
Contract
0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner
0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution
3.7
Source
Saccharomyces cerevisiae (strain ATCC 204508 / S288c); Saccharomyces cerevisiae…
UniProt
P0CX35, P26783, P0CX37, P26786, P0CX39, O13516, P0CX47, P48589, P05756, P06367, P0CX51, P0CX55, Q3E7Y3, P0CX29, P0CX31, Q3E7X9, P15646, Q12460, Q12499, Q06506, P39990, Q06679, Q04177, P53276, P38882, P42945, Q04305, Q02931, P25635, Q12220, Q05946, P40362, Q06078, Q02354, Q08492, P40055, P34247, P47083, P32899, P53941, Q12136, P33750, Q12035, Q05498, P48234, P40079, P25586, Q05022, P53254, P25368, Q06287, P36144, Q08965, Q08096, P53914, Q99207, Q06512, P35194, Q04500, P38333, P40546, P40470, Q06631
Ligands
GTP, ZN, MG

Structure

electron microscopy · resolution 3.7 · 71 distinct chains.

ChainMoleculeTypeResiduesSecondary structureUniProt
3A—rna175——
5A—rna523——
SA—rna1242——
SF—protein229—P0CX35
SG—protein213—P26783
SH—protein167—P0CX37
SI—protein165—P26786
SJ—protein166—P0CX39
SK—protein171—O13516
SM—protein123—P0CX47
SN—protein119—P48589
SO—protein134—P05756
SP—protein118—P06367
SR—protein125—P0CX51
ST—protein117—P0CX55
SX—protein127—Q3E7Y3
SY—protein103—P0CX29
SZ—protein102—P0CX31
Sd—protein63—Q3E7X9
3B—protein240—P15646
3C—protein225—P15646
3D—protein369—Q12460
3E—protein431—Q12499
3F—protein454—Q06506
3G, 3H—protein121—P39990
A4—protein662—Q06679
A5—protein514—Q04177
A8—protein548—P53276
A9—protein128—P38882
AE—protein1534—P42945
AF—protein493—Q04305
AG—protein826—Q02931
B1—protein834—P25635
B2—protein851—Q12220
B3—protein752—Q05946
B8—protein477—P40362
BE—protein865—Q06078
B6—protein374—Q02354
5B—protein60—Q08492
5C—protein516—P40055
5D—protein235—P34247
5E—protein204—P47083
5F—protein182—P32899
5G—protein282—P53941
5H—protein136—Q12136
5I—protein461—P33750
5J—protein151—Q12035
5K—protein175—Q05498
RA—protein338—P48234
RB—protein134—P40079
RC—protein175—P25586
RD—protein265—Q05022
RE—protein1079—P53254
RF—protein174—P25368
RG—protein216—Q06287
RH—protein230—Q06287
RI—protein252—P36144
RJ—protein796—Q08965
RK—protein360—Q08096
RL—protein805—P53914
RM—protein766—P53914
RN—protein607—Q99207
RO—protein525—Q06512
RP—protein2109—P35194
RQ—protein226—Q04500
RS—protein251—P38333
RT—protein171——
RV—protein190—P40546
RW—protein63—P40470
RY—protein37—Q06631
X1—protein61——

Ligands and binding sites

  • GTP · Guanosine-5'-triphosphate · ligand · chains RJ
  • ZN · Zinc ion · metal · chains 5K
  • MG · Magnesium ion · metal · chains RJ

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

Compared structures

  • Q08096 · AlphaFold monomer V2.0 prediction for RNA 3'-terminal phosphate cyclase-like protein… · a predicted model of the same protein · chain RK against A, TM-score 0.99
  • Q06679 · AlphaFold monomer V2.0 prediction for U3 small nucleolar RNA- associated protein 4… · a predicted model of the same protein · chain A4 against A, TM-score 0.98
  • P15646 · AlphaFold monomer V2.0 prediction for rRNA 2'-O-methyltransferase fibrillarin (P15646) · a predicted model of the same protein · chain 3B against A, TM-score 0.98
  • Q08965 · AlphaFold monomer V2.0 prediction for ribosome biogenesis protein BMS1 (Q08965) · a predicted model of the same protein · chain RJ against A, TM-score 0.97
  • P48234 · AlphaFold monomer V2.0 prediction for ribosome biogenesis protein ENP2 (P48234) · a predicted model of the same protein · chain RA against A, TM-score 0.97
  • P33750 · AlphaFold monomer V2.0 prediction for protein SOF1 (P33750) · a predicted model of the same protein · chain 5I against A, TM-score 0.96
  • P32899 · AlphaFold monomer V2.0 prediction for U3 small nucleolar ribonucleoprotein protein IMP3… · a predicted model of the same protein · chain 5F against A, TM-score 0.96
  • P53941 · AlphaFold monomer V2.0 prediction for U3 small nucleolar ribonucleoprotein protein IMP4… · a predicted model of the same protein · chain 5G against A, TM-score 0.95
  • Q06512 · AlphaFold monomer V2.0 prediction for nucleolar complex protein 4 (Q06512) · a predicted model of the same protein · chain RO against A, TM-score 0.92
  • Q05022 · AlphaFold monomer V2.0 prediction for rRNA biogenesis protein RRP5 (Q05022) · a predicted model of the same protein · chain RD against A, TM-score 0.92
  • P38333 · AlphaFold monomer V2.0 prediction for essential nuclear protein 1 (P38333) · a predicted model of the same protein · chain RS against A, TM-score 0.90

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