GL1X · GenesisL1 explorer

MolNFT v2 · #172983 · protein + RNA

The structure of the mitoribosome from Neurospora crassa with bound tRNA at the P-site

6YWY: “The structure of the mitoribosome from Neurospora crassa with bound tRNA at the P-site”. Electron microscopy at 3.05, 6 ligands (SPM, NAD, ATP). MolNFT v2 #172983 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
6YWY
Type
protein + RNA
Length
19,966 residues
Chains
85
Method
electron microscopy
Collection
MolNFT v2 / PDB Bank
Contract
0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner
0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution
3.05
Source
Neurospora crassa
UniProt
A0A0B0DJN7, Q873B3, V5IMN1, Q96U12, A0A0B0DQR9, A0A0B0DK80, Q6M9C4, A0A0B0DNH1, A0A0B0E388, A0A0B0E7L9, A0A0B0DM93, Q8X081, A0A0B0ECK1, A0A0B0DXI2, Q6MVF2, Q7S5N0, A0A0B0DT83, A0A0B0DQ90, Q8X0Q2, A0A0B0DNQ5, A0A0B0DW15, Q8X098, Q9C2E5, Q9HFL0, A0A0B0E6P7, Q96U95, Q7S4E7, A0A0B0DZ96, A0A0B0DWX0, A0A0B0E3D2, A0A0B0DUU4, A0A0B0DPP2, A0A0B0DTN8, Q7S518, Q7S711, Q6MVH6, A0A0B0E0Q5, A0A0B0E462, Q8NIR6, A0A0B0DMU6, A0A0B0EF55, A0A0B0ECJ7, A0A0B0DJR9, V5ILE0, A0A1W5YJW8, A0A0B0DXP8, Q8X048, A0A0B0DP65, A0A0B0E7P2, A0A0B0EEW5, A0A0B0ED13, A0A0B0EAU9, A0A0B0DQD8, A0A0B0DQD0, Q6MVY0, A0A0B0DHJ1, Q8X067, A0A0B0DKS9, A0A0B0DJ04, Q872A7, A0A0B0DRW6, A0A0B0DTH5, Q873E4, Q7SHR9, Q7RYW7, Q7SD06, A0A0B0DU00, Q9P5J2, A0A0B0E339, Q7SHR6, Q9HE52, A0A0B0DM95, Q7SHB2, A0A0B0DYB0, Q9C251, A0A0B0DIK4, Q870V5, Q7RWZ7
Ligands
SPM, NAD, ATP, MG, K, ZN

Structure

electron microscopy · resolution 3.05 · 85 distinct chains.

ChainMoleculeTypeResiduesSecondary structureUniProt
A—rna2843——
B—protein315—A0A0B0DJN7
C—protein307—Q873B3
D—protein254—V5IMN1
E—protein309—Q96U12
F—protein201—A0A0B0DQR9
G—protein74—A0A0B0DK80
f—protein245—Q6M9C4
g—protein147—A0A0B0DNH1
H—protein183—A0A0B0E388
I—protein119—A0A0B0E7L9
J—protein243—A0A0B0DM93
K—protein168—Q8X081
L—protein192—A0A0B0ECK1
M—protein194—A0A0B0DXI2
N—protein133—Q6MVF2
O—protein272—Q7S5N0
P—protein180—A0A0B0DT83
Q—protein353—A0A0B0DQ90
R—protein249—Q8X0Q2
S—protein179—A0A0B0DNQ5
T—protein180—A0A0B0DW15
U—protein138—Q8X098
V—protein94—Q9C2E5
W—protein59—Q9HFL0
X—protein48—A0A0B0E6P7
Y—protein46—Q96U95
0—protein46—Q7S4E7
1—protein367—A0A0B0DZ96
2—protein123—A0A0B0DWX0
3—protein95—A0A0B0E3D2
4—protein137—A0A0B0DUU4
5—protein350—A0A0B0DPP2
6—protein273—A0A0B0DTN8
7—protein84—Q7S518
8—protein331—Q7S711
h—protein98—Q6MVH6
i—protein124—A0A0B0E0Q5
9—protein206—A0A0B0E462
a—protein161—Q8NIR6
b—protein161—A0A0B0DMU6
c—protein98—A0A0B0EF55
d—protein235—A0A0B0ECJ7
AA—protein372—A0A0B0DJR9
BB—protein290—V5ILE0
CC—protein438—A0A1W5YJW8
DD—protein290—A0A0B0DXP8
EE—protein367—Q8X048
FF—protein117—A0A0B0DP65
GG—protein223—A0A0B0E7P2
HH—protein160—A0A0B0EEW5
II—protein247—A0A0B0ED13
JJ—protein188—A0A0B0EAU9
KK—protein124—A0A0B0DQD8
LL—protein128—A0A0B0DQD0
MM—protein118—Q6MVY0
NN—protein112—A0A0B0DHJ1
OO—protein276—Q8X067
PP—protein98—A0A0B0DKS9
QQ—protein158—A0A0B0DJ04
RR—protein134—Q872A7
SS—protein81—A0A0B0DRW6
TT—protein88—A0A0B0DTH5
UU—protein224—Q873E4
VV—protein261—Q7SHR9
WW—protein353—Q7RYW7
XX—protein408—Q7SD06
YY—protein99—A0A0B0DU00
ZZ—protein312—Q9P5J2
11—protein88—A0A0B0E339
22—protein33—Q7SHR6
33—protein191—Q9HE52
44—protein260—A0A0B0DM95
55—protein232—A0A0B0DM95
66—protein283—Q7SHB2
77—protein179—A0A0B0DYB0
88—protein467—Q9C251
00—protein48—A0A0B0DIK4
99—protein36—A0A0B0DIK4
aa—rna1435——
bb—rna73——
ee—rna11——
cc—protein7——
e—protein148—Q870V5
j—protein195—Q7RWZ7

Ligands and binding sites

  • SPM · Spermine · ligand · chains A, c
  • NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A, E, 2, 6
  • ATP · Adenosine-5'-triphosphate · ligand · chains XX
  • MG · Magnesium ion · metal · 250 copies · chains A, B, P, 3, C, D, Q, Y, J, T, c, M, S, K, L, BB, KK, aa, QQ, XX, YY, 00, LL, ee
  • K · Potassium ion · metal · 49 copies · chains A, C, J, 0, 2, 3, ZZ, 88, aa, KK
  • ZN · Zinc ion · metal · 2 copies · chains W, 0

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

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