MolNFT v2 · #163878 · protein

Cryo-EM structure of respiratory complex I from Yarrowia lipolytica at 3.2 A resolution

6RFR: “Cryo-EM structure of respiratory complex I from Yarrowia lipolytica at 3.2 A resolution”. Electron microscopy at 3.2, 13 ligands (3PE, PLC, SF4). MolNFT v2 #163878 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6RFR
Type: protein
Length: 8,057 residues
Chains: 42
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.2
Source: Yarrowia lipolytica
UniProt: Q9UUU3, Q9UUU2, Q9UUU1, A0A1D8NC63, A0A371BY45, A0A371C5F3, Q9UUU0, Q9UUT9, Q9UUT8, A0A371CB65, Q9UUT7, Q9B6D4, A0A1H6Q8Z5, A0A1H6PXT9, A0A1D8N3C8, A0A1D8NG21, A0A1D8NDL1, Q6ZY23, A0A371C2D0, A0A1H6PPE5, A0A1D8NKB4, A0A1D8N7X0, A0A1D8N3H5, A0A1D8ND94, A0A1D8NGI5, A0A371C0F2, A0A1D8N596, A0A1D8NFX6, A0A1H6PJS3, A0A1D8NJR0, A0A1D8N5V2, A0A1H6Q311, Q6ZY24, A0A371CFV9, S5U3V2, S5U4R9, S5TMS4, S5TMP9, S5TF58, Q9B6E9, A0A1H6PKH9, A0A1D8NNZ0
Ligands: 3PE, PLC, SF4, CDL, T7X, FES, LMN, ZMP, FMN, NDP, UQ9, CPL, ZN

Structure

electron microscopy · resolution 3.2 · 42 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	—	protein	692	—	Q9UUU3
B	—	protein	456	—	Q9UUU2
C	—	protein	438	—	Q9UUU1
D	—	protein	86	—	A0A1D8NC63
E	—	protein	349	—	A0A371BY45
F	—	protein	121	—	A0A371C5F3
G	—	protein	239	—	Q9UUU0
H	—	protein	216	—	Q9UUT9
I	—	protein	190	—	Q9UUT8
J	—	protein	179	—	A0A371CB65
K	—	protein	177	—	Q9UUT7
L	—	protein	89	—	Q9B6D4
M	—	protein	117	—	A0A1H6Q8Z5
O	—	protein	77	—	A0A1H6PXT9
P	—	protein	123	—	A0A1D8N3C8
Q	—	protein	85	—	A0A1D8NG21
R	—	protein	106	—	A0A1D8NDL1
S	—	protein	174	—	Q6ZY23
U	—	protein	171	—	A0A371C2D0
W	—	protein	121	—	A0A1H6PPE5
X	—	protein	167	—	A0A1D8NKB4
Y	—	protein	123	—	A0A1D8N7X0
Z	—	protein	181	—	A0A1D8N3H5
a	—	protein	124	—	A0A1D8ND94
b	—	protein	64	—	A0A1D8NGI5
c	—	protein	44	—	A0A371C0F2
d	—	protein	90	—	A0A1D8N596
e	—	protein	52	—	A0A1D8NFX6
f	—	protein	80	—	A0A1H6PJS3
g	—	protein	76	—	A0A1D8NJR0
h	—	protein	136	—	A0A1D8N5V2
i	—	protein	83	—	A0A1H6Q311
j	—	protein	90	—	Q6ZY24
n	—	protein	114	—	A0A371CFV9
1	—	protein	340	—	S5U3V2
2	—	protein	469	—	S5U4R9
3	—	protein	127	—	S5TMS4
4	—	protein	486	—	S5TMP9
5	—	protein	654	—	S5TF58
6	—	protein	183	—	Q9B6E9
8	—	protein	82	—	A0A1H6PKH9
9	—	protein	86	—	A0A1D8NNZ0

Ligands and binding sites

3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 15 copies · chains C, I, g, 1, E, K, J, 4, 2, 5, W, S, b, 3, D, 6, i, a
PLC · Diundecyl phosphatidyl choline · ligand · 7 copies · chains K, 1, I, W, Z, i, n, 4, 5, h, R
SF4 · Iron/sulfur cluster · ligand · 6 copies · chains A, B, I, C, K
CDL · Cardiolipin · ligand · 6 copies · chains E, 1, 3, X, g, 2, 6, D, I, Z, h, J, j, 5, S, i, n, 4
T7X · Phosphatidylinositol · ligand · 4 copies · chains X, b, 2, L, 5, 6, E, K, 1, 3, C, 4
FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains A, H
LMN · Lauryl Maltose Neopentyl Glycol · ligand · 2 copies · chains J, 2, 4, a, j
ZMP · S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy) butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate · ligand · 2 copies · chains O, P, Q, R
FMN · Flavin mononucleotide · ligand · chains B
NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains E
UQ9 · Ubiquinone-9 · ligand · chains K, 1
CPL · 1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphocholine · ligand · chains b, 2
ZN · Zinc ion · metal · chains M

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

Compared structures

6RFR · Cryo-EM structure of respiratory complex I from yarrowia lipolytica at 3.2 a resolution · the same entry in another collection · chain 2 against 2, TM-score 1.00

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