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Cryo-EM structure of polytomella complex-I (complete composition)

Analyse Cryo-EM structure of polytomella complex-I (complete composition) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7ARD
Type: protein
Length: 8,747 residues
Chains: 51
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ND3; Psst; ND9; ND7; 24 kda; 51 kda; 75 kda; ND1; Tyky; ND6; ND4L; ND5; ND4; ND2; C1-fdx…
UniProt: A0A024FSS5
Ligands: PC7, PTY, SF4, CDL, FES, 8Q1, FMN, NDP, ZN
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 51 distinct chains · 51% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ND3	protein	121	63% helix, 0% strand	—
B	Psst	protein	154	50% helix, 13% strand	—
C	ND9	protein	216	19% helix, 31% strand	—
D	ND7	protein	395	50% helix, 13% strand	—
E	24 kda	protein	235	34% helix, 13% strand	—
F	51 kda	protein	430	48% helix, 13% strand	—
G	75 kda	protein	682	34% helix, 18% strand	—
H	ND1	protein	293	72% helix, 1% strand	—
I	Tyky	protein	199	37% helix, 15% strand	—
J	ND6	protein	145	74% helix, 0% strand	—
K	ND4L	protein	104	78% helix, 0% strand	—
L	ND5	protein	536	75% helix, 5% strand	—
M	ND4	protein	438	74% helix, 3% strand	—
N	ND2	protein	375	79% helix, 0% strand	—
O	C1-fdx	protein	161	24% helix, 22% strand	—
P	39 kda	protein	347	36% helix, 14% strand	—
Q	18 kda	protein	162	28% helix, 14% strand	—
R	13 kda	protein	108	14% helix, 16% strand	—
S	B8	protein	95	47% helix, 24% strand	—
T	SDAP1	protein	83	57% helix, 2% strand	—
U	SDAP2	protein	84	52% helix, 2% strand	—
V	B13	protein	134	57% helix, 7% strand	—
W	B14	protein	127	60% helix, 0% strand	—
X	Pgiv	protein	99	74% helix, 1% strand	—
Y	B14.7	protein	205	55% helix, 3% strand	—
Z	B16.6	protein	124	53% helix, 0% strand	—
a	Mwfe	protein	60	85% helix, 0% strand	—
b	B9	protein	54	87% helix, 0% strand	—
c	Kfyi	protein	97	35% helix, 6% strand	—
d	B14.5B	protein	80	76% helix, 3% strand	—
e	15 kda	protein	71	72% helix, 0% strand	—
f	Mnll	protein	111	58% helix, 3% strand	—
g	Esss	protein	147	60% helix, 1% strand	—
h	NUOP4	protein	77	64% helix, 1% strand	—
i	NUOP5	protein	111	43% helix, 11% strand	—
j	Aggg	protein	87	45% helix, 10% strand	—
k	B12	protein	44	68% helix, 0% strand	—
l	Ashi	protein	127	41% helix, 6% strand	—
m	B15	protein	111	43% helix, 4% strand	—
n	Complex I-B22	protein	120	51% helix, 3% strand	A0A024FSS5
o	B18	protein	83	64% helix, 0% strand	—
p	Pdsw	protein	155	63% helix, 3% strand	—
q	B17.2	protein	28	0% helix, 7% strand	—
r	B14.5A	protein	60	15% helix, 17% strand	—
s	NUOP7	protein	115	43% helix, 2% strand	—
t	NUOP8	protein	82	59% helix, 0% strand	—
u	Unknown	protein	50	94% helix, 0% strand	—
w	Unknown	protein	41	78% helix, 2% strand	—
x	Cal	protein	250	23% helix, 26% strand	—
y	CA2	protein	308	28% helix, 26% strand	—
z	CA3	protein	226	30% helix, 30% strand	—

Ligands and binding sites

PC7 · (7S)-4-hydroxy-N,N,N-trimethyl-9-oxo-7-[(palmitoyloxy) methyl]-3,5,8-trioxa-4-phosphahexacosan-1-aminium 4-oxide · ligand · 7 copies · chains A, H, N, b, y, L, M, h, l, c, n, g, d, f, J, z
PTY · Phosphatidylethanolamine · ligand · 7 copies · chains D, H, I, Z, L, h, l, M, Y, g, N, O, m
SF4 · Iron/sulfur cluster · ligand · 6 copies · chains B, D, F, G, I
CDL · Cardiolipin · ligand · 5 copies · chains L, M, Y, m, s, t, N, d, n, f, i, y, z
FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains E, F, G
8Q1 · S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy) butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate · ligand · 2 copies · chains U, W, T, n, s
FMN · Flavin mononucleotide · ligand · chains F
NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains B, P
ZN · Zinc ion · metal · chains R

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1103	0.89	0.90	139	empty
2	979	0.89	0.91	130	empty
3	1089	0.88	0.89	107	empty
4	1042	0.87	0.87	88	CDL
5	962	0.86	0.88	82	empty

Interfaces

228 interfaces between chains.

x–y · 3522 Å² buried · 45 hydrogen bonds · protein-protein
E–F · 3217 Å² buried · 33 hydrogen bonds · protein-protein
J–K · 3213 Å² buried · 21 hydrogen bonds · protein-protein
C–D · 2969 Å² buried · 45 hydrogen bonds · protein-protein
y–z · 2745 Å² buried · 25 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

7ARD · Cryo-EM structure of Polytomella Complex-I (complete composition) · the same entry in another collection · chain B against B, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt A0A024FSS5
Elsewhere: RCSB PDB 7ARD · PDBe 7ARD · UniProt A0A024FSS5

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