National Center for
Biotechnology Information

8GYM: Cryo-EM structure of Tetrahymena thermophila respiratory mega-complex MC IV2+(I+III2+II)2

PDB ID:	8GYM Download
MMDB ID:	231718
PDB Deposition Date:	2022/9/23
Updated in MMDB:	2023/06
Experimental Method:	electron microscopy
Resolution:	2.96 Å
Source Organism:	Tetrahymena thermophila SB210
Similar Structures:

Biological Unit for 8GYM: 326-meric; determined by author

Molecular Components in 8GYM
Label	Count	Molecule
Proteins (326 molecules)
1t 1T	2	Tim10/ddp Family Zinc Finger Protein
2e 2E	2	Nmra Domain-containing Protein
2f 2F	2	Transmembrane Protein, Putative
2g 2G	2	Sdhtt3
2h 2H	2	Diphthamide Synthesis Protein
2i 2I	2	Duf4885 Domain-containing Protein
2j 2J	2	Transmembrane Protein, Putative
2k 2K	2	Transmembrane Protein, Putative
2l 2L	2	Transposase
2m 2M	2	Transmembrane Protein, Putative
2n 2N	2	Transmembrane Protein, Putative
2o 2O	2	Sdhtt11
2t 2T	2	Zf-tim10_ddp Domain-containing Protein
3t 3T	2	Zf-tim10_ddp Domain-containing Protein
4a 4A	2	Phage Protein
4t 4T	2	Transposase
5t 5T	2	Cullin Domain-containing Protein
6a 6A	2	Transmembrane Protein, Putative
6b 6B	2	Structural Protein
6c 6C	2	Transmembrane Protein, Putative
6l 6L	2	Decapping Nuclease
6t 6T	2	Annexin
7a 7A	2	Transmembrane Protein, Putative
7c 7C	2	Nadh Dehydrogenase [ubiquinone] 1 Beta Subcomplex Subunit 8, Mitochondrial
7l 7L	2	Ctf/nf-i Domain-containing Protein
a A	2	Transmembrane Protein, Putative
b B	2	Protein Phosphatase 2C, Putative
bp BP	2	Chromosome Condensation Regulator Rcc1 Repeat Protein
c1 C1	2	Cytochrome C Oxidase Subunit 1
c2 C2	2	Cytochrome C Oxidase Subunit 2
c3 C3	2	Ymf68
d D	2	Surf1-like Protein
e E	2	Trab Family Protein
f F	2	Transmembrane Protein, Putative
fs FS	2	Iron-binding Zinc Finger Cdgsh Type Protein
g G	2	Nadh Dehydrogenase [ubiquinone] 1 Alpha Subcomplex Subunit 8, Mitochondrial
h H	2	Surf1-like Protein
i I	2	Coxtt9
j J	2	Coxtt10
k K	2	39S Ribosomal Protein L9, Mitochondrial
l L	2	Ubiquinol-cytochrome C Reductase Complex Ubiquinone-binding Protein Qp-c
m M	2	Transmembrane Protein, Putative
m1 M1	2	Oxoglutarate/malate Translocator Protein, Putative
m2 M2	2	2-oxoglutarate/malate Carrier Protein
m3 M3	2	Carrier Protein
n N	2	Transmembrane Protein, Putative
o O	2	Mobilization Protein
p P	2	Yflt Domain-containing Protein
q Q	2	Transmembrane Protein, Putative
r R	2	Transmembrane Protein
s S	2	Complex III Subunit VII
sa SA	2	Succinate Dehydrogenase [ubiquinone] Flavoprotein Subunit, Mitochondrial
sb SB	2	Succinate Dehydrogenase (Quinone)
sc SC	2	Cytochrome B-c1 Complex Subunit 8
sd SD	2	Sdhd
t T	2	Transmembrane Protein, Putative
u U	2	Transmembrane Protein, Putative
v V	2	Coxtt22
vb VB	2	Cytochrome C Oxidase Subunit VB Protein
w W	2	Transmembrane Protein, Putative
x X	2	Transmembrane Protein, Putative
y Y	2	Lysozyme
y0 Y0	2	Ymf70
y5 Y5	2	Ymf75
y7 Y7	2	Ymf67
z Z	2	ABC Transporter
z1 Z1	2	Coxtt28
1b 1B	2	Nadh Dehydrogenase Subunit 1
2b 2B	2	Nadh Dehydrogenase Subunit 2
4l 4L	2	Ymf58
5b 5B	2	Ymf57
a1 A1	2	Transmembrane Protein, Putative
a2 A2	2	Ribosomal Protein L51/s25/ci-b8 Domain Protein
a3 A3	2	Transmembrane Protein, Putative
a5 A5	2	ETC Complex I Subunit Motif Protein
a6 A6	2	Nadh Dehydrogenase, Putative
a7 A7	2	37S Ribosomal Protein S25, Mitochondrial
a8 A8	2	Cx9c Domain-containing Protein
a9 A9	2	Nad-dependent Epimerase/dehydratase Family Protein
ab AB	2	Acyl Carrier Protein
ac AC	2	Acyl Carrier Protein
al AL	2	Nadh Dehydrogenase [ubiquinone] 1 Alpha Subcomplex Subunit 12
am AM	2	Ndua13
an AN	2	Transmembrane Protein, Putative
b2 B2	2	Ndub2
b3 B3	2	Transmembrane Protein, Putative
b4 B4	2	Ndub4
b6 B6	2	Ndub6
b7 B7	2	Chch Domain-containing Protein
b8 B8	2	Ndub8
b9 B9	2	Nadh Dehydrogenase [ubiquinone] 1 Alpha Subcomplex Subunit 10, Mitochondrial
bl BL	2	Ndub10
bm BM	2	Transmembrane Protein, Putative
c4 C4	2	Complex I-mnll
fx FX	2	2 Iron, 2 Sulfur Cluster-binding Protein
g1 G1	2	Gamma-carbonic Anhydrase
g2 G2	2	Gamma-carbonic Anhydrase
g3 G3	2	Transcription Factor Apfi Protein, Putative
j1 J1	2	Dnaj Domain Protein
n1 N1	2	Nadh-ubiquinone Oxidoreductase Chain 1
n2 N2	2	Ymf65
n3 N3	2	Nadh-ubiquinone Oxidoreductase Chain 3
n4 N4	2	Nadh-ubiquinone Oxidoreductase Chain 4
n5 N5	2	Nadh Dehydrogenase Subunit 5
n6 N6	2	Ymf62
p1 P1	2	Transmembrane Protein, Putative
p2 P2	2	Nduph2
qA qa QA Qa	4	M16 Family Peptidase, Putative
qB qb QB Qb	4	Peptidase M16 Inactive Domain Protein
qC qc QC Qc	4	Apocytochrome B
qD qd QD Qd	4	Cytochrome Protein C1
qE qe QE Qe	4	Rieske Iron-sulfur Protein, Ubiquinol-cytochrome C Reductase Iron-sulfur Subunit
qF qf QF Qf	4	Ubiquinol-cytochrome C Reductase Hinge Protein
qG qg QG Qg	4	Sulphotransf Domain-containing Protein
qH qh QH Qh	4	Transmembrane Protein, Putative
qI qi QI Qi	4	Transmembrane Protein, Putative
qJ qj QJ Qj	4	Transmembrane Protein, Putative
qL ql QL Ql	4	Uqcrtt2
qM qm Qm u2 U2 QM	6	Unknown Peptide
s1 S1	2	Nadh-ubiquinone Oxidoreductase 75 KDA Subunit
s2 S2	2	Nadh Dehydrogenase Subunit 7
s3 S3	2	Nadh Dehydrogenase Subunit 9
s4 S4	2	Nadh Dehydrogenase [ubiquinone] Iron-sulfur Protein 4, Mitochondrial
s5 S5	2	Gram Domain Protein
s6 S6	2	Zinc-finger Protein
s7 S7	2	Nadh Dehydrogenase Subunit 10
s8 S8	2	Nadh-ubiquinone Oxidoreductase 1, Chain, Putative
t1 T1	2	Lipid-a-disaccharide Synthase
t2 T2	2	Acyl-coa Synthetase (Amp-forming)/amp-acid Ligase II
t3 T3	2	Rnase III Domain-containing Protein
t4 T4	2	Transmembrane Protein
t5 T5	2	Transmembrane Protein, Putative
t6 T6	2	COX Assembly Mitochondrial Protein
t7 T7	2	Transmembrane Protein, Putative
t8 T8	2	PH Domain-containing Protein
t9 T9	2	Nadh Dehydrogenase [ubiquinone] 1 Alpha Subcomplex Subunit 8
ta TA	2	Nadh Dehydrogenase [ubiquinone] 1 Beta Subcomplex Subunit 4
tb TB	2	Transmembrane Protein, Putative
tc TC	2	ATP Synthase Subunit E, Mitochondrial
td TD	2	Transmembrane Protein, Putative
te TE	2	Transmembrane Protein, Putative
tf TF	2	Ndutt15
tg TG	2	Ndutt16
th TH	2	Ndutt17
tx TX	2	Thioredoxin
v1 V1	2	Nadh Dehydrogenase [ubiquinone] Flavoprotein 1, Mitochondrial
v2 V2	2	Nadh-ubiquinone Oxidoreductase 24 KDA Subunit
x1 X1	2	Nadh-ubiquinone Oxidoreductase Complex I, 21 KDA Subunit
C c	2	Coxtt3
u1 U1	2	Unknown Peptide
Chemicals and Non-standard biopolymers (510 molecules)
1	6	HEME C
2	168	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
3	198	CARDIOLIPIN
4	4	HEME-A
5	6	COPPER (II) ION
6	2	MAGNESIUM ION
7	16	FE2/S2 (INORGANIC) CLUSTER
8	48	1,2-Distearoyl-sn-glycerophosphoethanolamine
9	2	O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
10	6	1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE
11	2	FLAVIN-ADENINE DINUCLEOTIDE
12	14	IRON/SULFUR CLUSTER
13	2	FE3-S4 CLUSTER
14	10	UBIQUINONE-10
15	6	ZINC ION
16	10	PROTOPORPHYRIN IX CONTAINING FE
17	2	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
18	2	S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate
19	2	Phosphatidylinositol
20	2	ADENOSINE-5'-DIPHOSPHATE
21	2	FLAVIN MONONUCLEOTIDE