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2YBB: Fitted model for bovine mitochondrial supercomplex I1III2IV1 by single particle cryo-EM (EMD-1876)

PDB ID:

2YBB Download

MMDB ID:

94393

PDB Deposition Date:

2011

Updated in MMDB:

2022/11

Experimental Method:

electron microscopy

Resolution:

19 Å

Source Organism:

Escherichia coli BL21▼

Taxonomy	Molecule
Escherichia coli BL21	m, n, o, p
Thermus thermophilus HB8	1, 2, 3, 4, 5, 6, 7, 8
Bos taurus	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, a, b, c, d, e, f, g, h, i , j, k

Similar Structures:

Biological Unit for 2YBB: 48-meric; determined by author and by software (PISA)

Molecular Components in 2YBB
Label	Count	Molecule
Proteins (48 molecules)
1	1	Nadh-quinone Oxidoreductase Subunit 1
2	1	Nadh-quinone Oxidoreductase Subunit 2
3	1	Nadh-quinone Oxidoreductase Subunit 3
4	1	Nadh-quinone Oxidoreductase Subunit 4
5	1	Nadh-quinone Oxidoreductase Subunit 5
6	1	Nadh-quinone Oxidoreductase Subunit 6
7	1	Nadh-quinone Oxidoreductase Subunit 15
8	1	Nadh-quinone Oxidoreductase Subunit 9
A a	2	Cytochrome B-c1 Complex Subunit 1, Mitochondrial
B b	2	Cytochrome B-c1 Complex Subunit 2, Mitochondrial
C c	2	Cytochrome B
D d	2	Cytochrome C1, Heme Protein, Mitochondrial
E e	2	Cytochrome B-c1 Complex Subunit Rieske, Mitochondrial
F f	2	Cytochrome B-c1 Complex Subunit 7
G g	2	Cytochrome B-c1 Complex Subunit 8
H h	2	Cytochrome B-c1 Complex Subunit 6, Mitochondrial
I i	2	Cytochrome B-c1 Complex Subunit Rieske, Mitochondrial
J j	2	Cytochrome B-c1 Complex Subunit 9
K k	2	Cytochrome B-c1 Complex Subunit 10
L	1	Cytochrome C Oxidase Subunit 1
M	1	Cytochrome C Oxidase Subunit 2
N	1	Cytochrome C Oxidase Subunit 3
O	1	Cytochrome C Oxidase Subunit 4 Isoform 1, Mitochondrial
P	1	Cytochrome C Oxidase Subunit 5A, Mitochondrial
Q	1	Cytochrome C Oxidase Subunit 5B, Mitochondrial
R	1	Cytochrome C Oxidase Polypeptide Via, Cytochrome C Oxidase Polypeptide VB
S	1	Cytochrome C Oxidase Subunit 6B1
T	1	Cytochrome C Oxidase Subunit 6C
U	1	Cytochrome C Oxidase Subunit 7a1, Mitochondrial
V	1	Cytochrome C Oxidase Subunit 7B, Mitochondrial
W	1	Cytochrome C Oxidase Subunit 7C, Mitochondrial
X	1	Cytochrome C Oxidase Subunit 8B, Mitochondrial
Y	1	Cytochrome C
m	1	Nadh\: Ubiquinone Oxidoreductase, Membrane Subunit L,
n	1	Nadh\: Ubiquinone Oxidoreductase, Membrane Subunit M,
o	1	Nadh-quinone Oxidoreductase Subunit N
p	1	Nadh-quinone Oxidoreductase Subunit K
Chemicals and Non-standard biopolymers (42 molecules)
1	7	IRON/SULFUR CLUSTER (Link to PubChem not yet available)
2	1	FLAVIN MONONUCLEOTIDE (Link to PubChem not yet available)
3	1	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE (Link to PubChem not yet available)
4	7	MAGNESIUM ION (Link to PubChem not yet available)
5	4	FE2/S2 (INORGANIC) CLUSTER (Link to PubChem not yet available)
6	1	CALCIUM ION (Link to PubChem not yet available)
7	5	PROTOPORPHYRIN IX CONTAINING FE (Link to PubChem not yet available)
8	2	STIGMATELLIN A (Link to PubChem not yet available)
9	2	UBIQUINONE-1 (Link to PubChem not yet available)
10	2	HEME C (Link to PubChem not yet available)
11	4	CARDIOLIPIN (Link to PubChem not yet available)
12	2	HEME-A (Link to PubChem not yet available)
13	3	COPPER (II) ION (Link to PubChem not yet available)
14	1	ZINC ION (Link to PubChem not yet available)

* Click molecule labels to explore molecular sequence information.

Citing MMDB

Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. " MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2014 Jan; 42(Database issue):D297-303