3NBS: Dimeric cytochrome c from horse heart

Crystal structure of dimeric cytochrome c from horse heart. Determined by X-ray diffraction at 2.2 Å resolution. Released 14 Jul 2010.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Equus caballus
Chains: 4
Atoms: 3,776
Mol. weight: 50.18 kDa
Ligands: PO4, HEC
Released: 14 Jul 2010

Explore 3NBS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3NBS contains 28 α-helices and 12 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 7 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	3-13	11
α-helix	24-26	3
α-helix	38	1
β-strand	39	1	1
α-helix	50-54	5
β-strand	58	1	1
α-helix	61-69	9
α-helix	71-74	4
β-strand	80	1	2
α-helix	88-101	14

Chains B and D: 7 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	3-13	11
α-helix	24-26	3
β-strand	39	1	3
α-helix	50-54	5
β-strand	58	1	3
α-helix	61-69	9
α-helix	71-74	4
β-strand	80	1	2
α-helix	81-84	4
α-helix	88-101	14

Chain C: 7 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	3-13	11
α-helix	24-26	3
α-helix	38	1
β-strand	39	1	4
α-helix	50-53	4
β-strand	58	1	4
α-helix	61-69	9
α-helix	71-74	4
β-strand	80	1	5
α-helix	88-101	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cytochrome c	A, B, C, D	protein	104	Equus caballus	P00004 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>3NBS_1 Cytochrome c (chains A, B, C, D)
GDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGFTYTDANKNKGITWK
EETLMEYLENPKKYIPGTKMIFAGIKKKTEREDLIAYLKKATNE

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	2
HEC	Heme C	C34 H36 Fe N4 O4	4

Water and common crystallization additives (PEG, PG4) are not listed.

Primary citation

Cytochrome c polymerization by successive domain swapping at the C-terminal helix. Hirota, S., Hattori, Y., Nagao, S. et al. Proc Natl Acad Sci U S A (2010) 107:12854-12859. DOI 10.1073/pnas.1001839107 · PubMed

Other PDB entries of the same protein (UniProt P00004 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6K9J 0.98 Å, 0.98 A three-dimensional structure of horse heart cytochrome C at 110K
8ZXR 1.6 Å, Crystal structure of Ssr1698 in complex with heme c
3O1Y 1.75 Å, Electron transfer complexes: Experimental mapping of the redox-dependent cytochrome c…
1WEJ 1.8 Å, IgG1 FAB fragment (of E8 antibody) complexed with horse cytochrome C at 1.8 a resolution
3WC8 1.8 Å, Dimeric horse cytochrome c obtained by refolding with desalting method
3WUI 1.8 Å, Dimeric horse cytochrome c formed by refolding from molten globule state
6K9I 1.8 Å, High-resolution three-dimensional structure of horse heart cytochrome C at room…
1HRC 1.9 Å, High-resolution three-dimensional structure of horse heart cytochrome C
3O20 1.9 Å, Electron transfer complexes:experimental mapping of the Redox-dependent Cytochrome C…
5IY5 2.0 Å, Electron transfer complex of cytochrome c and cytochrome c oxidase at 2.0 angstrom…
1CRC 2.08 Å, Cytochrome C at low ionic strength
3NBT 2.1 Å, Crystal structure of trimeric cytochrome c from horse heart

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