3KS0: Heme domain of flavocytochrome b2

Crystal structure of the heme domain of flavocytochrome b2 in complex with Fab B2B4. Determined by X-ray diffraction at 2.7 Å resolution. Released 26 May 2010.

Method: X-ray diffraction
Resolution: 2.7 Å
Organisms: Mus musculus, Saccharomyces cerevisiae
Chains: 6
Atoms: 8,021
Mol. weight: 116.86 kDa
Ligands: HEM
Released: 26 May 2010

Explore 3KS0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3KS0 contains 40 α-helices and 108 β-strands across 6 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: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	11	1	13
α-helix	13-17	5
β-strand	20-21	2	14
β-strand	24-25	2	14
β-strand	26-29	4	15
β-strand	32-35	4	15
α-helix	40-42	3
α-helix	48-53	6
β-strand	56-57	2	15
α-helix	59-65	7
α-helix	71-74	4
α-helix	77-79	3
β-strand	80-83	4	15
β-strand	84	1	13
α-helix	90-92	3
β-strand	93	1	15
α-helix	94-96	3

Chain B: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	11	1	28
α-helix	13-16	4
β-strand	20-21	2	29
β-strand	24-25	2	29
β-strand	26-29	4	30
β-strand	32-35	4	30
α-helix	37-42	6
α-helix	48-53	6
β-strand	57	1	30
α-helix	59-62	4
α-helix	71-74	4
α-helix	77-79	3
β-strand	80-83	4	30
β-strand	84	1	28
α-helix	90-92	3
β-strand	93	1	30
α-helix	94-96	3

Chain H: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	11-12	2	8
β-strand	18-25	8	7
β-strand	33-40	8	9
β-strand	44-52	9	9
β-strand	57-59	3	9
β-strand	67-72	6	7
α-helix	73-75	3
β-strand	77-82	6	7
α-helix	87-89	3
β-strand	91-98	8	9
β-strand	107	1	9
β-strand	111-113	3	9
β-strand	114-115	2	8
β-strand	121	1	10
β-strand	124-128	5	11
β-strand	139-149	11	11
β-strand	150	1	10
β-strand	155-158	4	12
α-helix	159-161	3
β-strand	167-169	3	11
α-helix	170-172	3
β-strand	173-175	3	11
β-strand	178-188	11	11
β-strand	198-203	6	12
α-helix	204-206	3
β-strand	208-213	6	12
α-helix	214	1

Chain J: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	16
β-strand	9-12	4	17
β-strand	17-22	6	18
β-strand	23-24	2	16
α-helix	31-33	3
β-strand	36-41	6	17
β-strand	45-51	7	17
β-strand	55-56	2	17
α-helix	57	1
β-strand	64-69	6	18
β-strand	72-78	7	18
α-helix	82-84	3
β-strand	86-94	9	17
β-strand	97-100	4	17
β-strand	104-108	5	17
β-strand	114	1	19
β-strand	117-121	5	20
α-helix	125-128	4
β-strand	132-142	11	20
β-strand	143	1	19
β-strand	148-153	6	21
β-strand	156-157	2	21
β-strand	162-164	3	20
α-helix	165-167	3
β-strand	168-169	2	20
β-strand	175-184	10	20
α-helix	185-189	5
β-strand	194-199	6	21
β-strand	204-209	6	21

Chain K: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	22
β-strand	11-12	2	23
β-strand	18-25	8	22
β-strand	33-39	7	24
β-strand	45-51	7	24
β-strand	57-59	3	24
β-strand	67-72	6	22
β-strand	77-82	6	22
α-helix	87-89	3
β-strand	91-98	8	24
β-strand	107	1	24
β-strand	111-113	3	24
β-strand	114-115	2	23
β-strand	121	1	25
α-helix	122-123	2
β-strand	124-128	5	26
β-strand	139-149	11	26
β-strand	150	1	25
β-strand	155-158	4	27
α-helix	159-161	3
β-strand	167-169	3	26
α-helix	170-172	3
β-strand	173-175	3	26
β-strand	178-188	11	26
α-helix	189-191	3
β-strand	198-203	6	27
β-strand	208-213	6	27
α-helix	214	1

Chain L: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	1
β-strand	9-12	4	2
β-strand	17-22	6	3
β-strand	23-24	2	1
α-helix	31-33	3
β-strand	36-41	6	2
β-strand	45-51	7	2
β-strand	55-56	2	2
α-helix	57	1
β-strand	64-69	6	3
β-strand	72-78	7	3
α-helix	82-84	3
β-strand	86-94	9	2
β-strand	97-100	4	2
β-strand	104-108	5	2
β-strand	114	1	4
β-strand	117-121	5	5
α-helix	125-128	4
β-strand	132-142	11	5
β-strand	143	1	4
β-strand	148-153	6	6
β-strand	156-157	2	6
β-strand	162-164	3	5
α-helix	165-167	3
β-strand	168-169	2	5
β-strand	175-184	10	5
α-helix	185-190	6
β-strand	194-199	6	6
β-strand	204-209	6	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
heme domain of flavocytochrome b2	J, L	protein	214	Mus musculus
Fragment Antigen Binding B2B4	H, K	protein	225	Mus musculus
Cytochrome b2, mitochondrial	A, B	protein	95	Saccharomyces cerevisiae	P00175 (AlphaFold model)

Sequence of entity 1 (J, L), FASTA

>3KS0_1 heme domain of flavocytochrome b2 (chains J, L)
QAVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLFTGLIGGTNKRAPGV
PARFSGSLIGDKAALTITGAQTEDEAIYFCALWDSNHLVFGGGTKLTVLGQPKSSPSVTL
FPPSSEELETNKATLVCTITDFYPGVVTVDWKVDGTPVTQGMETTQPSKQSNNKYMASSY
LTLTARAWERHSSYSCQVTHEGHTVEKSLSPADC

Sequence of entity 2 (H, K), FASTA

>3KS0_2 Fragment Antigen Binding B2B4 (chains H, K)
EVQLQESGPSLVKPSQTLSLTCSVTGDSITSGYWNWIRKFPGNKLEYMGYISYGGSTYYN
PSLESRISITRDTSKNQYYLQLNSVTTEDTATYFCARLFGSYYFDYWGQGTTLTVSSAKT
TPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYT
LSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDCGCKPCI

Sequence of entity 3 (A, B), FASTA

>3KS0_3 Cytochrome b2, mitochondrial (chains A, B)
MNKQKISPAEVAKHNKPDDCWVVINGYVYDLTRFLPNHPGGQDVIKFNAGKDVTAIFEPL
HAPNVIDKYIAPEKKLGPLQGSMPPELVCPPYAPG

Ligands and cofactors

ID	Name	Formula	Copies
HEM	Protoporphyrin IX containing FE	C34 H32 Fe N4 O4	2

Primary citation

Structural evidence for the functional importance of the heme domain mobility in flavocytochrome b2. Diep Le, K.H., Lederer, F., Golinelli-Pimpaneau, B. J Mol Biol (2010) 400:518-530. DOI 10.1016/j.jmb.2010.05.035 · PubMed

Other PDB entries of the same protein (UniProt P00175 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1KBI 2.3 Å, Crystallographic Study of the Recombinant Flavin-binding Domain of Baker's Yeast…
1FCB 2.4 Å, Molecular structure of flavocytochrome B2 at 2.4 Å resolution
1KBJ 2.5 Å, Crystallographic Study of the Recombinant Flavin-binding Domain of Baker's Yeast…
1LTD 2.6 Å, The 2.6 Å refined structure of the escherichia coli recombinant saccharomyces cerevisiae…
1SZF 2.7 Å, A198G:L230A mutant flavocytochrome b2 with pyruvate bound
1SZG 2.7 Å, A198G:L230A flavocytochrome b2 with sulfite bound
1QCW 2.75 Å, Flavocytochrome B2, ARG289LYS mutant
2OZ0 2.8 Å, Mechanistic and Structural Studies of H373Q Flavocytochrome b2: Effects of Mutating the…
1LCO 2.9 Å, X-ray structure of two complexes of the Y143F flavocytochrome B2 mutant crystallized in…
1LDC 2.9 Å, X-ray structure of two complexes of the Y143F flavocytochrome B2 mutant crystallized in…
1SZE 3.0 Å, L230A mutant flavocytochrome b2 with benzoylformate
9J9B 3.83 Å, Substrate-engaged TIM23 complex from yeast

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