5H8Y: Sulfite reductase [ferredoxin], chloroplastic

Crystal structure of the complex between maize sulfite reductase and ferredoxin in the form-2 crystal. Determined by X-ray diffraction at 2.2 Å resolution. Released 13 Apr 2016.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Zea mays
Chains: 6
Atoms: 19,620
Mol. weight: 287.01 kDa
Ligands: SRM, FES, MG, SF4
Released: 13 Apr 2016

Explore 5H8Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5H8Y contains 150 α-helices and 128 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: 37 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	66-73	8
α-helix	81-84	4
α-helix	94-100	7
α-helix	101-103	3
β-strand	105-109	5	1
β-strand	119-124	6	1
α-helix	128-130	3
β-strand	131-132	2	2
α-helix	134-147	14
β-strand	152-154	3	1
β-strand	160-165	6	1
α-helix	167-169	3
α-helix	170-179	10
β-strand	192	1	3
α-helix	194-195	2
β-strand	196	1	4
α-helix	205-220	16
α-helix	227-233	7
α-helix	241-244	4
α-helix	245-251	7
β-strand	277	1	3
β-strand	279-283	5	4
β-strand	286	1	5
α-helix	291-293	3
β-strand	296-302	7	4
β-strand	308-315	8	4
β-strand	318	1	6
β-strand	322	1	7
β-strand	325	1	7
β-strand	331	1	6
α-helix	332-333	2
β-strand	334-340	7	4
α-helix	341-343	3
α-helix	344-358	15
α-helix	364-366	3
α-helix	369-376	8
α-helix	378-389	12
α-helix	392-393	2
β-strand	394	1	4
α-helix	395-398	4
α-helix	400-402	3
β-strand	403	1	5
β-strand	409-412	4	2
β-strand	418-422	5	2
α-helix	423	1
α-helix	425-427	3
β-strand	428-429	2	1
α-helix	433-443	11
β-strand	448-450	3	2
β-strand	456-461	6	2
α-helix	463-465	3
α-helix	466-475	10
α-helix	481-483	3
α-helix	486-490	5
β-strand	492-493	2	8
α-helix	508-525	18
β-strand	535-538	4	8
α-helix	547-549	3
β-strand	552-558	7	8
β-strand	561-566	6	8
β-strand	577-584	8	8
α-helix	585-587	3
α-helix	588-602	15
α-helix	603-604	2
α-helix	609-616	8
α-helix	618-627	10

Chain B: 36 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	66-73	8
α-helix	81-84	4
α-helix	94-102	9
β-strand	105-109	5	9
β-strand	119-124	6	9
α-helix	128-130	3
β-strand	131-132	2	10
α-helix	134-146	13
β-strand	152-154	3	9
β-strand	160-165	6	9
α-helix	167-169	3
α-helix	170-179	10
β-strand	192	1	11
α-helix	194-195	2
β-strand	196	1	12
α-helix	205-220	16
α-helix	227-233	7
α-helix	241-244	4
α-helix	245-251	7
β-strand	277	1	11
β-strand	279-283	5	12
β-strand	286	1	13
α-helix	291-293	3
β-strand	296-302	7	12
β-strand	308-315	8	12
β-strand	318	1	14
β-strand	322	1	15
β-strand	325	1	15
β-strand	331	1	14
α-helix	332-333	2
β-strand	334-340	7	12
α-helix	341-343	3
α-helix	344-358	15
α-helix	364-366	3
α-helix	369-376	8
α-helix	378-389	12
α-helix	392-393	2
β-strand	394	1	12
α-helix	395-398	4
α-helix	400-402	3
β-strand	403	1	13
β-strand	409-412	4	10
β-strand	418-422	5	10
α-helix	423	1
α-helix	425-427	3
β-strand	428-429	2	9
α-helix	433-443	11
β-strand	448-450	3	10
β-strand	456-461	6	10
α-helix	463-465	3
α-helix	466-475	10
α-helix	481-483	3
α-helix	486-490	5
β-strand	492-493	2	16
α-helix	508-525	18
β-strand	535-538	4	16
α-helix	547-549	3
β-strand	552-558	7	16
β-strand	561-566	6	16
β-strand	577-584	8	16
α-helix	585-587	3
α-helix	588-601	14
α-helix	603-604	2
α-helix	609-616	8
α-helix	618-627	10

Chain C: 37 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	66-73	8
α-helix	81-85	5
α-helix	94-100	7
α-helix	101-103	3
β-strand	105-109	5	17
β-strand	119-124	6	17
α-helix	128-130	3
β-strand	131-132	2	18
α-helix	134-147	14
β-strand	152-154	3	17
β-strand	160-165	6	17
α-helix	167-169	3
α-helix	170-179	10
β-strand	192	1	19
α-helix	194-195	2
β-strand	196	1	20
α-helix	205-220	16
α-helix	227-232	6
α-helix	241-244	4
α-helix	245-252	8
β-strand	277	1	19
β-strand	279-283	5	20
β-strand	286	1	21
α-helix	291-293	3
β-strand	296-302	7	20
β-strand	308-315	8	20
β-strand	318	1	22
β-strand	322	1	23
β-strand	325	1	23
β-strand	331	1	22
α-helix	332-333	2
β-strand	334-340	7	20
α-helix	341-343	3
α-helix	344-358	15
α-helix	364-366	3
α-helix	369-376	8
α-helix	378-389	12
α-helix	392-393	2
β-strand	394	1	20
α-helix	395-398	4
α-helix	400-402	3
β-strand	403	1	21
β-strand	409-412	4	18
β-strand	418-422	5	18
α-helix	425-427	3
β-strand	428-429	2	17
α-helix	433-443	11
β-strand	448-450	3	18
β-strand	456-461	6	18
α-helix	463-465	3
α-helix	466-475	10
α-helix	478-480	3
α-helix	481-483	3
α-helix	486-490	5
β-strand	492-493	2	24
α-helix	508-525	18
β-strand	535-538	4	24
α-helix	547-549	3
β-strand	552-558	7	24
β-strand	561-566	6	24
β-strand	577-584	8	24
α-helix	585-587	3
α-helix	588-602	15
α-helix	603-604	2
α-helix	609-616	8
α-helix	618-627	10

Chain D: 33 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	66-73	8
α-helix	81-84	4
α-helix	94-100	7
α-helix	101-103	3
β-strand	105-109	5	25
β-strand	119-124	6	25
α-helix	128-130	3
β-strand	131-132	2	26
α-helix	134-147	14
β-strand	152-154	3	25
β-strand	160-165	6	25
α-helix	167-169	3
α-helix	170-179	10
β-strand	192	1	27
α-helix	194-195	2
β-strand	196	1	28
α-helix	205-220	16
α-helix	227-232	6
α-helix	245-252	8
β-strand	277	1	27
β-strand	279-283	5	28
β-strand	286	1	29
α-helix	291-293	3
β-strand	296-302	7	28
β-strand	308-315	8	28
β-strand	318	1	30
β-strand	322	1	31
β-strand	325	1	31
β-strand	331	1	30
α-helix	332-333	2
β-strand	334-340	7	28
α-helix	341-343	3
α-helix	344-357	14
α-helix	369-376	8
α-helix	378-389	12
α-helix	392-393	2
β-strand	394	1	28
α-helix	395-398	4
β-strand	403	1	29
β-strand	409-412	4	26
β-strand	418-422	5	26
α-helix	425-427	3
β-strand	428-429	2	25
α-helix	433-443	11
β-strand	448-450	3	26
β-strand	456-461	6	26
α-helix	463-465	3
α-helix	466-475	10
α-helix	481-483	3
α-helix	486-490	5
β-strand	492-493	2	32
α-helix	508-525	18
β-strand	535-538	4	32
α-helix	547-549	3
β-strand	552-558	7	32
β-strand	561-566	6	32
β-strand	577-584	8	32
α-helix	585-587	3
α-helix	588-602	15
α-helix	603-604	2
α-helix	609-616	8
α-helix	618-627	10

Chain E: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	33
β-strand	12-19	8	33
α-helix	24-30	7
β-strand	48-53	6	33
β-strand	56-57	2	34
α-helix	66-70	5
β-strand	73-75	3	33
α-helix	76-78	3
β-strand	80-81	2	34
β-strand	85-88	4	33
α-helix	92-94	3

Chain F: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	8	1	35
β-strand	13	1	35
β-strand	48-53	6	35
α-helix	69-71	3
β-strand	73-75	3	35
α-helix	76-78	3
β-strand	86-88	3	35
α-helix	92-95	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sulfite reductase [ferredoxin], chloroplastic	A, B, C, D	protein	583	Zea mays	O23813 (AlphaFold model)
Ferredoxin-1, chloroplastic	E, F	protein	98	Zea mays	P27787 (AlphaFold model)

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

>5H8Y_1 Sulfite reductase [ferredoxin], chloroplastic (chains A, B, C, D)
APAKKDASEVKRSKVEIIKEKSNFLRYPLNEELVSEAPNINESAVQLIKFHGSYQQTDRD
VRGQKNYSFMLRTKNPCGKVPNQLYLAMDTLADEFGIGTLRLTTRQTFQLHGVLKKNLKT
VLSTVIKNMGSTLGACGDLNRNVLAPAAPYVKKDILFAQQTAENIAALLTPQSGAYYDLW
VDGEKIMSAEEPPEVTKARNDNSHGTNFPDSPEPIYGTQYLPRKFKVAVTAAGDNSVDIL
TNDIGVVVVSDDAGEPIGFNIYVGGGMGRTHRVETTFPRLADPLGYVPKEDILYAIKAIV
VTQRENGRRDDRKYSRMKYMIDRWGIDRFRAEVEKYYGKKFESFRPLPEWQFNSYLGWQE
QGDGKLFYGVHVDNGRVGGQAKKTLREIIEKYNLDVSITPNQNLILCGIDQAWREPITTA
LAQAGLLEPKDVDPLNLTAMACPALPLCPLAQTEAERGILPILKRIRAVFNKVGIKDSES
VVVRITGCPNGCARPYMAELGFVGDGPKSYQIWLGGTPNQSTLAESFMDKVKLDDIEKVL
EPLFTYWNGTRQEGESFGSFTNRTGFDKLKEVVNKWAESPSAA

Sequence of entity 2 (E, F), FASTA

>5H8Y_2 Ferredoxin-1, chloroplastic (chains E, F)
ATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSD
QSYLDDGQIADGWVLTCHAYPTSDVVIETHKEEELTGA

Ligands and cofactors

ID	Name	Formula	Copies
SRM	Siroheme	C42 H44 Fe N4 O16	4
FES	FE2/S2 (inorganic) cluster	Fe2 S2	2
MG	Magnesium ion	Mg	4
SF4	Iron/sulfur cluster	Fe4 S4	4

Water and common crystallization additives (CL) are not listed.

Primary citation

Structural and mutational studies of an electron transfer complex of maize sulfite reductase and ferredoxin. Kim, J.Y., Nakayama, M., Toyota, H. et al. J Biochem (2016) 160:101-109. DOI 10.1093/jb/mvw016 · PubMed

Other PDB entries of the same protein (UniProt O23813 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5H92 2.08 Å, Crystal structure of the complex between maize Sulfite Reductase and ferredoxin in the…
5H8V 2.2 Å, Crystal structure of the complex between maize Sulfite Reductase and ferredoxin in the…

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