3W5U: Ferredoxin

Cross-linked complex between Ferredoxin and Ferredoxin-NADP+ reductase. Determined by X-ray diffraction at 2.7 Å resolution. Released 19 Jun 2013.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Zea mays
Chains: 8
Atoms: 12,485
Mol. weight: 187.32 kDa
Ligands: FES, FAD
Released: 19 Jun 2013

Explore 3W5U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3W5U contains 62 α-helices and 128 β-strands across 8 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: 14 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	22	1	1
β-strand	32	1	2
β-strand	38-41	4	3
β-strand	42-47	6	4
β-strand	57-63	7	4
β-strand	75-79	5	3
β-strand	83	1	5
α-helix	88	1
β-strand	89	1	5
α-helix	90-91	2
β-strand	93-96	4	3
β-strand	97	1	4
β-strand	110-116	7	4
β-strand	119-121	3	6
β-strand	127-129	3	6
α-helix	131-138	8
α-helix	139-140	2
β-strand	144-151	8	3
α-helix	156-157	2
β-strand	158	1	1
β-strand	164-170	7	7
α-helix	171-174	4
α-helix	175-185	11
β-strand	189	1	8
β-strand	192	1	8
β-strand	197-204	8	7
α-helix	207-209	3
α-helix	213-222	10
β-strand	227-233	7	7
β-strand	238	1	9
β-strand	244	1	9
α-helix	247-251	5
α-helix	252-254	3
α-helix	255-261	7
β-strand	267-273	7	7
α-helix	277-290	14
α-helix	296-304	9
β-strand	309-313	5	7

Chains B, D, F and H: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	10
β-strand	12-19	8	10
α-helix	24-30	7
β-strand	48-53	6	10
β-strand	56-57	2	11
α-helix	66-70	5
β-strand	73-75	3	10
β-strand	80-81	2	11
β-strand	85-88	4	10

Chain C: 13 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	22	1	12
β-strand	32	1	13
β-strand	33	1	14
β-strand	36	1	14
β-strand	38-41	4	15
β-strand	42-47	6	16
β-strand	57-63	7	16
β-strand	75-79	5	15
β-strand	83	1	17
α-helix	88	1
β-strand	89	1	17
α-helix	90-92	3
β-strand	93-96	4	15
β-strand	97	1	16
β-strand	110-116	7	16
β-strand	119-121	3	18
β-strand	127-129	3	18
α-helix	131-138	8
α-helix	139-140	2
β-strand	144-151	8	15
α-helix	156-157	2
β-strand	158	1	12
β-strand	164-170	7	19
α-helix	171-174	4
α-helix	175-185	11
β-strand	189	1	20
β-strand	192	1	20
β-strand	197-204	8	19
α-helix	207-209	3
α-helix	213-222	10
β-strand	227-233	7	19
β-strand	238	1	21
β-strand	244	1	21
α-helix	247-252	6
α-helix	255-261	7
β-strand	267-273	7	19
α-helix	277-290	14
α-helix	296-304	9
β-strand	309-313	5	19

Chain E: 13 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	22	1	24
β-strand	32	1	25
β-strand	33	1	26
β-strand	36	1	26
β-strand	38-41	4	27
β-strand	42-47	6	28
β-strand	57-63	7	28
β-strand	75-79	5	27
β-strand	83	1	29
α-helix	88	1
β-strand	89	1	29
α-helix	90-92	3
β-strand	93-96	4	27
β-strand	97	1	28
β-strand	110-116	7	28
β-strand	119-121	3	30
β-strand	127-129	3	30
α-helix	131-138	8
α-helix	139-140	2
β-strand	144-151	8	27
α-helix	156-157	2
β-strand	158	1	24
β-strand	164-170	7	31
α-helix	171-174	4
α-helix	175-185	11
β-strand	189	1	32
β-strand	192	1	32
β-strand	197-204	8	31
α-helix	207-209	3
α-helix	213-222	10
β-strand	227-233	7	31
β-strand	238	1	33
β-strand	244	1	33
α-helix	247-252	6
α-helix	255-261	7
β-strand	267-273	7	31
α-helix	277-290	14
α-helix	296-305	10
β-strand	309-313	5	31

Chain G: 14 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	22	1	36
β-strand	32	1	37
β-strand	38-41	4	38
β-strand	42-47	6	39
β-strand	57-63	7	39
β-strand	75-79	5	38
β-strand	83	1	40
α-helix	88	1
β-strand	89	1	40
α-helix	90-91	2
β-strand	93-96	4	38
β-strand	97	1	39
β-strand	110-116	7	39
β-strand	119-121	3	41
β-strand	127-129	3	41
α-helix	131-138	8
α-helix	139-140	2
β-strand	144-151	8	38
α-helix	156-157	2
β-strand	158	1	36
β-strand	164-170	7	42
α-helix	171-174	4
α-helix	175-185	11
β-strand	189	1	43
β-strand	192	1	43
β-strand	197-204	8	42
α-helix	207-209	3
α-helix	213-222	10
β-strand	227-233	7	42
β-strand	238	1	44
β-strand	244	1	44
α-helix	247-251	5
α-helix	252-254	3
α-helix	255-261	7
β-strand	267-273	7	42
α-helix	277-291	15
α-helix	296-304	9
β-strand	309-313	5	42

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ferredoxin	A, C, E, G	protein	314	Zea mays	Q9SLP6 (AlphaFold model)
Ferredoxin-1, chloroplastic	B, D, F, H	protein	98	Zea mays	P27787 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>3W5U_1 Ferredoxin (chains A, C, E, G)
IRAQASAVEAPATAKAKKCSKKQEEGVVTNLYKPKEPYVGRCLLNTKITGDDAPGETWHM
VFSTEGKIPYREGQSIGVIADGVDKNGKPHKVRLYSIASSAIGDFGDSKTVSLCVKRLIY
TNDAGEIVKGVCSNFLCDLQPGDNVQITGPVGKEMLMPKDPNATIIMLATGTGIAPFRSF
LWKMFFEKHDDYKFNGLGWLFLGVPTSSSLLYKEEFGKMKERAPENFRVDYAVSREQTNA
AGERMYIQTRMAEYKEELWELLKKDNTYVYMCGLKGMEKGIDDIMVSLAEKDGIDWFDYK
KQLKRGDQWNVEVY

Sequence of entity 2 (B, D, F, H), FASTA

>3W5U_2 Ferredoxin-1, chloroplastic (chains B, D, F, H)
ATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQCD
QSYLDDGQIADGWVLTCHAYPTSDVVIETHKEEELTGA

Ligands and cofactors

ID	Name	Formula	Copies
FES	FE2/S2 (inorganic) cluster	Fe2 S2	4
FAD	Flavin-adenine dinucleotide	C27 H33 N9 O15 P2	4

Primary citation

Concentration-dependent oligomerization of cross-linked complexes between ferredoxin and ferredoxin-NADP(+) reductase. Kimata-Ariga, Y., Kubota-Kawai, H., Lee, Y.-H. et al. Biochem Biophys Res Commun (2013) 434:867-872. DOI 10.1016/j.bbrc.2013.04.033 · PubMed

Other PDB entries of the same protein (UniProt Q9SLP6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1GAW 2.2 Å, Crystal structure analysis of the ferredoxin-NADP+ reductase from maize leaf
1GAQ 2.59 Å, Crystal structure of the complex between ferredoxin and ferredoxin-NADP+ reductase
3W5V 3.81 Å, Cross-linked complex between Ferredoxin and Ferredoxin-NADP+ reductase

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