9CQ5: Ribulose bisphosphate carboxylase large chain

Mn-bound RuBisCO from spinach with CABP inhibitor. Determined by X-ray diffraction at 2.5 Å resolution. Released 5 Feb 2025.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Spinacia oleracea
Chains: 16
Atoms: 38,560
Mol. weight: 543.2 kDa
Ligands: CAP, MN
Released: 5 Feb 2025

Explore 9CQ5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9CQ5 contains 257 α-helices and 224 β-strands across 16 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: 25 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	21-24	4
β-strand	25	1	1
β-strand	36-44	9	1
α-helix	45	1
α-helix	50-59	10
α-helix	70-74	5
α-helix	77-80	4
β-strand	83-89	7	1
β-strand	97-103	7	1
α-helix	105-107	3
α-helix	113-121	9
α-helix	124-126	3
β-strand	127	1	2
β-strand	130-139	10	1
α-helix	142-145	4
α-helix	154-162	9
β-strand	169-171	3	3
β-strand	173	1	4
α-helix	182-194	13
β-strand	199-201	3	4
α-helix	214-232	19
β-strand	237-239	3	4
β-strand	240-241	2	3
α-helix	247-260	14
β-strand	264-268	5	3
α-helix	269-272	4
α-helix	274-287	14
β-strand	290-294	5	3
α-helix	298-302	5
β-strand	308-309	2	1
α-helix	311-321	11
β-strand	325-327	3	3
β-strand	335	1	5
α-helix	339-350	12
β-strand	353-354	2	6
β-strand	357	1	7
α-helix	358-360	3
β-strand	362	1	7
β-strand	366-367	2	6
α-helix	371-373	3
β-strand	375-379	5	3
α-helix	387-394	8
β-strand	399-401	3	3
α-helix	404-407	4
α-helix	413-433	21
α-helix	437-449	13
α-helix	453-462	10

Chain B: 26 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	21-24	4
β-strand	25	1	8
β-strand	36-44	9	8
α-helix	45	1
α-helix	50-60	11
α-helix	70-74	5
α-helix	77-80	4
β-strand	83-89	7	8
α-helix	90	1
β-strand	97-103	7	8
α-helix	105-107	3
α-helix	113-121	9
α-helix	124-126	3
β-strand	127	1	5
β-strand	130-139	10	8
α-helix	142-145	4
α-helix	154-162	9
β-strand	169-173	5	9
α-helix	182-194	13
β-strand	199-201	3	9
α-helix	214-232	19
β-strand	237-241	5	9
α-helix	247-260	14
β-strand	264-268	5	9
α-helix	269-272	4
α-helix	274-287	14
β-strand	290-294	5	9
α-helix	298-302	5
β-strand	308-309	2	8
α-helix	311-321	11
β-strand	325-327	3	9
β-strand	335	1	2
α-helix	339-350	12
β-strand	353-354	2	10
β-strand	357	1	11
β-strand	362	1	11
β-strand	366-367	2	10
α-helix	371-373	3
β-strand	375-379	5	9
α-helix	384-386	3
α-helix	387-394	8
β-strand	399-401	3	9
α-helix	403-407	5
α-helix	413-433	21
α-helix	437-451	15
α-helix	453-461	9

Chain C: 26 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	20-24	5
β-strand	25	1	12
β-strand	36-44	9	12
α-helix	45	1
α-helix	50-61	12
α-helix	70-73	4
α-helix	77-80	4
β-strand	83-89	7	12
α-helix	90	1
β-strand	97-103	7	12
α-helix	105-107	3
α-helix	113-120	8
α-helix	124-126	3
β-strand	127	1	13
β-strand	130-139	10	12
α-helix	142-145	4
α-helix	154-162	9
β-strand	169-173	5	14
α-helix	182-194	13
β-strand	199-201	3	14
β-strand	209	1	15
β-strand	212	1	15
α-helix	214-232	19
β-strand	237-241	5	14
α-helix	247-260	14
β-strand	264-268	5	14
α-helix	269-272	4
α-helix	274-287	14
β-strand	290-294	5	14
α-helix	298-302	5
β-strand	308-309	2	12
α-helix	311-321	11
β-strand	325-327	3	14
β-strand	335	1	16
α-helix	339-350	12
β-strand	353-354	2	17
β-strand	357	1	18
β-strand	362	1	18
β-strand	366-367	2	17
α-helix	371-374	4
β-strand	375-379	5	14
α-helix	384-386	3
α-helix	387-394	8
β-strand	399-401	3	14
α-helix	404-407	4
α-helix	413-433	21
α-helix	437-451	15
α-helix	453-461	9

Chain D: 29 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	11-13	3
α-helix	21-24	4
β-strand	25	1	19
α-helix	29-32	4
β-strand	36-44	9	19
α-helix	45	1
α-helix	50-60	11
α-helix	70-74	5
α-helix	77-80	4
β-strand	83-89	7	19
α-helix	90	1
β-strand	97-103	7	19
α-helix	105-107	3
α-helix	113-120	8
α-helix	124-126	3
β-strand	127	1	16
β-strand	130-139	10	19
α-helix	142-145	4
α-helix	155-162	8
β-strand	169-173	5	20
α-helix	182-194	13
β-strand	199-201	3	20
α-helix	214-232	19
β-strand	237-241	5	20
α-helix	247-260	14
β-strand	264-268	5	20
α-helix	269-272	4
α-helix	274-287	14
β-strand	290-294	5	20
α-helix	298-302	5
β-strand	308-309	2	19
α-helix	311-321	11
β-strand	325-327	3	20
β-strand	335	1	13
α-helix	339-350	12
β-strand	353-354	2	21
β-strand	357	1	22
α-helix	358-360	3
β-strand	362	1	22
β-strand	366-367	2	21
α-helix	371-373	3
β-strand	375-379	5	20
α-helix	384-386	3
α-helix	387-394	8
β-strand	399-401	3	20
α-helix	404-407	4
α-helix	413-432	20
α-helix	437-451	15
α-helix	453-461	9

Chain E: 28 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	11-13	3
α-helix	20-24	5
β-strand	25	1	23
α-helix	29-32	4
β-strand	36-44	9	23
α-helix	45	1
α-helix	50-61	12
α-helix	70-74	5
α-helix	77-80	4
β-strand	83-89	7	23
β-strand	97-103	7	23
α-helix	105-107	3
α-helix	113-121	9
α-helix	124-126	3
β-strand	127	1	24
β-strand	130-139	10	23
α-helix	142-145	4
α-helix	154-162	9
β-strand	169-171	3	25
β-strand	173	1	26
α-helix	182-194	13
β-strand	199-201	3	26
β-strand	209	1	27
β-strand	212	1	27
α-helix	214-232	19
β-strand	237-239	3	26
β-strand	240-241	2	25
α-helix	247-260	14
β-strand	264-268	5	25
α-helix	269-272	4
α-helix	274-287	14
β-strand	290-294	5	25
α-helix	298-302	5
β-strand	308-309	2	23
α-helix	311-321	11
β-strand	325-327	3	25
β-strand	335	1	28
α-helix	339-350	12
β-strand	353-354	2	29
β-strand	357	1	30
α-helix	358-360	3
β-strand	362	1	30
β-strand	366-367	2	29
α-helix	371-374	4
β-strand	375-379	5	25
α-helix	384-386	3
α-helix	387-394	8
β-strand	399-401	3	25
α-helix	404-407	4
α-helix	413-433	21
α-helix	437-451	15
α-helix	453-461	9

Chain F: 28 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	21-24	4
β-strand	25	1	31
α-helix	29-32	4
β-strand	36-44	9	31
α-helix	45	1
α-helix	50-60	11
α-helix	70-74	5
α-helix	77-80	4
β-strand	83-89	7	31
α-helix	90	1
β-strand	97-103	7	31
α-helix	105-107	3
α-helix	113-121	9
α-helix	124-126	3
β-strand	127	1	28
β-strand	130-139	10	31
α-helix	142-145	4
α-helix	155-162	8
β-strand	169-173	5	32
α-helix	182-194	13
β-strand	199-201	3	32
α-helix	214-232	19
β-strand	237-241	5	32
α-helix	247-260	14
β-strand	264-268	5	32
α-helix	269-272	4
α-helix	274-287	14
β-strand	290-294	5	32
α-helix	298-302	5
β-strand	308-309	2	31
α-helix	311-321	11
β-strand	325-327	3	32
β-strand	335	1	24
α-helix	339-350	12
β-strand	353-354	2	33
β-strand	357	1	34
α-helix	358-360	3
β-strand	362	1	34
β-strand	366-367	2	33
α-helix	371-373	3
β-strand	375-379	5	32
α-helix	384-386	3
α-helix	387-394	8
β-strand	399-401	3	32
α-helix	404-407	4
α-helix	413-433	21
α-helix	437-449	13
α-helix	453-461	9

Chain G: 28 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	16	1	35
α-helix	20-24	5
β-strand	25	1	36
α-helix	29-32	4
β-strand	36-44	9	36
α-helix	45	1
α-helix	50-60	11
β-strand	68	1	35
α-helix	70-73	4
α-helix	77-80	4
β-strand	83-89	7	36
α-helix	90	1
β-strand	97-103	7	36
α-helix	105-107	3
α-helix	113-120	8
α-helix	124-126	3
β-strand	127	1	37
β-strand	130-139	10	36
α-helix	142-145	4
α-helix	155-162	8
β-strand	169-171	3	38
β-strand	173	1	39
α-helix	182-194	13
β-strand	199-201	3	39
β-strand	209	1	40
β-strand	212	1	40
α-helix	214-232	19
β-strand	237-239	3	39
β-strand	240-241	2	38
α-helix	247-260	14
β-strand	264-268	5	38
α-helix	269-272	4
α-helix	274-286	13
β-strand	290-294	5	38
α-helix	298-302	5
β-strand	308-309	2	36
α-helix	311-321	11
β-strand	325-327	3	38
β-strand	335	1	41
α-helix	339-350	12
β-strand	353-354	2	42
β-strand	357	1	43
α-helix	358-360	3
β-strand	362	1	43
β-strand	366-367	2	42
α-helix	371-373	3
β-strand	375-379	5	38
α-helix	384-386	3
α-helix	387-394	8
β-strand	399-401	3	38
α-helix	404-407	4
α-helix	413-432	20
α-helix	437-451	15
α-helix	453-462	10

Chain H: 29 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	11-13	3
α-helix	21-24	4
β-strand	25	1	44
α-helix	29-32	4
β-strand	36-44	9	44
α-helix	45	1
α-helix	50-61	12
α-helix	70-74	5
α-helix	77-80	4
β-strand	83-89	7	44
α-helix	90	1
β-strand	97-103	7	44
α-helix	105-107	3
α-helix	113-120	8
α-helix	124-126	3
β-strand	127	1	41
β-strand	130-139	10	44
α-helix	142-146	5
α-helix	155-162	8
β-strand	169-173	5	45
α-helix	182-195	14
β-strand	199-201	3	45
β-strand	209	1	46
β-strand	212	1	46
α-helix	214-232	19
β-strand	237-241	5	45
α-helix	247-260	14
β-strand	264-268	5	45
α-helix	269-272	4
α-helix	274-286	13
β-strand	290-294	5	45
α-helix	298-302	5
β-strand	308-309	2	44
α-helix	311-321	11
β-strand	325-327	3	45
β-strand	335	1	37
α-helix	339-350	12
β-strand	353-354	2	47
β-strand	357	1	48
α-helix	358-360	3
β-strand	362	1	48
β-strand	366-367	2	47
α-helix	371-374	4
β-strand	375-379	5	45
α-helix	384-386	3
α-helix	387-394	8
β-strand	399-401	3	45
α-helix	403-407	5
α-helix	413-433	21
α-helix	437-451	15
α-helix	453-462	10

5 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ribulose bisphosphate carboxylase large chain	A, B, C, D, E, F, G, H	protein	475	Spinacia oleracea	P00875 (AlphaFold model)
Ribulose bisphosphate carboxylase small subunit, chloroplastic 2	I, J, K, L, M, N, O, P	protein	123	Spinacia oleracea	Q43832 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H), FASTA

>9CQ5_1 Ribulose bisphosphate carboxylase large chain (chains A, B, C, D, E, F, G, H)
MSPQTETKASVEFKAGVKDYKLTYYTPEYETLDTDILAAFRVSPQPGVPPEEAGAAVAAE
SSTGTWTTVWTDGLTNLDRYKGRCYHIEPVAGEENQYICYVAYPLDLFEEGSVTNMFTSI
VGNVFGFKALRALRLEDLRIPVAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGL
SAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYL
NATAGTCEDMMKRAVFARELGVPIVMHDYLTGGFTANTTLSHYCRDNGLLLHIHRAMHAV
IDRQKNHGMHFRVLAKALRLSGGDHIHSGTVVGKLEGERDITLGFVDLLRDDYTEKDRSR
GIYFTQSWVSTPGVLPVASGGIHVWHMPALTEIFGDDSVLQFGGGTLGHPWGNAPGAVAN
RVALEACVQARNEGRDLAREGNTIIREATKWSPELAAACEVWKEIKFEFPAMDTV

Sequence of entity 2 (I, J, K, L, M, N, O, P), FASTA

>9CQ5_2 Ribulose bisphosphate carboxylase small subunit, chloroplastic 2 (chains I, J, K, L, M, N, O, P)
MQVWPILNLKKYETLSYLPPLTTDQLARQVDYLLNNKWVPCLEFETDHGFVYREHHNSPG
YYDGRYWTMWKLPMFGCTDPAQVLNELEECKKEYPNAFIRIIGFDSNREVQCISFIAYKP
AGY

Ligands and cofactors

ID	Name	Formula	Copies
CAP	2-carboxyarabinitol-1,5-diphosphate	C6 H14 O13 P2	8
MN	Manganese (II) ion	Mn	8

Primary citation

The structure of Mn(II)-bound Rubisco from Spinacia oleracea. Voland, R.W., Coleman, R.E., Lancaster, K.M. J Inorg Biochem (2024) 260:112682-112682. DOI 10.1016/j.jinorgbio.2024.112682 · PubMed

Other PDB entries of the same protein (UniProt P00875 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8RUC 1.6 Å, Activated spinach rubisco complexed with 2-carboxyarabinitol bisphosphate
1IR1 1.8 Å, Crystal Structure of Spinach Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco)…
1AA1 2.2 Å, Activated spinach rubisco in complex with the product 3-phosphoglycerate
1AUS 2.2 Å, Activated unliganded spinach rubisco
1RXO 2.2 Å, Activated spinach rubisco in complex with its substrate ribulose-1,5-bisphosphate and…
1RBO 2.3 Å, Spinach rubisco in complex with the inhibitor 2-carboxyarabinitol-1,5-diphosphate
1RCO 2.3 Å, Spinach rubisco in complex with the inhibitor D-xylulose-2,2-diol-1,5-bisphosphate
1UPM 2.3 Å, Activated spinach rubisco complexed with 2-carboxyarabinitol 2 bisphosphat and CA2+.
1UPP 2.3 Å, Spinach rubisco in complex with 2-carboxyarabinitol 2 bisphosphate and calcium.
8QJ0 2.3 Å, Room-temperature Serial Synchrotron Crystallography structure of Spinacia oleracea RuBisCO
1RCX 2.4 Å, Non-activated spinach rubisco in complex with its substrate ribulose-1,5-bisphosphate

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