1IR1: Large subunit of Rubisco

Crystal Structure of Spinach Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Complexed with CO2, Mg2+ and 2-Carboxyarabinitol-1,5-Bisphosphate. Determined by X-ray diffraction at 1.8 Å resolution. Released 13 Mar 2002.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Spinacia oleracea
Chains: 8
Atoms: 21,056
Mol. weight: 271.67 kDa
Ligands: CAP, MG
Released: 13 Mar 2002

Explore 1IR1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1IR1 contains 130 α-helices and 112 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.

Chains A and C: 28 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	21-24	4
β-strand	25	1	1
α-helix	29-32	4
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
α-helix	90	1
β-strand	97-103	7	1
α-helix	105-107	3
α-helix	113-120	8
α-helix	124-126	3
β-strand	130-139	10	1
α-helix	142-145	4
α-helix	155-162	8
β-strand	169-171	3	2
β-strand	173	1	3
α-helix	182-194	13
β-strand	199-201	3	3
β-strand	209	1	4
β-strand	212	1	4
α-helix	214-232	19
β-strand	237-239	3	3
β-strand	240-241	2	2
α-helix	247-260	14
β-strand	264-268	5	2
α-helix	269-272	4
α-helix	274-287	14
β-strand	290-294	5	2
α-helix	298-302	5
β-strand	308-309	2	1
α-helix	311-321	11
β-strand	325-327	3	2
α-helix	339-350	12
β-strand	353-354	2	5
β-strand	357	1	6
α-helix	358-360	3
β-strand	362	1	6
β-strand	366-367	2	5
α-helix	371-373	3
β-strand	375-379	5	2
α-helix	384-386	3
α-helix	387-394	8
β-strand	399-401	3	2
α-helix	404-407	4
α-helix	413-432	20
α-helix	437-449	13
α-helix	453-462	10

Chain B: 27 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	21-24	4
β-strand	25	1	9
β-strand	36-44	9	9
α-helix	45	1
α-helix	50-60	11
α-helix	70-74	5
α-helix	77-80	4
β-strand	83-89	7	9
α-helix	90	1
β-strand	97-103	7	9
α-helix	105-107	3
α-helix	113-120	8
α-helix	124-126	3
β-strand	130-139	10	9
α-helix	142-145	4
α-helix	155-162	8
β-strand	169-171	3	10
β-strand	173	1	11
α-helix	182-194	13
β-strand	199-201	3	11
β-strand	209	1	12
β-strand	212	1	12
α-helix	214-232	19
β-strand	237-239	3	11
β-strand	240-241	2	10
α-helix	247-260	14
β-strand	264-268	5	10
α-helix	269-272	4
α-helix	274-287	14
β-strand	290-294	5	10
α-helix	298-302	5
β-strand	308-309	2	9
α-helix	311-321	11
β-strand	325-327	3	10
α-helix	339-350	12
β-strand	353-354	2	13
β-strand	357	1	14
α-helix	358-360	3
β-strand	362	1	14
β-strand	366-367	2	13
α-helix	371-373	3
β-strand	375-379	5	10
α-helix	384-386	3
α-helix	387-394	8
β-strand	399-401	3	10
α-helix	404-407	4
α-helix	413-432	20
α-helix	437-449	13
α-helix	453-462	10

Chain D: 27 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	21-24	4
β-strand	25	1	25
β-strand	36-44	9	25
α-helix	45	1
α-helix	50-59	10
α-helix	70-74	5
α-helix	77-80	4
β-strand	83-89	7	25
α-helix	90	1
β-strand	97-103	7	25
α-helix	105-107	3
α-helix	113-120	8
α-helix	124-126	3
β-strand	130-139	10	25
α-helix	142-145	4
α-helix	155-162	8
β-strand	169-171	3	26
β-strand	173	1	27
α-helix	182-193	12
β-strand	199-201	3	27
β-strand	209	1	28
β-strand	212	1	28
α-helix	214-232	19
β-strand	237-239	3	27
β-strand	240-241	2	26
α-helix	247-260	14
β-strand	264-268	5	26
α-helix	269-272	4
α-helix	274-287	14
β-strand	290-294	5	26
α-helix	298-302	5
β-strand	308-309	2	25
α-helix	311-321	11
β-strand	325-327	3	26
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	371-373	3
β-strand	375-379	5	26
α-helix	384-386	3
α-helix	387-394	8
β-strand	399-401	3	26
α-helix	404-407	4
α-helix	413-432	20
α-helix	437-449	13
α-helix	453-462	10

Chain S: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	20-22	3
α-helix	23-35	13
α-helix	38	1
β-strand	39-45	7	7
β-strand	52	1	8
β-strand	63	1	8
β-strand	68-70	3	7
α-helix	80-93	14
β-strand	98-105	8	7
β-strand	110-118	9	7

Chains T, U and V: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
α-helix	20-21	2
α-helix	23-35	13
α-helix	38	1
β-strand	39-45	7	15
β-strand	52	1	16
β-strand	63	1	16
β-strand	68-70	3	15
α-helix	80-93	14
β-strand	98-105	8	15
β-strand	110-118	9	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Large subunit of Rubisco	A, B, C, D	protein	475	Spinacia oleracea	P00875 (AlphaFold model)
Small subunit of Rubisco	S, T, U, V	protein	123	Spinacia oleracea	Q43832 (AlphaFold model)

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

>1IR1_1 Large subunit of Rubisco (chains A, B, C, D)
MSPQTETKASVEFKAGVKDYKLTYYTPEYETLDTDILAAFRVSPQPGVPPEEAGAAVAAE
SSTGTWTTVWTDGLTNLDRYKGRCYHIEPVAGEENQYICYVAYPLDLFEEGSVTNMFTSI
VGNVFGFKALRALRLEDLRIPVAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGL
SAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYL
NATAGTCEDMMKRAVFARELGVPIVMHDYLTGGFTANTTLSHYCRDNGLLLHIHRAMHAV
IDRQKNHGMHFRVLAKALRLSGGDHIHSGTVVGKLEGERDITLGFVDLLRDDYTEKDRSR
GIYFTQSWVSTPGVLPVASGGIHVWHMPALTEIFGDDSVLQFGGGTLGHPWGNAPGAVAN
RVALEACVQARNEGRDLAREGNTIIREATKWSPELAAACEVWKEIKFEFPAMDTV

Sequence of entity 2 (S, T, U, V), FASTA

>1IR1_2 Small subunit of Rubisco (chains S, T, U, V)
MKVWPTQNMKRYETLSYLPPLTTDQLARQVDYLLNNKWVPCLEFETDHGFVYREHHNSPG
YYDGRYWTMWKLPMFGCTDPAQVLNELEECKKEYPNAFIRIIGFDSNRQVQCVSFIAYKP
AGY

Ligands and cofactors

ID	Name	Formula	Copies
CAP	2-carboxyarabinitol-1,5-diphosphate	C6 H14 O13 P2	4
MG	Magnesium ion	Mg	4

Primary citation

Crystal structure of activated ribulose-1,5-bisphosphate carboxylase/oxygenase from green alga Chlamydomonas reinhardtii complexed with 2-carboxyarabinitol-1,5-bisphosphate. Mizohata, E., Matsumura, H., Okano, Y. et al. J Mol Biol (2002) 316:679-691. DOI 10.1006/jmbi.2001.5381 · 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
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
9CQ5 2.5 Å, Mn-bound RuBisCO from spinach with CABP inhibitor

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