1RXO: Activated spinach rubisco

Activated spinach rubisco in complex with its substrate ribulose-1,5-bisphosphate and calcium. Determined by X-ray diffraction at 2.2 Å resolution. Released 16 Jun 1997.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Spinacia oleracea
Chains: 8
Atoms: 19,440
Mol. weight: 271.07 kDa
Ligands: CA, RUB
Released: 16 Jun 1997

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

Secondary structure: helices and β-sheets

1RXO contains 124 α-helices and 104 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 B, E, H and L: 26 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	25	1	8
β-strand	36-44	9	8
α-helix	45	1
α-helix	50-59	10
α-helix	70-74	5
α-helix	77-79	3
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	130-139	10	8
α-helix	142-145	4
α-helix	155-162	8
β-strand	169-173	5	9
α-helix	182-194	13
β-strand	199-201	3	9
β-strand	209	1	10
β-strand	212	1	10
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
α-helix	338-350	13
β-strand	353-354	2	11
β-strand	357	1	12
α-helix	358-360	3
β-strand	362	1	12
β-strand	366-367	2	11
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	404-407	4
α-helix	413-432	20
α-helix	437-449	13
α-helix	453-461	9

Chains C, F, I and S: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
α-helix	20-22	3
α-helix	23-35	13
α-helix	38	1
β-strand	39-45	7	13
β-strand	52	1	14
β-strand	63	1	14
β-strand	68-70	3	13
α-helix	80-93	14
β-strand	98-105	8	13
β-strand	110-118	9	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ribulose bisphosphate carboxylase/oxygenase	B, E, H, L	protein	475	Spinacia oleracea	P00875 (AlphaFold model)
Ribulose bisphosphate carboxylase/oxygenase	C, F, I, S	protein	123	Spinacia oleracea	P00870 (AlphaFold model)

Sequence of entity 1 (B, E, H, L), FASTA

>1RXO_1 RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE (chains B, E, H, L)
MSPQTETKASVGFKAGVKDYKLTYYTPEYETLDTDILAAFRVSPQPGVPPEEAGAAVAAE
SSTGTWTTVWTDGLTNLDRYKGRCYHIEPVAGEENQYICYVAYPLDLFEEGSVTNMFTSI
VGNVFGFKALRALRLEDLRIPVAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGL
SAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYL
NATAGTCEDMMKRAVFARELGVPIVMHDYLTGGFTANTTLSHYCRDNGLLLHIHRAMHAV
IDRQKNHGMHFRVLAKALRLSGGDHIHSGTVVGKLEGERDITLGFVDLLRDDYTEKDRSR
GIYFTQSWVSTPGVLPVASGGIHVWHMPALTEIFGDDSVLQFGGGTLGHPWGNAPGAVAN
RVALEACVQARNEGRDLAREGNTIIREATKWSPELAAACEVWKEIKFEFPAMDTV

Sequence of entity 2 (C, F, I, S), FASTA

>1RXO_2 RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE (chains C, F, I, S)
MQVWPILNLKKYETLSYLPPLTTDQLARQVDYLLNNKWVPCLEFETDHGFVYREHHNSPG
YYDGRYWTMWKLPMFGCTDPAQVLNELEECKKEYPNAFIRIIGFDSNREVQCISFIAYKP
AGY

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	4
RUB	Ribulose-1,5-diphosphate	C5 H12 O11 P2	4

Primary citation

The structure of the complex between rubisco and its natural substrate ribulose 1,5-bisphosphate. Taylor, T.C., Andersson, I. J Mol Biol (1997) 265:432-444. DOI 10.1006/jmbi.1996.0738 · 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
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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