1RBO: Spinach rubisco

Spinach rubisco in complex with the inhibitor 2-carboxyarabinitol-1,5-diphosphate. Determined by X-ray diffraction at 2.3 Å resolution. Released 12 Mar 1997.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Spinacia oleracea
Chains: 8
Atoms: 19,900
Mol. weight: 270.92 kDa
Ligands: CAP
Released: 12 Mar 1997

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

Secondary structure: helices and β-sheets

1RBO contains 132 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 B, E, H and L: 28 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	21-24	4
β-strand	25	1	9
α-helix	29-32	4
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	113-121	9
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

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	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
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

>1RBO_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

>1RBO_2 RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE (chains C, F, I, S)
MQVWPILNLKKYETLSYLPPLTTDQLARQVDYLLNNKWVPCLEFETDHGFVYREHHNSPG
YYDGRYWTMWKLPMFGCTDPAQVLNELEECKKEYPNAFIRIIGFDSNREVQCISFIAYKP
AGY

Ligands and cofactors

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

Primary citation

A common structural basis for the inhibition of ribulose 1,5-bisphosphate carboxylase by 4-carboxyarabinitol 1,5-bisphosphate and xylulose 1,5-bisphosphate. Taylor, T.C., Fothergill, M.D., Andersson, I. J Biol Chem (1996) 271:32894-32899. DOI 10.1074/jbc.271.51.32894 · 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…
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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