1UPP: Spinach rubisco

Spinach rubisco in complex with 2-carboxyarabinitol 2 bisphosphate and calcium. Determined by X-ray diffraction at 2.3 Å resolution. Released 14 Oct 2003.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: SPINACIA OLERACEA
Chains: 8
Atoms: 19,504
Mol. weight: 271.54 kDa
Ligands: CAP, CA
Released: 14 Oct 2003

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

Secondary structure: helices and β-sheets

1UPP contains 122 α-helices and 120 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: 26 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	16	1	1
α-helix	21-24	4
β-strand	25	1	2
α-helix	29-32	4
β-strand	36-44	9	2
α-helix	50-60	11
β-strand	68	1	1
α-helix	70-74	5
α-helix	77-80	4
β-strand	83-89	7	2
α-helix	90	1
β-strand	97-103	7	2
α-helix	105-107	3
α-helix	113-120	8
α-helix	124-126	3
β-strand	130-139	10	2
α-helix	142-145	4
α-helix	155-162	8
β-strand	169-171	3	3
β-strand	173	1	4
α-helix	182-194	13
β-strand	199-201	3	4
β-strand	209	1	5
β-strand	212	1	5
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	2
α-helix	311-321	11
β-strand	325-327	3	3
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
β-strand	375-379	5	3
α-helix	384-386	3
α-helix	387-394	8
β-strand	399-401	3	3
α-helix	404-407	4
α-helix	413-433	21
α-helix	437-451	15
α-helix	453-461	9

Chain C: 25 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	16	1	8
α-helix	21-24	4
β-strand	25	1	9
β-strand	36-44	9	9
α-helix	50-60	11
β-strand	68	1	8
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
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	413-433	21
α-helix	437-449	13
α-helix	453-462	10

Chain E: 28 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	16	1	15
α-helix	21-24	4
β-strand	25	1	16
α-helix	29-32	4
β-strand	36-44	9	16
α-helix	50-60	11
β-strand	68	1	15
α-helix	70-74	5
α-helix	77-80	4
β-strand	83-89	7	16
α-helix	90	1
β-strand	97-103	7	16
α-helix	105-107	3
α-helix	109	1
α-helix	113-120	8
α-helix	124-126	3
β-strand	130-139	10	16
α-helix	142-145	4
α-helix	155-162	8
β-strand	169-171	3	17
β-strand	173	1	18
α-helix	182-194	13
β-strand	199-201	3	18
β-strand	209	1	19
β-strand	212	1	19
α-helix	214-232	19
β-strand	237-239	3	18
β-strand	240-241	2	17
α-helix	247-260	14
β-strand	264-268	5	17
α-helix	269-272	4
α-helix	274-285	12
β-strand	290-294	5	17
α-helix	298-302	5
β-strand	308-309	2	16
α-helix	311-321	11
β-strand	325-327	3	17
α-helix	339-350	12
β-strand	353-354	2	20
β-strand	357	1	21
α-helix	358-360	3
β-strand	362	1	21
β-strand	366-367	2	20
α-helix	371-373	3
β-strand	375-378	4	17
α-helix	384-386	3
α-helix	387-394	8
β-strand	399-401	3	17
α-helix	404-407	4
α-helix	413-433	21
α-helix	437-451	15
α-helix	453-462	10

Chain G: 28 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	16	1	22
α-helix	21-24	4
β-strand	25	1	23
α-helix	29-32	4
β-strand	36-44	9	23
α-helix	45	1
α-helix	50-60	11
β-strand	68	1	22
α-helix	70-74	5
α-helix	77-79	3
β-strand	83-89	7	23
α-helix	90	1
β-strand	97-103	7	23
α-helix	105-107	3
α-helix	113-121	9
α-helix	124-126	3
β-strand	130-139	10	23
α-helix	142-145	4
α-helix	155-162	8
β-strand	169-171	3	24
β-strand	173	1	25
α-helix	182-193	12
β-strand	199-201	3	25
β-strand	209	1	26
β-strand	212	1	26
α-helix	214-232	19
β-strand	237-239	3	25
β-strand	240-241	2	24
α-helix	247-260	14
β-strand	264-267	4	24
α-helix	269-272	4
α-helix	274-287	14
β-strand	290-293	4	24
α-helix	294	1
α-helix	298-302	5
β-strand	308-309	2	23
α-helix	311-321	11
β-strand	325-327	3	24
α-helix	339-350	12
β-strand	353-354	2	27
β-strand	357	1	28
α-helix	358-360	3
β-strand	362	1	28
β-strand	366-367	2	27
β-strand	375-379	5	24
α-helix	384-386	3
α-helix	387-394	8
β-strand	399-401	3	24
α-helix	404-407	4
α-helix	413-433	21
α-helix	437-449	13
α-helix	453-462	10

Chains I and L: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
α-helix	23-35	13
α-helix	38	1
β-strand	39-45	7	29
β-strand	52	1	30
β-strand	63	1	30
β-strand	68-70	3	29
α-helix	80-93	14
β-strand	98-105	8	29
β-strand	110-118	9	29

Chain J: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
α-helix	23-35	13
α-helix	38	1
β-strand	39-45	7	31
β-strand	52	1	32
β-strand	63	1	32
β-strand	68-69	2	31
α-helix	80-93	14
β-strand	98-105	8	31
β-strand	110-118	9	31

Chain K: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
α-helix	23-35	13
β-strand	39-45	7	33
β-strand	52	1	34
β-strand	63	1	34
β-strand	68-69	2	33
α-helix	80-93	14
β-strand	98-105	8	33
β-strand	110-118	9	33

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ribulose bisphosphate carboxylase large chain	A, C, E, G	protein	475	SPINACIA OLERACEA	P00875 (AlphaFold model)
Ribulose bisphosphate carboxylase small chain	I, J, K, L	protein	123	SPINACIA OLERACEA	Q43832 (AlphaFold model)

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

>1UPP_1 RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN (chains A, C, E, G)
MSPQTETKASVEFKAGVKDYKLTYYTPEYETLDTDILAAFRVSPQPGVPPEEAGAAVAAE
SSTGTWTTVWTDGLTNLDRYKGRCYHIEPVAGEENQYICYVAYPLDLFEEGSVTNMFTSI
VGNVFGFKALRALRLEDLRIPVAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGL
SAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYL
NATAGTCEDMMKRAVFARELGVPIVMHDYLTGGFTANTTLSHYCRDNGLLLHIHRAMHAV
IDRQKNHGMHFRVLAKALRLSGGDHIHSGTVVGKLEGERDITLGFVDLLRDDYTEKDRSR
GIYFTQSWVSTPGVLPVASGGIHVWHMPALTEIFGDDSVLQFGGGTLGHPWGNAPGAVAN
RVALEACVQARNEGRDLAREGNTIIREATKWSPELAAACEVWKEIKFEFPAMDTV

Sequence of entity 2 (I, J, K, L), FASTA

>1UPP_2 RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN (chains I, J, K, L)
MQVWPILNLKKYETLSYLPPLTTDQLARQVDYLLNNKWVPCLEFETDHGFVYREHHNSPG
YYDGRYWTMWKLPMFGCTDPAQVLNELEECKKEYPNAFIRIIGFDSNREVQCISFIAYKP
AGY

Ligands and cofactors

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

Primary citation

Calcium Supports Loop Closure But not Catalysis in Rubisco. Karehabadi, S., Taylor, T.C., Andersson, I. J Mol Biol (2003) 334:65. DOI 10.1016/J.JMB.2003.09.025 · 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+.
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

Browse structure collections

About this viewer

MolViewer shows 1UPP directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.