1UPM: Activated spinach rubisco

Activated spinach rubisco complexed with 2-carboxyarabinitol 2 bisphosphat and CA2+. 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: 16
Atoms: 40,436
Mol. weight: 543.08 kDa
Ligands: CAP, CA
Released: 14 Oct 2003

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

Secondary structure: helices and β-sheets

1UPM contains 277 α-helices and 240 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 B: 28 helices, 24 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	50-60	11
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	127	1	2
β-strand	130-139	10	1
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	1
α-helix	311-321	11
β-strand	325-327	3	3
β-strand	335	1	6
α-helix	339-350	12
β-strand	353-354	2	7
β-strand	357	1	8
α-helix	358-360	3
β-strand	362	1	8
β-strand	366-367	2	7
α-helix	372-374	3
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	413-432	20
α-helix	437-449	13
α-helix	453-462	10

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

Element	Residues	Length	Sheet
α-helix	2-5	4
α-helix	19-22	4
α-helix	23-35	13
α-helix	38	1
β-strand	39-45	7	9
β-strand	52	1	10
β-strand	63	1	10
β-strand	68-70	3	9
α-helix	80-93	14
β-strand	98-105	8	9
β-strand	110-118	9	9

Chains E and H: 30 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	11-13	3
α-helix	21-24	4
β-strand	25	1	11
α-helix	29-32	4
β-strand	36-44	9	11
α-helix	45	1
α-helix	50-60	11
α-helix	70-74	5
α-helix	77-80	4
β-strand	83-89	7	11
α-helix	90	1
β-strand	97-103	7	11
α-helix	105-107	3
α-helix	109	1
α-helix	113-121	9
α-helix	124-126	3
β-strand	127	1	12
β-strand	130-139	10	11
α-helix	142-145	4
α-helix	155-162	8
β-strand	169-171	3	13
β-strand	173	1	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	237-239	3	14
β-strand	240-241	2	13
α-helix	247-260	14
β-strand	264-268	5	13
α-helix	269-272	4
α-helix	274-287	14
β-strand	290-294	5	13
α-helix	298-302	5
β-strand	308-309	2	11
α-helix	311-321	11
β-strand	325-327	3	13
β-strand	335	1	16
α-helix	339-350	12
β-strand	353-354	2	17
β-strand	357	1	18
α-helix	358-360	3
β-strand	362	1	18
β-strand	366-367	2	17
α-helix	372-374	3
β-strand	375-379	5	13
α-helix	384-386	3
α-helix	387-394	8
β-strand	399-401	3	13
α-helix	404-407	4
α-helix	413-432	20
α-helix	437-449	13
α-helix	453-462	10

Chain K: 31 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	11-13	3
α-helix	21-24	4
β-strand	25	1	29
α-helix	29-32	4
α-helix	35	1
β-strand	36-44	9	29
α-helix	45	1
α-helix	50-60	11
α-helix	70-74	5
α-helix	77-80	4
β-strand	83-89	7	29
α-helix	90	1
β-strand	97-103	7	29
α-helix	105-107	3
α-helix	109	1
α-helix	113-120	8
α-helix	124-126	3
β-strand	127	1	30
β-strand	130-139	10	29
α-helix	142-145	4
α-helix	155-162	8
β-strand	169-171	3	31
β-strand	173	1	32
α-helix	182-193	12
β-strand	199-201	3	32
β-strand	209	1	33
β-strand	212	1	33
α-helix	214-232	19
β-strand	237-239	3	32
β-strand	240-241	2	31
α-helix	247-260	14
β-strand	264-268	5	31
α-helix	269-272	4
α-helix	274-287	14
β-strand	290-294	5	31
α-helix	298-302	5
β-strand	308-309	2	29
α-helix	311-321	11
β-strand	325-327	3	31
β-strand	335	1	34
α-helix	339-350	12
β-strand	353-354	2	35
β-strand	357	1	36
α-helix	358-360	3
β-strand	362	1	36
β-strand	366-367	2	35
α-helix	372-374	3
β-strand	375-379	5	31
α-helix	384-386	3
α-helix	387-394	8
β-strand	399-401	3	31
α-helix	404-407	4
α-helix	413-432	20
α-helix	437-449	13
α-helix	453-462	10

Chain L: 30 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	11-13	3
α-helix	21-24	4
β-strand	25	1	37
α-helix	29-32	4
β-strand	36-44	9	37
α-helix	45	1
α-helix	50-60	11
α-helix	70-74	5
α-helix	77-80	4
β-strand	83-89	7	37
α-helix	90	1
β-strand	97-103	7	37
α-helix	105-107	3
α-helix	109	1
α-helix	113-120	8
α-helix	124-126	3
β-strand	127	1	6
β-strand	130-139	10	37
α-helix	142-145	4
α-helix	155-162	8
β-strand	169-171	3	38
β-strand	173	1	39
α-helix	182-193	12
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	274-287	14
β-strand	290-294	5	38
α-helix	298-302	5
β-strand	308-309	2	37
α-helix	311-321	11
β-strand	325-327	3	38
β-strand	335	1	2
α-helix	339-350	12
β-strand	353-354	2	41
β-strand	357	1	42
α-helix	358-360	3
β-strand	362	1	42
β-strand	366-367	2	41
α-helix	372-374	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	437-449	13
α-helix	453-462	10

Chain M: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
α-helix	19-22	4
α-helix	23-35	13
α-helix	38	1
β-strand	39-45	7	43
β-strand	52	1	44
β-strand	63	1	44
β-strand	68-69	2	43
α-helix	80-93	14
β-strand	98-105	8	43
β-strand	110-118	9	43

Chain O: 30 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	11-13	3
α-helix	21-24	4
β-strand	25	1	45
α-helix	29-32	4
β-strand	36-44	9	45
α-helix	45	1
α-helix	50-60	11
α-helix	70-74	5
α-helix	77-80	4
β-strand	83-89	7	45
α-helix	90	1
β-strand	97-103	7	45
α-helix	105-107	3
α-helix	109	1
α-helix	113-120	8
α-helix	124-126	3
β-strand	127	1	34
β-strand	130-139	10	45
α-helix	142-145	4
α-helix	155-162	8
β-strand	169-171	3	46
β-strand	173	1	47
α-helix	182-194	13
β-strand	199-201	3	47
β-strand	209	1	48
β-strand	212	1	48
α-helix	214-232	19
β-strand	237-239	3	47
β-strand	240-241	2	46
α-helix	247-260	14
β-strand	264-268	5	46
α-helix	269-272	4
α-helix	274-287	14
β-strand	290-294	5	46
α-helix	298-302	5
β-strand	308-309	2	45
α-helix	311-321	11
β-strand	325-327	3	46
β-strand	335	1	30
α-helix	339-350	12
β-strand	353-354	2	49
β-strand	357	1	50
α-helix	358-360	3
β-strand	362	1	50
β-strand	366-367	2	49
α-helix	372-374	3
β-strand	375-379	5	46
α-helix	384-386	3
α-helix	387-394	8
β-strand	399-401	3	46
α-helix	404-407	4
α-helix	413-432	20
α-helix	437-448	12
α-helix	453-462	10

Chain P: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	19-22	4
α-helix	23-35	13
α-helix	38	1
β-strand	39-45	7	51
β-strand	52	1	52
β-strand	63	1	52
β-strand	68-70	3	51
α-helix	80-93	14
β-strand	98-105	8	51
β-strand	110-118	9	51

2 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	B, E, H, K, L, O, R, V	protein	475	SPINACIA OLERACEA	P00875 (AlphaFold model)
Ribulose bisphosphate carboxylase small chain	C, F, I, M, P, S, T, W	protein	123	SPINACIA OLERACEA	Q43832 (AlphaFold model)

Sequence of entity 1 (B, E, H, K, L, O, R, V), FASTA

>1UPM_1 RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN (chains B, E, H, K, L, O, R, V)
MSPQTETKASVEFKAGVKDYKLTYYTPEYETLDTDILAAFRVSPQPGVPPEEAGAAVAAE
SSTGTWTTVWTDGLTNLDRYKGRCYHIEPVAGEENQYICYVAYPLDLFEEGSVTNMFTSI
VGNVFGFKALRALRLEDLRIPVAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGL
SAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYL
NATAGTCEDMMKRAVFARELGVPIVMHDYLTGGFTANTTLSHYCRDNGLLLHIHRAMHAV
IDRQKNHGMHFRVLAKALRLSGGDHIHSGTVVGKLEGERDITLGFVDLLRDDYTEKDRSR
GIYFTQSWVSTPGVLPVASGGIHVWHMPALTEIFGDDSVLQFGGGTLGHPWGNAPGAVAN
RVALEACVQARNEGRDLAREGNTIIREATKWSPELAAACEVWKEIKFEFPAMDTV

Sequence of entity 2 (C, F, I, M, P, S, T, W), FASTA

>1UPM_2 RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN (chains C, F, I, M, P, S, T, W)
MQVWPILNLKKYETLSYLPPLTTDQLARQVDYLLNNKWVPCLEFETDHGFVYREHHNSPG
YYDGRYWTMWKLPMFGCTDPAQVLNELEECKKEYPNAFIRIIGFDSNREVQCISFIAYKP
AGY

Ligands and cofactors

ID	Name	Formula	Copies
CAP	2-carboxyarabinitol-1,5-diphosphate	C6 H14 O13 P2	8
CA	Calcium ion	Ca	8

Primary citation

Calcium Supports Loop Closure But not Catalysis in Rubisco. Karkehabadi, 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
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

Browse structure collections

About this viewer

MolViewer shows 1UPM 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.