7JN4: Rubisco in the apo state

Rubisco in the apo state. Determined by electron microscopy at 2.68 Å resolution. Released 18 Nov 2020.

Method: Electron microscopy
Resolution: 2.68 Å
Organism: Chlamydomonas reinhardtii
Chains: 16
Atoms: 35,712
Mol. weight: 586.21 kDa
Released: 18 Nov 2020

Explore 7JN4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7JN4 contains 209 α-helices and 216 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.

Chains A, E and I: 22 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	25	1	1
β-strand	36-44	9	1
α-helix	50-59	10
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	182-195	14
β-strand	199-201	3	3
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	274-286	13
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	338-350	13
β-strand	353-354	2	4
β-strand	357	1	5
α-helix	358-360	3
β-strand	362	1	5
β-strand	366-367	2	4
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	414-432	19
α-helix	441-451	11
α-helix	453-459	7

Chains B, D, F, H, J, L, N and P: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	6
α-helix	19-22	4
α-helix	23-35	13
β-strand	38-45	8	6
β-strand	53	1	7
α-helix	55-59	5
β-strand	69	1	7
β-strand	74-76	3	6
α-helix	86-99	14
β-strand	104-111	8	6
β-strand	117-124	8	6

Chains C, G, K and M: 22 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	25	1	8
β-strand	36-44	9	8
α-helix	50-59	10
β-strand	83-89	7	8
α-helix	90	1
β-strand	97-103	7	8
α-helix	105-107	3
α-helix	113-120	8
α-helix	124-126	3
β-strand	130-139	10	8
α-helix	142-145	4
α-helix	155-162	8
β-strand	169-171	3	9
β-strand	173	1	10
α-helix	182-195	14
β-strand	199-201	3	10
α-helix	214-232	19
β-strand	237-239	3	10
β-strand	240-241	2	9
α-helix	247-260	14
β-strand	264-268	5	9
α-helix	269-272	4
α-helix	274-286	13
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	414-432	19
α-helix	441-451	11
α-helix	453-460	8

Chain O: 23 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	25	1	50
α-helix	29-32	4
β-strand	36-44	9	50
α-helix	50-59	10
β-strand	83-89	7	50
α-helix	90	1
β-strand	97-103	7	50
α-helix	105-107	3
α-helix	113-120	8
α-helix	124-126	3
β-strand	130-139	10	50
α-helix	142-145	4
α-helix	155-162	8
β-strand	169-171	3	51
β-strand	173	1	52
α-helix	182-195	14
β-strand	199-201	3	52
α-helix	214-232	19
β-strand	237-239	3	52
β-strand	240-241	2	51
α-helix	247-260	14
β-strand	264-268	5	51
α-helix	269-272	4
α-helix	274-286	13
β-strand	290-294	5	51
α-helix	298-302	5
β-strand	308-309	2	50
α-helix	311-321	11
β-strand	325-327	3	51
α-helix	338-350	13
β-strand	353-354	2	53
β-strand	357	1	54
α-helix	358-360	3
β-strand	362	1	54
β-strand	366-367	2	53
α-helix	371-373	3
β-strand	375-379	5	51
α-helix	384-386	3
α-helix	387-394	8
β-strand	399-401	3	51
α-helix	414-432	19
α-helix	441-451	11
α-helix	453-459	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ribulose bisphosphate carboxylase large chain	A, C, E, G, I, K, M, O	protein	475	Chlamydomonas reinhardtii	P00877 (AlphaFold model)
Ribulose bisphosphate carboxylase small chain 2, chloroplastic	B, D, F, H, J, L, N, P	protein	185	Chlamydomonas reinhardtii	P08475 (AlphaFold model)

Sequence of entity 1 (A, C, E, G, I, K, M, O), FASTA

>7JN4_1 Ribulose bisphosphate carboxylase large chain (chains A, C, E, G, I, K, M, O)
MVPQTETKAGAGFKAGVKDYRLTYYTPDYVVRDTDILAAFRMTPQPGVPPEECGAAVAAE
SSTGTWTTVWTDGLTSLDRYKGRCYDIEPVPGEDNQYIAYVAYPIDLFEEGSVTNMFTSI
VGNVFGFKALRALRLEDLRIPPAYVKTFVGPPHGIQVERDKLNKYGRGLLGCTIKPKLGL
SAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEAIYKAQAETGEVKGHYL
NATAGTCEEMMKRAVCAKELGVPIIMHDYLTGGFTANTSLAIYCRDNGLLLHIHRAMHAV
IDRQRNHGIHFRVLAKALRMSGGDHLHSGTVVGKLEGEREVTLGFVDLMRDDYVEKDRSR
GIYFTQDWCSMPGVMPVASGGIHVWHMPALVEIFGDDACLQFGGGTLGHPWGNAPGAAAN
RVALEACTQARNEGRDLAREGGDVIRSACKWSPELAAACEVWKEIKFEFDTIDKL

Sequence of entity 2 (B, D, F, H, J, L, N, P), FASTA

>7JN4_2 Ribulose bisphosphate carboxylase small chain 2, chloroplastic (chains B, D, F, H, J, L, N, P)
MAAVIAKSSVSAAVARPARSSVRPMAALKPAVKAAPVAAPAQANQMMVWTPVNNKMFETF
SYLPPLSDEQIAAQVDYIVANGWIPCLEFAESDKAYVSNESAIRFGSVSCLYYDNRYWTM
WKLPMFGCRDPMQVLREIVACTKAFPDAYVRLVAFDNQKQVQIMGFLVQRPKSARDWQPA
NKRSV

Primary citation

The structural basis of Rubisco phase separation in the pyrenoid. He, S., Chou, H.T., Matthies, D. et al. Nat Plants (2020) 6:1480-1490. DOI 10.1038/s41477-020-00811-y · PubMed

Other PDB entries of the same protein (UniProt P00877 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1GK8 1.4 Å, Rubisco from Chlamydomonas reinhardtii
2V6A 1.5 Å, Crystal structure of Chlamydomonas reinhardtii Rubisco with large- subunit mutations…
2V63 1.8 Å, Crystal structure of Rubisco from Chlamydomonas reinhardtii with a large-subunit V331A…
1IR2 1.84 Å, Crystal Structure of Activated Ribulose-1,5-bisphosphate Carboxylase/oxygenase (Rubisco)…
5BS2 1.97 Å, Crystal structure of RbcX-IIa from Chlamydomonas reinhardtii in complex with RbcL…
2V67 2.0 Å, Crystal structure of Chlamydomonas reinhardtii Rubisco with a large- subunit supressor…
1UW9 2.05 Å, L290F-A222T chlamydomonas Rubisco mutant
7JSX 2.06 Å, EPYC1(106-135) peptide-bound Rubisco
7JFO 2.13 Å, EPYC1(49-72)-bound Rubisco
1UZH 2.2 Å, A chimeric chlamydomonas, synechococcus rubisco enzyme
1UWA 2.3 Å, L290F mutant rubisco from chlamydomonas
2V68 2.3 Å, Crystal structure of Chlamydomonas reinhardtii Rubisco with large- subunit mutations…

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