7JFO: EPYC1(49-72)-bound Rubisco

EPYC1(49-72)-bound Rubisco. Determined by electron microscopy at 2.13 Å resolution. Released 18 Nov 2020.

Method: Electron microscopy
Resolution: 2.13 Å
Organism: Chlamydomonas reinhardtii
Chains: 24
Atoms: 38,958
Mol. weight: 608.83 kDa
Released: 18 Nov 2020

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

Secondary structure: helices and β-sheets

7JFO contains 248 α-helices and 208 β-strands across 24 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 and E: 24 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	25	1	1
α-helix	29-32	4
β-strand	36-44	9	1
α-helix	45	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	113-121	9
α-helix	124-126	3
β-strand	130-139	10	1
α-helix	142-145	4
α-helix	154-162	9
β-strand	169-173	5	2
α-helix	182-194	13
β-strand	199-201	3	2
β-strand	209	1	3
β-strand	212	1	3
α-helix	214-232	19
β-strand	237-241	5	2
α-helix	247-260	14
β-strand	264-268	5	2
α-helix	269-272	4
α-helix	274-287	14
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	336-350	15
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	387-394	8
β-strand	399-402	4	2
α-helix	405-408	4
α-helix	413-432	20
α-helix	437-451	15
α-helix	453-460	8

Chains B, D, J and P: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	19-22	4
α-helix	23-35	13
β-strand	39-46	8	6
α-helix	47-49	3
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	103-111	9	6
β-strand	116-124	9	6

Chains C, I, K, M and O: 24 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	25	1	8
α-helix	29-32	4
β-strand	36-44	9	8
α-helix	45	1
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	113-121	9
α-helix	124-126	3
β-strand	130-139	10	8
α-helix	142-145	4
α-helix	154-162	9
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	325-330	6	9
α-helix	336-350	15
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	387-394	8
β-strand	399-402	4	9
α-helix	405-408	4
α-helix	413-432	20
α-helix	437-451	15
α-helix	453-460	8

Chains F, H, L and N: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	19-22	4
α-helix	23-35	13
β-strand	39-46	8	20
α-helix	47-50	4
β-strand	53	1	21
α-helix	55-59	5
β-strand	69	1	21
β-strand	74-76	3	20
α-helix	86-99	14
β-strand	103-111	9	20
β-strand	116-124	9	20

Chain G: 24 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	25	1	22
α-helix	29-32	4
β-strand	36-44	9	22
α-helix	45	1
α-helix	50-59	10
β-strand	83-89	7	22
α-helix	90	1
β-strand	97-103	7	22
α-helix	105-107	3
α-helix	113-121	9
α-helix	124-126	3
β-strand	130-139	10	22
α-helix	142-145	4
α-helix	154-162	9
β-strand	169-173	5	23
α-helix	182-194	13
β-strand	199-201	3	23
β-strand	209	1	24
β-strand	212	1	24
α-helix	214-232	19
β-strand	237-241	5	23
α-helix	247-260	14
β-strand	264-268	5	23
α-helix	269-272	4
α-helix	274-287	14
β-strand	290-294	5	23
α-helix	298-302	5
β-strand	308-309	2	22
α-helix	311-321	11
β-strand	325-327	3	23
α-helix	336-350	15
β-strand	353-354	2	25
β-strand	357	1	26
α-helix	358-360	3
β-strand	362	1	26
β-strand	366-367	2	25
α-helix	371-373	3
β-strand	375-380	6	23
α-helix	387-394	8
β-strand	399-402	4	23
α-helix	405-408	4
α-helix	413-432	20
α-helix	437-451	15
α-helix	453-460	8

Chains q, r, s, t, u, v, w and x: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	58-60	3
α-helix	63-71	9

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)
LCI5	q, r, s, t, u, v, w, x	protein	24	Chlamydomonas reinhardtii	Q94ET8 (AlphaFold model)

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

>7JFO_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

>7JFO_2 Ribulose bisphosphate carboxylase small chain 2, chloroplastic (chains B, D, F, H, J, L, N, P)
MAAVIAKSSVSAAVARPARSSVRPMAALKPAVKAAPVAAPAQANQMMVWTPVNNKMFETF
SYLPPLSDEQIAAQVDYIVANGWIPCLEFAESDKAYVSNESAIRFGSVSCLYYDNRYWTM
WKLPMFGCRDPMQVLREIVACTKAFPDAYVRLVAFDNQKQVQIMGFLVQRPKSARDWQPA
NKRSV

Sequence of entity 3 (q, r, s, t, u, v, w, x), FASTA

>7JFO_3 LCI5 (chains q, r, s, t, u, v, w, x)
TNRVSPTRSVLPANWRQELESLRN

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
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…
2VDH 2.3 Å, Crystal structure of Chlamydomonas reinhardtii Rubisco with a large- subunit C172S…

Browse structure collections

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