2VDI: Ribulose bisphosphate carboxylase large chain

Crystal structure of Chlamydomonas reinhardtii Rubisco with a large- subunit C192S mutation. Determined by X-ray diffraction at 2.65 Å resolution. Released 4 Nov 2008.

Method: X-ray diffraction
Resolution: 2.65 Å
Organism: CHLAMYDOMONAS REINHARDTII
Chains: 16
Atoms: 40,074
Mol. weight: 557.43 kDa
Ligands: CAP, MG
Released: 4 Nov 2008

Explore 2VDI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2VDI contains 263 α-helices and 260 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 A: 27 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	21-24	4
β-strand	25	1	1
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	154-162	9
β-strand	169-171	3	3
β-strand	173	1	4
α-helix	182-193	12
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	371-374	4
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

Chain B: 27 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	21-24	4
β-strand	25	1	9
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	113-120	8
α-helix	124-126	3
β-strand	127	1	6
β-strand	130-139	10	9
α-helix	142-145	4
α-helix	154-162	9
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
β-strand	335	1	2
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	371-374	4
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

Chain C: 27 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	16	1	15
α-helix	21-24	4
β-strand	25	1	16
β-strand	36-44	9	16
α-helix	45	1
α-helix	50-59	10
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	113-120	8
α-helix	124-126	3
β-strand	127	1	17
β-strand	130-139	10	16
α-helix	142-145	4
α-helix	154-162	9
β-strand	169-171	3	18
β-strand	173	1	19
α-helix	182-193	12
β-strand	199-201	3	19
β-strand	209	1	20
β-strand	212	1	20
α-helix	214-232	19
β-strand	237-239	3	19
β-strand	240-241	2	18
α-helix	247-260	14
β-strand	264-268	5	18
α-helix	269-272	4
α-helix	274-287	14
β-strand	290-294	5	18
α-helix	298-302	5
β-strand	308-309	2	16
α-helix	311-321	11
β-strand	325-327	3	18
β-strand	335	1	21
α-helix	339-350	12
β-strand	353-354	2	22
β-strand	357	1	23
α-helix	358-360	3
β-strand	362	1	23
β-strand	366-367	2	22
α-helix	371-374	4
β-strand	375-379	5	18
α-helix	384-386	3
α-helix	387-394	8
β-strand	399-401	3	18
α-helix	404-407	4
α-helix	413-433	21
α-helix	441-451	11
α-helix	453-462	10

Chain D: 27 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	16	1	24
α-helix	21-24	4
β-strand	25	1	25
β-strand	36-44	9	25
α-helix	45	1
α-helix	50-60	11
β-strand	68	1	24
α-helix	70-74	5
α-helix	77-80	4
β-strand	83-89	7	25
α-helix	90	1
β-strand	97-103	7	25
α-helix	105-107	3
α-helix	113-121	9
α-helix	124-126	3
β-strand	127	1	21
β-strand	130-139	10	25
α-helix	142-145	4
α-helix	155-162	8
β-strand	169-171	3	26
β-strand	173	1	27
α-helix	182-193	12
β-strand	199-201	3	27
β-strand	209	1	28
β-strand	212	1	28
α-helix	214-232	19
β-strand	237-239	3	27
β-strand	240-241	2	26
α-helix	247-260	14
β-strand	264-268	5	26
α-helix	269-272	4
α-helix	274-287	14
β-strand	290-294	5	26
α-helix	298-302	5
β-strand	308-309	2	25
α-helix	311-321	11
β-strand	325-327	3	26
β-strand	335	1	17
α-helix	339-350	12
β-strand	353-354	2	29
β-strand	357	1	30
α-helix	358-360	3
β-strand	362	1	30
β-strand	366-367	2	29
α-helix	371-374	4
β-strand	375-379	5	26
α-helix	384-386	3
α-helix	387-394	8
β-strand	399-401	3	26
α-helix	404-407	4
α-helix	413-432	20
α-helix	437-449	13
α-helix	453-462	10

Chain E: 27 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	21-24	4
β-strand	25	1	31
β-strand	36-44	9	31
α-helix	45	1
α-helix	50-60	11
α-helix	70-74	5
α-helix	77-80	4
β-strand	83-89	7	31
α-helix	90	1
β-strand	97-103	7	31
α-helix	105-107	3
α-helix	113-121	9
α-helix	124-126	3
β-strand	127	1	32
β-strand	130-139	10	31
α-helix	142-145	4
α-helix	154-162	9
β-strand	169-171	3	33
β-strand	173	1	34
α-helix	182-193	12
β-strand	199-201	3	34
β-strand	209	1	35
β-strand	212	1	35
α-helix	214-232	19
β-strand	237-239	3	34
β-strand	240-241	2	33
α-helix	247-260	14
β-strand	264-268	5	33
α-helix	269-272	4
α-helix	274-287	14
β-strand	290-294	5	33
α-helix	298-302	5
β-strand	308-309	2	31
α-helix	311-321	11
β-strand	325-327	3	33
β-strand	335	1	36
α-helix	339-350	12
β-strand	353-354	2	37
β-strand	357	1	38
α-helix	358-360	3
β-strand	362	1	38
β-strand	366-367	2	37
α-helix	371-374	4
β-strand	375-379	5	33
α-helix	384-386	3
α-helix	387-394	8
β-strand	399-401	3	33
α-helix	404-407	4
α-helix	413-432	20
α-helix	437-449	13
α-helix	453-462	10

Chain F: 27 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	21-24	4
β-strand	25	1	39
β-strand	36-44	9	39
α-helix	45	1
α-helix	50-60	11
α-helix	70-74	5
α-helix	77-80	4
β-strand	83-89	7	39
α-helix	90	1
β-strand	97-103	7	39
α-helix	105-107	3
α-helix	113-120	8
α-helix	124-126	3
β-strand	127	1	36
β-strand	130-139	10	39
α-helix	142-145	4
α-helix	154-162	9
β-strand	169-171	3	40
β-strand	173	1	41
α-helix	182-193	12
β-strand	199-201	3	41
β-strand	209	1	42
β-strand	212	1	42
α-helix	214-232	19
β-strand	237-239	3	41
β-strand	240-241	2	40
α-helix	247-260	14
β-strand	264-268	5	40
α-helix	269-272	4
α-helix	274-287	14
β-strand	290-294	5	40
α-helix	298-302	5
β-strand	308-309	2	39
α-helix	311-321	11
β-strand	325-327	3	40
β-strand	335	1	32
α-helix	339-350	12
β-strand	353-354	2	43
β-strand	357	1	44
α-helix	358-360	3
β-strand	362	1	44
β-strand	366-367	2	43
α-helix	371-374	4
β-strand	375-379	5	40
α-helix	384-386	3
α-helix	387-394	8
β-strand	399-401	3	40
α-helix	404-407	4
α-helix	413-432	20
α-helix	437-449	13
α-helix	453-461	9

Chain G: 27 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	21-24	4
β-strand	25	1	45
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	113-120	8
α-helix	124-126	3
β-strand	127	1	46
β-strand	130-139	10	45
α-helix	142-145	4
α-helix	154-162	9
β-strand	169-171	3	47
β-strand	173	1	48
α-helix	182-193	12
β-strand	199-201	3	48
β-strand	209	1	49
β-strand	212	1	49
α-helix	214-232	19
β-strand	237-239	3	48
β-strand	240-241	2	47
α-helix	247-259	13
β-strand	264-268	5	47
α-helix	269-272	4
α-helix	274-287	14
β-strand	290-294	5	47
α-helix	298-302	5
β-strand	308-309	2	45
α-helix	311-321	11
β-strand	325-327	3	47
β-strand	335	1	50
α-helix	339-350	12
β-strand	353-354	2	51
β-strand	357	1	52
α-helix	358-360	3
β-strand	362	1	52
β-strand	366-367	2	51
α-helix	371-374	4
β-strand	375-379	5	47
α-helix	384-386	3
α-helix	387-394	8
β-strand	399-401	3	47
α-helix	404-407	4
α-helix	413-432	20
α-helix	437-449	13
α-helix	453-462	10

Chain H: 27 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	21-24	4
β-strand	25	1	53
α-helix	29-32	4
β-strand	36-44	9	53
α-helix	45	1
α-helix	50-60	11
α-helix	70-74	5
α-helix	77-80	4
β-strand	83-89	7	53
β-strand	97-103	7	53
α-helix	105-107	3
α-helix	113-121	9
α-helix	124-126	3
β-strand	127	1	50
β-strand	130-139	10	53
α-helix	142-145	4
α-helix	155-162	8
β-strand	169-171	3	54
β-strand	173	1	55
α-helix	182-193	12
β-strand	199-201	3	55
β-strand	209	1	56
β-strand	212	1	56
α-helix	214-232	19
β-strand	237-239	3	55
β-strand	240-241	2	54
α-helix	247-260	14
β-strand	264-268	5	54
α-helix	269-272	4
α-helix	274-287	14
β-strand	290-294	5	54
α-helix	298-302	5
β-strand	308-309	2	53
α-helix	311-321	11
β-strand	325-327	3	54
β-strand	335	1	46
α-helix	339-350	12
β-strand	353-354	2	57
β-strand	357	1	58
α-helix	358-360	3
β-strand	362	1	58
β-strand	366-367	2	57
α-helix	371-374	4
β-strand	375-379	5	54
α-helix	384-386	3
α-helix	387-394	8
β-strand	399-401	3	54
α-helix	404-407	4
α-helix	413-432	20
α-helix	437-449	13
α-helix	453-462	10

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	A, B, C, D, E, F, G, H	protein	475	CHLAMYDOMONAS REINHARDTII	P00877 (AlphaFold model)
Ribulose bisphosphate carboxylase small chain 1	I, J, K, L, M, N, O, P	protein	140	CHLAMYDOMONAS REINHARDTII	P00873 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H), FASTA

>2VDI_1 RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN (chains A, B, C, D, E, F, G, H)
MVPQTETKAGAGFKAGVKDYRLTYYTPDYVVRDTDILAAFRMTPQPGVPPEECGAAVAAE
SSTGTWTTVWTDGLTSLDRYKGRCYDIEPVPGEDNQYIAYVAYPIDLFEEGSVTNMFTSI
VGNVFGFKALRALRLEDLRIPPAYVKTFVGPPHGIQVERDKLNKYGRGLLGCTIKPKLGL
SAKNYGRAVYESLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEAIYKAQAETGEVKGHYL
NATAGTCEEMMKRAVCAKELGVPIIMHDYLTGGFTANTSLAIYCRDNGLLLHIHRAMHAV
IDRQRNHGIHFRVLAKALRMSGGDHLHSGTVVGKLEGEREVTLGFVDLMRDDYVEKDRSR
GIYFTQDWCSMPGVMPVASGGIHVWHMPALVEIFGDDACLQFGGGTLGHPWGNAPGAAAN
RVALEACTQARNEGRDLAREGGDVIRSACKWSPELAAACEVWKEIKFEFDTIDKL

Sequence of entity 2 (I, J, K, L, M, N, O, P), FASTA

>2VDI_2 RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1 (chains I, J, K, L, M, N, O, P)
MMVWTPVNNKMFETFSYLPPLTDEQIAAQVDYIVANGWIPCLEFAEADKAYVSNESAIRF
GSVSCLYYDNRYWTMWKLPMFGCRDPMQVLREIVACTKAFPDAYVRLVAFDNQKQVQIMG
FLVQRPKTARDFQPANKRSV

Ligands and cofactors

ID	Name	Formula	Copies
CAP	2-carboxyarabinitol-1,5-diphosphate	C6 H14 O13 P2	8
MG	Magnesium ion	Mg	8

Water and common crystallization additives (EDO) are not listed.

Primary citation

Structural and Functional Consequences of the Replacement of Proximal Residues Cys-172 and Cys-192 in the Large Subunit of Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase from Chlamydomonas Reinhardtii. Garcia-Murria, M.-J., Karkehabadi, S., Marin-Navarro, J. et al. Biochem J (2008) 411:241. DOI 10.1042/BJ20071422 · 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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