2V6A: Ribulose bisphosphate carboxylase large chain

Crystal structure of Chlamydomonas reinhardtii Rubisco with large- subunit mutations V331A, G344S. Determined by X-ray diffraction at 1.5 Å resolution. Released 31 Jul 2007.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: CHLAMYDOMONAS REINHARDTII
Chains: 16
Atoms: 42,413
Mol. weight: 558.57 kDa
Ligands: MG, CAP
Released: 31 Jul 2007

Explore 2V6A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2V6A contains 266 α-helices and 256 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
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
β-strand	97-103	7	1
α-helix	105-107	3
α-helix	113-121	9
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	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	437-451	15
α-helix	453-462	10

Chains B and E: 26 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
β-strand	97-103	7	9
α-helix	105-107	3
α-helix	113-121	9
α-helix	124-126	3
β-strand	127	1	6
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
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	437-451	15
α-helix	453-462	10

Chains C and G: 27 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	21-24	4
β-strand	25	1	15
β-strand	36-44	9	15
α-helix	45	1
α-helix	50-60	11
α-helix	70-74	5
α-helix	77-80	4
β-strand	83-89	7	15
α-helix	90	1
β-strand	97-103	7	15
α-helix	105-107	3
α-helix	113-121	9
α-helix	124-126	3
β-strand	127	1	16
β-strand	130-139	10	15
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	274-287	14
β-strand	290-294	5	17
α-helix	298-302	5
β-strand	308-309	2	15
α-helix	311-321	11
β-strand	325-327	3	17
β-strand	335	1	20
α-helix	339-350	12
β-strand	353-354	2	21
β-strand	357	1	22
α-helix	358-360	3
β-strand	362	1	22
β-strand	366-367	2	21
α-helix	371-374	4
β-strand	375-379	5	17
α-helix	384-386	3
α-helix	387-394	8
β-strand	399-401	3	17
α-helix	404-407	4
α-helix	413-432	20
α-helix	437-451	15
α-helix	453-462	10

Chains D and H: 28 helices, 24 β-strands

Element	Residues	Length	Sheet
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
α-helix	70-74	5
α-helix	77-80	4
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	127	1	20
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	182-194	13
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	264-268	5	24
α-helix	269-272	4
α-helix	274-287	14
β-strand	290-294	5	24
α-helix	298-302	5
β-strand	308-309	2	23
α-helix	311-321	11
β-strand	325-327	3	24
β-strand	335	1	16
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
α-helix	371-374	4
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	413-432	20
α-helix	437-451	15
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	37
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	113-121	9
α-helix	124-126	3
β-strand	127	1	34
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	182-194	13
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	30
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	371-373	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	437-451	15
α-helix	453-462	10

Chains I, K, L, M, N and O: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	57
α-helix	20-22	3
α-helix	23-35	13
β-strand	39-45	7	58
α-helix	47-49	3
β-strand	53	1	59
α-helix	55-59	5
β-strand	69	1	59
β-strand	74-76	3	58
α-helix	86-99	14
β-strand	104-111	8	58
β-strand	116-124	9	58
α-helix	135-137	3
β-strand	139	1	57

Chain J: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	60
α-helix	20-22	3
α-helix	23-36	14
β-strand	39-45	7	61
α-helix	47-49	3
β-strand	53	1	62
α-helix	55-59	5
β-strand	69	1	62
β-strand	74-76	3	61
α-helix	86-99	14
β-strand	104-111	8	61
β-strand	116-124	9	61
α-helix	135-137	3
β-strand	139	1	60

Chain P: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3	1
β-strand	4	1	78
α-helix	5	1
α-helix	20-22	3
α-helix	23-35	13
β-strand	39-45	7	79
α-helix	47-49	3
β-strand	53	1	80
α-helix	55-59	5
β-strand	69	1	80
β-strand	74-76	3	79
α-helix	86-99	14
β-strand	104-111	8	79
β-strand	116-124	9	79
α-helix	135-137	3
β-strand	139	1	78

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

>2V6A_1 RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN (chains A, B, C, D, E, F, G, H)
MVPQTETKAGAGFKAGVKDYRLTYYTPDYVVRDTDILAAFRMTPQPGVPPEECGAAVAAE
SSTGTWTTVWTDGLTSLDRYKGRCYDIEPVPGEDNQYIAYVAYPIDLFEEGSVTNMFTSI
VGNVFGFKALRALRLEDLRIPPAYVKTFVGPPHGIQVERDKLNKYGRGLLGCTIKPKLGL
SAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEAIYKAQAETGEVKGHYL
NATAGTCEEMMKRAVCAKELGVPIIMHDYLTGGFTANTSLAIYCRDNGLLLHIHRAMHAV
IDRQRNHGIHFRVLAKALRMSGGDHLHSGTAVGKLEGEREVTLSFVDLMRDDYVEKDRSR
GIYFTQDWCSMPGVMPVASGGIHVWHMPALVEIFGDDACLQFGGGTLGHPWGNAPGAAAN
RVALEACTQARNEGRDLAREGGDVIRSACKWSPELAAACEVWKEIKFEFDTIDKL

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

>2V6A_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
MG	Magnesium ion	Mg	8
CAP	2-carboxyarabinitol-1,5-diphosphate	C6 H14 O13 P2	8

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

Primary citation

Structural Analysis of Altered Large-Subunit Loop-6-Carboxy-Terminus Interactions that Influence Catalytic Efficiency and Co2-O2 Specificity of Ribulose-1,5-Bisphosphate Carboxylase Oxygenase. Karkehabadi, S., Satagopan, S., Taylor, T.C. et al. Biochemistry (2007) 46:11080. DOI 10.1021/BI701063F · 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
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…
2VDH 2.3 Å, Crystal structure of Chlamydomonas reinhardtii Rubisco with a large- subunit C172S…

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