PDB-4mjn: Structure of the c ring of the CF1FO ATP synthases.

Basic information

• Entry: Database: PDB / ID: 4mjn
• Title: Structure of the c ring of the CF1FO ATP synthases.
• Components: ATP synthase subunit c, chloroplastic
• Keywords: HYDROLASE

Function / homology

Function:

: / chloroplast thylakoid membrane / proton motive force-driven ATP synthesis / proton-transporting ATP synthase activity, rotational mechanism / lipid binding

Domain/homology:

ATP synthase, F0 complex, subunit C, bacterial/chloroplast / ATP synthase, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C

Component:

ATP synthase subunit c, chloroplastic

• Biological species: Triticum aestivum (bread wheat)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6 Å
• Authors: Balakrishna, A.M. / Gruber, G.

Citation

Journal: Biosci. Rep. / Year: 2014
Title: Crystallographic structure of the turbine C-ring from spinach chloroplast F-ATP synthase.
Authors: Balakrishna, A.M. / Seelert, H. / Marx, S.H. / Dencher, N.A. / Gruber, G.

#1: Journal: J.Biol.Chem. / Year: 2009
Title: Structure of the c14 rotor ring of the proton translocating chloroplast ATP Synthase
Authors: Vollmar, M. / Schlieper, D. / Winn, M. / Buchner, C. / Groth, G.

History

Deposition	Sep 4, 2013	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Mar 19, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jun 5, 2019	Group: Data collection / Database references / Category: citation Item: _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Nov 8, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Assembly

Deposited unit

A: ATP synthase subunit c, chloroplastic

B: ATP synthase subunit c, chloroplastic

C: ATP synthase subunit c, chloroplastic

D: ATP synthase subunit c, chloroplastic

E: ATP synthase subunit c, chloroplastic

F: ATP synthase subunit c, chloroplastic

G: ATP synthase subunit c, chloroplastic

H: ATP synthase subunit c, chloroplastic

I: ATP synthase subunit c, chloroplastic

J: ATP synthase subunit c, chloroplastic

K: ATP synthase subunit c, chloroplastic

L: ATP synthase subunit c, chloroplastic

M: ATP synthase subunit c, chloroplastic

N: ATP synthase subunit c, chloroplastic

Summary:

• 112 kDa, 14 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	111,683	14
Polymers	111,683	14
Non-polymers	0	0
Water	0	0

1

Summary:

• Idetical with deposited unit
• defined by author

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Unit cell

Length a, b, c (Å)	144.420, 99.295, 123.510
Angle α, β, γ (deg.)	90.00, 104.34, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	A
2	4	E
1	5	A
2	5	F
1	6	A
2	6	G
1	7	A
2	7	H
1	8	A
2	8	I
1	9	A
2	9	J
1	10	A
2	10	K
1	11	A
2	11	L
1	12	A
2	12	M
1	13	A
2	13	N
1	14	B
2	14	C
1	15	B
2	15	D
1	16	B
2	16	E
1	17	B
2	17	F
1	18	B
2	18	G
1	19	B
2	19	H
1	20	B
2	20	I
1	21	B
2	21	J
1	22	B
2	22	K
1	23	B
2	23	L
1	24	B
2	24	M
1	25	B
2	25	N
1	26	C
2	26	D
1	27	C
2	27	E
1	28	C
2	28	F
1	29	C
2	29	G
1	30	C
2	30	H
1	31	C
2	31	I
1	32	C
2	32	J
1	33	C
2	33	K
1	34	C
2	34	L
1	35	C
2	35	M
1	36	C
2	36	N
1	37	D
2	37	E
1	38	D
2	38	F
1	39	D
2	39	G
1	40	D
2	40	H
1	41	D
2	41	I
1	42	D
2	42	J
1	43	D
2	43	K
1	44	D
2	44	L
1	45	D
2	45	M
1	46	D
2	46	N
1	47	E
2	47	F
1	48	E
2	48	G
1	49	E
2	49	H
1	50	E
2	50	I
1	51	E
2	51	J
1	52	E
2	52	K
1	53	E
2	53	L
1	54	E
2	54	M
1	55	E
2	55	N
1	56	F
2	56	G
1	57	F
2	57	H
1	58	F
2	58	I
1	59	F
2	59	J
1	60	F
2	60	K
1	61	F
2	61	L
1	62	F
2	62	M
1	63	F
2	63	N
1	64	G
2	64	H
1	65	G
2	65	I
1	66	G
2	66	J
1	67	G
2	67	K
1	68	G
2	68	L
1	69	G
2	69	M
1	70	G
2	70	N
1	71	H
2	71	I
1	72	H
2	72	J
1	73	H
2	73	K
1	74	H
2	74	L
1	75	H
2	75	M
1	76	H
2	76	N
1	77	I
2	77	J
1	78	I
2	78	K
1	79	I
2	79	L
1	80	I
2	80	M
1	81	I
2	81	N
1	82	J
2	82	K
1	83	J
2	83	L
1	84	J
2	84	M
1	85	J
2	85	N
1	86	K
2	86	L
1	87	K
2	87	M
1	88	K
2	88	N
1	89	L
2	89	M
1	90	L
2	90	N
1	91	M
2	91	N

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 2 - 75 / Label seq-ID: 2 - 75

Dom-ID	Ens-ID	Auth asym-ID	Label asym-ID
1	1	A	A
2	1	B	B
1	2	A	A
2	2	C	C
1	3	A	A
2	3	D	D
1	4	A	A
2	4	E	E
1	5	A	A
2	5	F	F
1	6	A	A
2	6	G	G
1	7	A	A
2	7	H	H
1	8	A	A
2	8	I	I
1	9	A	A
2	9	J	J
1	10	A	A
2	10	K	K
1	11	A	A
2	11	L	L
1	12	A	A
2	12	M	M
1	13	A	A
2	13	N	N
1	14	B	B
2	14	C	C
1	15	B	B
2	15	D	D
1	16	B	B
2	16	E	E
1	17	B	B
2	17	F	F
1	18	B	B
2	18	G	G
1	19	B	B
2	19	H	H
1	20	B	B
2	20	I	I
1	21	B	B
2	21	J	J
1	22	B	B
2	22	K	K
1	23	B	B
2	23	L	L
1	24	B	B
2	24	M	M
1	25	B	B
2	25	N	N
1	26	C	C
2	26	D	D
1	27	C	C
2	27	E	E
1	28	C	C
2	28	F	F
1	29	C	C
2	29	G	G
1	30	C	C
2	30	H	H
1	31	C	C
2	31	I	I
1	32	C	C
2	32	J	J
1	33	C	C
2	33	K	K
1	34	C	C
2	34	L	L
1	35	C	C
2	35	M	M
1	36	C	C
2	36	N	N
1	37	D	D
2	37	E	E
1	38	D	D
2	38	F	F
1	39	D	D
2	39	G	G
1	40	D	D
2	40	H	H
1	41	D	D
2	41	I	I
1	42	D	D
2	42	J	J
1	43	D	D
2	43	K	K
1	44	D	D
2	44	L	L
1	45	D	D
2	45	M	M
1	46	D	D
2	46	N	N
1	47	E	E
2	47	F	F
1	48	E	E
2	48	G	G
1	49	E	E
2	49	H	H
1	50	E	E
2	50	I	I
1	51	E	E
2	51	J	J
1	52	E	E
2	52	K	K
1	53	E	E
2	53	L	L
1	54	E	E
2	54	M	M
1	55	E	E
2	55	N	N
1	56	F	F
2	56	G	G
1	57	F	F
2	57	H	H
1	58	F	F
2	58	I	I
1	59	F	F
2	59	J	J
1	60	F	F
2	60	K	K
1	61	F	F
2	61	L	L
1	62	F	F
2	62	M	M
1	63	F	F
2	63	N	N
1	64	G	G
2	64	H	H
1	65	G	G
2	65	I	I
1	66	G	G
2	66	J	J
1	67	G	G
2	67	K	K
1	68	G	G
2	68	L	L
1	69	G	G
2	69	M	M
1	70	G	G
2	70	N	N
1	71	H	H
2	71	I	I
1	72	H	H
2	72	J	J
1	73	H	H
2	73	K	K
1	74	H	H
2	74	L	L
1	75	H	H
2	75	M	M
1	76	H	H
2	76	N	N
1	77	I	I
2	77	J	J
1	78	I	I
2	78	K	K
1	79	I	I
2	79	L	L
1	80	I	I
2	80	M	M
1	81	I	I
2	81	N	N
1	82	J	J
2	82	K	K
1	83	J	J
2	83	L	L
1	84	J	J
2	84	M	M
1	85	J	J
2	85	N	N
1	86	K	K
2	86	L	L
1	87	K	K
2	87	M	M
1	88	K	K
2	88	N	N
1	89	L	L
2	89	M	M
1	90	L	L
2	90	N	N
1	91	M	M
2	91	N	N

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91

Components

#1: Protein

A B C D E F G H I J K L M N
ATP synthase subunit c, chloroplastic / ATP synthase F(0) sector subunit c / ATPase subunit III / F-type ATPase subunit c / F-ATPase subunit c / Lipid-binding protein

Details:

Mass: 7977.366 Da / Num. of mol.: 14 / Fragment: c 14 rotor ring chloroplast ATP synthase / Source method: isolated from a natural source / Details: Thylakoid membrane / Source: (natural) Triticum aestivum (bread wheat)
References: UniProt: P69448, H+-transporting two-sector ATPase

Experimental details

Experiment

• Experiment: Method: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

• Crystal: Density Matthews: 3.84 ų/Da / Density % sol: 67.98 %
• Crystal grow: Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.3 ; Details: 33%(v/v) PEG550 MME, 0.05M Sodium acetate, pH 4.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999 Å
• Detector: Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2013 / Details: mirrors
• Radiation: Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.9999 Å / Relative weight: 1
• Reflection: Resolution: 6→30 Å / Num. all: 4238 / Num. obs: 4091 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 2.8 % / R_merge(I) obs: 0.049 / Net I/σ(I): 9.6
• Reflection shell: Resolution: 6→6.32 Å / Redundancy: 2.8 % / R_merge(I) obs: 0.106 / Mean I/σ(I) obs: 5.3 / Num. unique all: 433 / % possible all: 96.76

Processing

Software

Name	Version	Classification
PHASER		phasing
REFMAC	5.7.0029	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: 2W5J

2w5j

Resolution: 6→19.76 Å / Cor.coef. F_o:F_c: 0.926 / Cor.coef. F_o:F_c free: 0.91 / SU B: 829.803 / SU ML: 3.483 / Cross valid method: THROUGHOUT / ESU R Free: 2.68 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.37784	204	5 %	RANDOM
Rwork	0.35777	-	-	-
obs	0.35885	3887	93.77 %	-
all	-	4091	-	-

• Solvent computation: Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 41.177 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	23.28 Å2	-0 Å2	60.04 Å2
2-	-	-54.45 Å2	-0 Å2
3-	-	-	14 Å2

Refinement step

Cycle: LAST / Resolution: 6→19.76 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5026	0	0	0	5026

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.019	5012
X-RAY DIFFRACTION	r_bond_other_d	0.013	0.02	3332
X-RAY DIFFRACTION	r_angle_refined_deg	2.105	1.938	6902
X-RAY DIFFRACTION	r_angle_other_deg	3.803	3	7252
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.993	5	1022
X-RAY DIFFRACTION	r_chiral_restr	0.103	0.2	882
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	7028
X-RAY DIFFRACTION	r_gen_planes_other	0.006	0.02	980
X-RAY DIFFRACTION	r_rigid_bond_restr	26.308	3	8340
X-RAY DIFFRACTION	r_sphericity_bonded	87.741	5	8358

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	969	0.16
1	2	B	969	0.16
2	1	A	1012	0.13
2	2	C	1012	0.13
3	1	A	1013	0.12
3	2	D	1013	0.12
4	1	A	1019	0.1
4	2	E	1019	0.1
5	1	A	1009	0.11
5	2	F	1009	0.11
6	1	A	1016	0.12
6	2	G	1016	0.12
7	1	A	1010	0.13
7	2	H	1010	0.13
8	1	A	1018	0.11
8	2	I	1018	0.11
9	1	A	1013	0.11
9	2	J	1013	0.11
10	1	A	1004	0.11
10	2	K	1004	0.11
11	1	A	1011	0.12
11	2	L	1011	0.12
12	1	A	1009	0.12
12	2	M	1009	0.12
13	1	A	998	0.11
13	2	N	998	0.11
14	1	B	983	0.19
14	2	C	983	0.19
15	1	B	983	0.17
15	2	D	983	0.17
16	1	B	998	0.17
16	2	E	998	0.17
17	1	B	969	0.17
17	2	F	969	0.17
18	1	B	984	0.18
18	2	G	984	0.18
19	1	B	978	0.18
19	2	H	978	0.18
20	1	B	985	0.17
20	2	I	985	0.17
21	1	B	980	0.17
21	2	J	980	0.17
22	1	B	988	0.17
22	2	K	988	0.17
23	1	B	969	0.18
23	2	L	969	0.18
24	1	B	994	0.18
24	2	M	994	0.18
25	1	B	968	0.17
25	2	N	968	0.17
26	1	C	1028	0.11
26	2	D	1028	0.11
27	1	C	1027	0.1
27	2	E	1027	0.1
28	1	C	1021	0.09
28	2	F	1021	0.09
29	1	C	1023	0.14
29	2	G	1023	0.14
30	1	C	1025	0.12
30	2	H	1025	0.12
31	1	C	1028	0.12
31	2	I	1028	0.12
32	1	C	1029	0.13
32	2	J	1029	0.13
33	1	C	1029	0.12
33	2	K	1029	0.12
34	1	C	1022	0.12
34	2	L	1022	0.12
35	1	C	1030	0.11
35	2	M	1030	0.11
36	1	C	1017	0.08
36	2	N	1017	0.08
37	1	D	1045	0.09
37	2	E	1045	0.09
38	1	D	1019	0.1
38	2	F	1019	0.1
39	1	D	1020	0.12
39	2	G	1020	0.12
40	1	D	1032	0.11
40	2	H	1032	0.11
41	1	D	1033	0.09
41	2	I	1033	0.09
42	1	D	1033	0.11
42	2	J	1033	0.11
43	1	D	1028	0.1
43	2	K	1028	0.1
44	1	D	1022	0.13
44	2	L	1022	0.13
45	1	D	1031	0.12
45	2	M	1031	0.12
46	1	D	1011	0.11
46	2	N	1011	0.11
47	1	E	1024	0.08
47	2	F	1024	0.08
48	1	E	1028	0.12
48	2	G	1028	0.12
49	1	E	1035	0.11
49	2	H	1035	0.11
50	1	E	1042	0.09
50	2	I	1042	0.09
51	1	E	1037	0.1
51	2	J	1037	0.1
52	1	E	1037	0.1
52	2	K	1037	0.1
53	1	E	1021	0.12
53	2	L	1021	0.12
54	1	E	1033	0.11
54	2	M	1033	0.11
55	1	E	1015	0.1
55	2	N	1015	0.1
56	1	F	1019	0.11
56	2	G	1019	0.11
57	1	F	1016	0.11
57	2	H	1016	0.11
58	1	F	1029	0.07
58	2	I	1029	0.07
59	1	F	1023	0.09
59	2	J	1023	0.09
60	1	F	1013	0.09
60	2	K	1013	0.09
61	1	F	1016	0.11
61	2	L	1016	0.11
62	1	F	1020	0.09
62	2	M	1020	0.09
63	1	F	1013	0.1
63	2	N	1013	0.1
64	1	G	1049	0.12
64	2	H	1049	0.12
65	1	G	1026	0.11
65	2	I	1026	0.11
66	1	G	1029	0.1
66	2	J	1029	0.1
67	1	G	1029	0.12
67	2	K	1029	0.12
68	1	G	1018	0.12
68	2	L	1018	0.12
69	1	G	1037	0.12
69	2	M	1037	0.12
70	1	G	1013	0.13
70	2	N	1013	0.13
71	1	H	1022	0.1
71	2	I	1022	0.1
72	1	H	1031	0.1
72	2	J	1031	0.1
73	1	H	1032	0.12
73	2	K	1032	0.12
74	1	H	1010	0.12
74	2	L	1010	0.12
75	1	H	1033	0.11
75	2	M	1033	0.11
76	1	H	1013	0.11
76	2	N	1013	0.11
77	1	I	1043	0.09
77	2	J	1043	0.09
78	1	I	1028	0.1
78	2	K	1028	0.1
79	1	I	1022	0.13
79	2	L	1022	0.13
80	1	I	1033	0.11
80	2	M	1033	0.11
81	1	I	1020	0.1
81	2	N	1020	0.1
82	1	J	1022	0.11
82	2	K	1022	0.11
83	1	J	1018	0.12
83	2	L	1018	0.12
84	1	J	1036	0.1
84	2	M	1036	0.1
85	1	J	1012	0.11
85	2	N	1012	0.11
86	1	K	1018	0.14
86	2	L	1018	0.14
87	1	K	1034	0.13
87	2	M	1034	0.13
88	1	K	1016	0.11
88	2	N	1016	0.11
89	1	L	1021	0.1
89	2	M	1021	0.1
90	1	L	1006	0.13
90	2	N	1006	0.13
91	1	M	1010	0.12
91	2	N	1010	0.12

LS refinement shell

Resolution: 6→6.142 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.539	15	-
Rwork	0.466	288	-
obs	-	-	98.06 %

Refinement TLS params.

Method: refined / Origin x: 160.176 Å / Origin y: 0.8528 Å / Origin z: 26.9438 Å

	11	12	13	21	22	23	31	32	33
T	2.4114 Å2	0.1017 Å2	-0.6038 Å2	-	3.3097 Å2	0.1523 Å2	-	-	3.3777 Å2
L	5.8117 °2	0.3238 °2	8.5344 °2	-	0.0344 °2	0.4429 °2	-	-	12.9269 °2
S	0.1126 Å °	-0.3647 Å °	-0.5158 Å °	0.1177 Å °	0.1863 Å °	-0.1243 Å °	-0.8026 Å °	-0.2864 Å °	-0.2989 Å °

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 75
2	X-RAY DIFFRACTION	1	B	2 - 75
3	X-RAY DIFFRACTION	1	C	2 - 75
4	X-RAY DIFFRACTION	1	D	2 - 75
5	X-RAY DIFFRACTION	1	E	2 - 75
6	X-RAY DIFFRACTION	1	F	2 - 75
7	X-RAY DIFFRACTION	1	G	2 - 75
8	X-RAY DIFFRACTION	1	H	2 - 75
9	X-RAY DIFFRACTION	1	I	2 - 75
10	X-RAY DIFFRACTION	1	J	2 - 75
11	X-RAY DIFFRACTION	1	K	2 - 75
12	X-RAY DIFFRACTION	1	L	2 - 75
13	X-RAY DIFFRACTION	1	M	2 - 75
14	X-RAY DIFFRACTION	1	N	2 - 75