PDB-6tqj: Crystal structure of the c14 ring of the F1FO ATP synthase from s...

Basic information

• Entry: Database: PDB / ID: 6tqj
• Title: Crystal structure of the c14 ring of the F1FO ATP synthase from spinach chloroplast
• Components: ATP synthase subunit c, chloroplastic
• Keywords: MEMBRANE PROTEIN / ATP synthase / c ring / spinach / chloroplast

Function / homology

Function:

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

Domain/homology:

F1F0 ATP synthase subunit C / F1FO ATP Synthase / 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 / Up-down Bundle / Mainly Alpha

Component:

EICOSANE / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / ATP synthase subunit c, chloroplastic

• Biological species: Spinacia oleracea (spinach)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
• Authors: Kovalev, K. / Gushchin, I. / Vlasov, A. / Round, E. / Polovinkin, V. / Gordeliy, V.

Funding support

Russian Federation, France, 4items

Organization	Grant number	Country
Russian Science Foundation	16-15-00242	Russian Federation
French National Research Agency	ANR-10-INSB-05-02	France
Grenoble Alliance for Integrated Structural Cell Biology (GRAL)	ANR-10-LABX-49-01	France
Russian Foundation for Basic Research	18-34-00256	Russian Federation

• Citation: Journal: Sci Rep / Year: 2019; Title: Unusual features of the c-ring of F1FOATP synthases.; Authors: Vlasov, A.V. / Kovalev, K.V. / Marx, S.H. / Round, E.S. / Gushchin, I.Y. / Polovinkin, V.A. / Tsoy, N.M. / Okhrimenko, I.S. / Borshchevskiy, V.I. / Buldt, G.D. / Ryzhykau, Y.L. / Rogachev, A.V. / Chupin, V.V. / Kuklin, A.I. / Dencher, N.A. / Gordeliy, V.I.

History

Deposition	Dec 16, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 25, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jan 24, 2024	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

hetero molecules

Summary:

• 119 kDa, 14 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	119,386	41
Polymers	111,683	14
Non-polymers	7,703	27
Water	3,477	193

1

Summary:

• Idetical with deposited unit
• defined by author&software
• Evidence: native gel electrophoresis

Symmetry operations:

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

Calculated values:

Buried area	62580 Å2
ΔGint	-558 kcal/mol
Surface area	29500 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	93.136, 96.336, 158.684
Angle α, β, γ (deg.)	90.000, 106.720, 90.000
Int Tables number	5
Space group name H-M	I121

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: MET / Beg label comp-ID: MET / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 1 - 81 / Label seq-ID: 1 - 81

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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spinacia oleracea (spinach) / Gene: atpH / Production host: Spinacia oleracea (spinach) / References: UniProt: P69447

#2: Chemical

A-101 B-101 C-101 C-102 C-103 D-101 E-101 F-101 G-101 G-102 G-103 H-101 H-102 H-103 H-104 I-101 I-102 J-101 L-101 L-102 ...
ChemComp-LFA / EICOSANE / LIPID FRAGMENT

Details:

Mass: 282.547 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C₂₀H₄₂

#3: Chemical

H-105 ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol

Details:

Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₁H₄₀O₄

#4: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H₂O

• Has ligand of interest: N

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 3.05 ų/Da / Density % sol: 59.7 %
• Crystal grow: Temperature: 293 K / Method: lipidic cubic phase / Details: 0.1 M MES pH 5.8, 1.4 M ammonium sulfate

Data collection

• Diffraction: Mean temperature: 100 K / Serial crystal experiment: N
• Diffraction source: Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.978 Å
• Detector: Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 8, 2015
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.978 Å / Relative weight: 1
• Reflection: Resolution: 2.3→48.17 Å / Num. obs: 57691 / % possible obs: 96.7 % / Redundancy: 3.7 % / CC_1/2: 0.993 / R_merge(I) obs: 0.192 / R_pim(I) all: 0.114 / R_rim(I) all: 0.225 / Net I/σ(I): 4.9 / Num. measured all: 214591 / Scaling rejects: 10

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	Rmerge(I) obs	Num. measured all	Num. unique obs	CC1/2	Rpim(I) all	Rrim(I) all	Net I/σ(I) obs	% possible all
2.3-2.36	3.5	1.169	12342	3484	0.421	0.704	1.369	1.2	75.6
10.03-48.17	3.4	0.051	2592	753	0.998	0.031	0.06	11.5	98.2

Processing

Software

Name	Version	Classification
Aimless	0.7.1	data scaling
REFMAC	5.8.0257	refinement
PDB_EXTRACT	3.25	data extraction
XDS		data reduction
MOLREP		phasing

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V3C

3v3c

Resolution: 2.3→20 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.928 / SU B: 8.026 / SU ML: 0.182 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.308 / ESU R Free: 0.221
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.2369	2844	4.9 %	RANDOM
Rwork	0.2042	-	-	-
obs	0.2058	54743	96.34 %	-

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

Displacement parameters

B_iso max: 122.05 Ų / B_iso mean: 30.937 Ų / B_iso min: 14.26 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	-1.53 Å2	-0 Å2	-1.57 Å2
2-	-	3.14 Å2	-0 Å2
3-	-	-	-0.56 Å2

Refinement step

Cycle: final / Resolution: 2.3→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7761	0	328	193	8282
Biso mean	-	-	71.29	34.47	-
Num. residues	-	-	-	-	1134

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.002	0.013	8363
X-RAY DIFFRACTION	r_bond_other_d	0	0.017	8749
X-RAY DIFFRACTION	r_angle_refined_deg	1.068	1.622	11325
X-RAY DIFFRACTION	r_angle_other_deg	1.115	1.551	20199
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.083	5	1172
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.177	25.254	236
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.412	15	1146
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.208	15	14
X-RAY DIFFRACTION	r_chiral_restr	0.034	0.2	1133
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	9308
X-RAY DIFFRACTION	r_gen_planes_other	0	0.02	1426

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	2272	0.05
1	2	B	2272	0.05
2	1	A	2264	0.06
2	2	C	2264	0.06
3	1	A	2268	0.05
3	2	D	2268	0.05
4	1	A	2267	0.04
4	2	E	2267	0.04
5	1	A	2273	0.03
5	2	F	2273	0.03
6	1	A	2265	0.05
6	2	G	2265	0.05
7	1	A	2274	0.04
7	2	H	2274	0.04
8	1	A	2276	0.03
8	2	I	2276	0.03
9	1	A	2279	0.03
9	2	J	2279	0.03
10	1	A	2269	0.05
10	2	K	2269	0.05
11	1	A	2262	0.05
11	2	L	2262	0.05
12	1	A	2268	0.04
12	2	M	2268	0.04
13	1	A	2270	0.03
13	2	N	2270	0.03
14	1	B	2298	0.04
14	2	C	2298	0.04
15	1	B	2303	0.04
15	2	D	2303	0.04
16	1	B	2293	0.05
16	2	E	2293	0.05
17	1	B	2289	0.05
17	2	F	2289	0.05
18	1	B	2302	0.04
18	2	G	2302	0.04
19	1	B	2304	0.04
19	2	H	2304	0.04
20	1	B	2295	0.04
20	2	I	2295	0.04
21	1	B	2295	0.03
21	2	J	2295	0.03
22	1	B	2307	0.03
22	2	K	2307	0.03
23	1	B	2303	0.03
23	2	L	2303	0.03
24	1	B	2301	0.04
24	2	M	2301	0.04
25	1	B	2289	0.04
25	2	N	2289	0.04
26	1	C	2308	0.05
26	2	D	2308	0.05
27	1	C	2289	0.05
27	2	E	2289	0.05
28	1	C	2279	0.06
28	2	F	2279	0.06
29	1	C	2306	0.03
29	2	G	2306	0.03
30	1	C	2306	0.04
30	2	H	2306	0.04
31	1	C	2295	0.05
31	2	I	2295	0.05
32	1	C	2293	0.04
32	2	J	2293	0.04
33	1	C	2302	0.04
33	2	K	2302	0.04
34	1	C	2300	0.04
34	2	L	2300	0.04
35	1	C	2302	0.04
35	2	M	2302	0.04
36	1	C	2280	0.05
36	2	N	2280	0.05
37	1	D	2297	0.05
37	2	E	2297	0.05
38	1	D	2281	0.05
38	2	F	2281	0.05
39	1	D	2315	0.04
39	2	G	2315	0.04
40	1	D	2306	0.03
40	2	H	2306	0.03
41	1	D	2299	0.05
41	2	I	2299	0.05
42	1	D	2301	0.04
42	2	J	2301	0.04
43	1	D	2307	0.04
43	2	K	2307	0.04
44	1	D	2306	0.03
44	2	L	2306	0.03
45	1	D	2305	0.04
45	2	M	2305	0.04
46	1	D	2291	0.05
46	2	N	2291	0.05
47	1	E	2283	0.05
47	2	F	2283	0.05
48	1	E	2298	0.04
48	2	G	2298	0.04
49	1	E	2292	0.05
49	2	H	2292	0.05
50	1	E	2293	0.04
50	2	I	2293	0.04
51	1	E	2287	0.04
51	2	J	2287	0.04
52	1	E	2295	0.05
52	2	K	2295	0.05
53	1	E	2289	0.05
53	2	L	2289	0.05
54	1	E	2290	0.05
54	2	M	2290	0.05
55	1	E	2291	0.04
55	2	N	2291	0.04
56	1	F	2293	0.06
56	2	G	2293	0.06
57	1	F	2297	0.04
57	2	H	2297	0.04
58	1	F	2294	0.03
58	2	I	2294	0.03
59	1	F	2289	0.04
59	2	J	2289	0.04
60	1	F	2299	0.05
60	2	K	2299	0.05
61	1	F	2294	0.05
61	2	L	2294	0.05
62	1	F	2293	0.04
62	2	M	2293	0.04
63	1	F	2282	0.04
63	2	N	2282	0.04
64	1	G	2306	0.04
64	2	H	2306	0.04
65	1	G	2289	0.05
65	2	I	2289	0.05
66	1	G	2294	0.04
66	2	J	2294	0.04
67	1	G	2304	0.04
67	2	K	2304	0.04
68	1	G	2309	0.03
68	2	L	2309	0.03
69	1	G	2302	0.04
69	2	M	2302	0.04
70	1	G	2285	0.05
70	2	N	2285	0.05
71	1	H	2297	0.03
71	2	I	2297	0.03
72	1	H	2298	0.02
72	2	J	2298	0.02
73	1	H	2303	0.03
73	2	K	2303	0.03
74	1	H	2304	0.02
74	2	L	2304	0.02
75	1	H	2311	0.03
75	2	M	2311	0.03
76	1	H	2285	0.04
76	2	N	2285	0.04
77	1	I	2299	0.03
77	2	J	2299	0.03
78	1	I	2297	0.05
78	2	K	2297	0.05
79	1	I	2286	0.04
79	2	L	2286	0.04
80	1	I	2296	0.03
80	2	M	2296	0.03
81	1	I	2289	0.03
81	2	N	2289	0.03
82	1	J	2277	0.04
82	2	K	2277	0.04
83	1	J	2269	0.04
83	2	L	2269	0.04
84	1	J	2277	0.04
84	2	M	2277	0.04
85	1	J	2270	0.04
85	2	N	2270	0.04
86	1	K	2291	0.03
86	2	L	2291	0.03
87	1	K	2288	0.03
87	2	M	2288	0.03
88	1	K	2274	0.05
88	2	N	2274	0.05
89	1	L	2299	0.03
89	2	M	2299	0.03
90	1	L	2280	0.04
90	2	N	2280	0.04
91	1	M	2282	0.04
91	2	N	2282	0.04

LS refinement shell

Resolution: 2.3→2.359 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.317	187	-
Rwork	0.307	3070	-
all	-	3257	-
obs	-	-	74.67 %