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- PDB-3v3c: Crystal Structure of Chloroplast ATP synthase c-ring from Pisum s... -

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Basic information

Entry
Database: PDB / ID: 3v3c
TitleCrystal Structure of Chloroplast ATP synthase c-ring from Pisum sativum
ComponentsATP synthase subunit c, chloroplastic
KeywordsPHOTOSYNTHESIS / c-ring / Proton translocation / proton binding
Function / homology
Function and homology information


chloroplast thylakoid membrane / proton-transporting ATP synthase complex, coupling factor F(o) / proton-transporting ATP synthase activity, rotational mechanism / membrane => GO:0016020 / lipid binding
Similarity search - Function
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 ...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
Similarity search - Domain/homology
DIGALACTOSYL DIACYL GLYCEROL (DGDG) / YTTRIUM (III) ION / ATP synthase subunit c, chloroplastic
Similarity search - Component
Biological speciesPisum sativum (garden pea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.402 Å
AuthorsSaroussi, S. / Nelson, N.
CitationJournal: Plos One / Year: 2012
Title: Structure and flexibility of the C-ring in the electromotor of rotary F(o)F(1)-ATPase of pea chloroplasts.
Authors: Saroussi, S. / Schushan, M. / Ben-Tal, N. / Junge, W. / Nelson, N.
History
DepositionDec 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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


Theoretical massNumber of molelcules
Total (without water)111,22239
Polymers109,06114
Non-polymers2,16025
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.130, 102.380, 122.430
Angle α, β, γ (deg.)90.000, 101.220, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11E-105-

YT3

21L-110-

YT3

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11N
21A
31B
41C
51D
61E
71F
81G
91H
101I
111J
121K
131L
141M

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO

Dom-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1VALVALchain 'N' and (resseq 3:81 )NN3 - 811 - 79
2VALVALchain 'A' and (resseq 3:81 )AA3 - 811 - 79
3VALVALchain 'B' and (resseq 3:81 )BB3 - 811 - 79
4VALVALchain 'C' and (resseq 3:81 )CC3 - 811 - 79
5VALVALchain 'D' and (resseq 3:81 )DD3 - 811 - 79
6VALVALchain 'E' and (resseq 3:81 )EE3 - 811 - 79
7PROPROchain 'F' and (resseq 3:79 )FF3 - 791 - 77
8VALVALchain 'G' and (resseq 3:81 )GG3 - 811 - 79
9VALVALchain 'H' and (resseq 3:81 )HH3 - 811 - 79
10VALVALchain 'I' and (resseq 3:81 )II3 - 811 - 79
11VALVALchain 'J' and (resseq 3:81 )JJ3 - 811 - 79
12VALVALchain 'K' and (resseq 3:81 )KK3 - 811 - 79
13VALVALchain 'L' and (resseq 3:81 )LL3 - 811 - 79
14VALVALchain 'M' and (resseq 3:81 )MM3 - 811 - 79

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Components

#1: Protein
ATP synthase subunit c, chloroplastic / / ATP synthase F(0) sector subunit c / ATPase subunit III / F-type ATPase subunit c / F-ATPase ...ATP synthase F(0) sector subunit c / ATPase subunit III / F-type ATPase subunit c / F-ATPase subunit c / Lipid-binding protein


Mass: 7790.104 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Details: chloroplast / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P08212
#2: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharideCarbohydrate / Mass: 949.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H96O15
#3: Chemical
ChemComp-YT3 / YTTRIUM (III) ION / Yttrium


Mass: 88.906 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Y
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Na

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.92 Å3/Da / Density % sol: 68.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 100mM Na-acetate (pH 4.5), 50mM MgCl2, 50mM NaCl, 10mM Yttrium chloride and 14-24% PEG 550 Mono, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 21, 2011
RadiationMonochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→29.32 Å / Num. obs: 23125 / Observed criterion σ(F): 3 / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 48 Å2 / Rmerge(I) obs: 0.167 / Net I/σ(I): 6.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
3.4-3.584.30.03327.1718123.4
3.4-3.584.51.92113379122.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.402→28.889 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 1.42 / σ(F): 1.34 / Phase error: 35.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3215 1044 5.18 %
Rwork0.2995 --
obs0.3006 20148 86.59 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 0.001 Å2 / ksol: 0.207 e/Å3
Displacement parametersBiso max: 563.6 Å2 / Biso mean: 92.7648 Å2 / Biso min: 7.04 Å2
Baniso -1Baniso -2Baniso -3
1--19.5646 Å2-0 Å25.3136 Å2
2---32.4647 Å20 Å2
3----16.4348 Å2
Refinement stepCycle: LAST / Resolution: 3.402→28.889 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7492 0 86 0 7578
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057661
X-RAY DIFFRACTIONf_angle_d1.0310457
X-RAY DIFFRACTIONf_chiral_restr0.1331367
X-RAY DIFFRACTIONf_plane_restr0.0051311
X-RAY DIFFRACTIONf_dihedral_angle_d16.2682574
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11N532X-RAY DIFFRACTIONPOSITIONAL0.165
12A532X-RAY DIFFRACTIONPOSITIONAL0.165
13B527X-RAY DIFFRACTIONPOSITIONAL0.174
14C520X-RAY DIFFRACTIONPOSITIONAL0.058
15D533X-RAY DIFFRACTIONPOSITIONAL0.093
16E533X-RAY DIFFRACTIONPOSITIONAL0.084
17F512X-RAY DIFFRACTIONPOSITIONAL0.041
18G533X-RAY DIFFRACTIONPOSITIONAL0.04
19H530X-RAY DIFFRACTIONPOSITIONAL0.04
110I530X-RAY DIFFRACTIONPOSITIONAL0.04
111J536X-RAY DIFFRACTIONPOSITIONAL0.04
112K532X-RAY DIFFRACTIONPOSITIONAL0.053
113L536X-RAY DIFFRACTIONPOSITIONAL0.04
114M536X-RAY DIFFRACTIONPOSITIONAL0.048
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4021-3.58120.3544470.418968973622
3.5812-3.80510.36511620.35042800296290
3.8051-4.09810.31571660.29273142330899
4.0981-4.50910.27741740.26073102327699
4.5091-5.15840.30071600.23893135329599
5.1584-6.48690.29711850.2943113329899
6.4869-28.890.37091500.34233123327396
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.10160.0503-0.1153-0.0009-0.03320.08910.0431-0.0942-0.0062-0.02620.01780.0046-0.0130.0780.2199-0.2319-0.41060.33690.59160.3848-0.2004-15.6719-17.477722.4089
20.2106-0.12840.28470.4413-0.19380.4160.10990.11910.09060.00290.2244-0.0079-0.1892-0.04570.39581.141-0.0412-0.36070.97150.09030.1646-7.3509-19.460119.2902
30.1085-0.0014-0.08810.00290.01160.10930.0163-0.2070.00140.0966-0.0123-0.0721-0.02240.09790.0415-0.26880.17490.38570.61070.0028-0.1283-15.962-25.206621.7123
40.1702-0.0340.13950.18960.05880.1893-0.0228-0.17610.0470.23250.0575-0.067-0.03040.11340.05051.0486-0.0529-0.44631.0153-0.10610.2035-8.4866-30.701820.7739
50.0561-0.0333-0.00280.04250.04110.103-0.0245-0.07290.0230.06030.11140.021-0.0135-0.02640.29880.34250.4325-0.00850.6508-0.2547-0.1367-18.8579-32.168823.568
60.0317-0.0247-0.01550.09070.03220.0354-0.1374-0.13610.00070.12630.0738-0.06710.08630.1186-0.3530.40720.2851-0.20730.4193-0.51530.1114-14.7503-40.221523.2103
70.5096-0.09020.70390.03940.01740.94880.03980.1085-0.0757-0.2338-0.10510.1565-0.0256-0.0782-0.27040.49530.7193-0.27610.0552-0.55710.2462-23.697-36.821727.4929
80.1135-0.0009-0.03450.19480.04120.04470.01510.1688-0.1386-0.3073-0.17890.3157-0.0696-0.1289-0.3680.4177-0.0699-0.51310.1307-0.30990.333-22.464-45.749929.4672
90.1179-0.018-0.04020.42320.13580.1061-0.04440.1064-0.1115-0.2558-0.08550.3693-0.0324-0.1605-0.4940.31460.32830.0091-0.2448-0.05140.2842-30.0245-38.519131.4573
100.1786-0.0215-0.09360.02110.04810.2011-0.10540.07960.0157-0.04220.14150.05170.24650.00590.01910.4424-0.0866-0.21720.0973-0.11260.2399-32.4247-46.577234.8935
110.07630.0886-0.0350.2484-0.06520.02730.0169-0.19330.07070.22960.0296-0.1156-0.05690.00390.12550.6202-0.6249-0.7985-0.0457-0.0084-0.0478-38.2749-39.862639.15
120.16790.0582-0.08740.0386-0.04270.0344-0.1025-0.1803-0.1299-0.15910.00620.13430.04790.0612-0.3775-0.1552-0.48480.27130.51120.4168-0.1023-41.4747-32.01938.6821
130.24440.0091-0.10770.0872-0.00940.0373-0.0305-0.0832-0.2113-0.1847-0.18080.03230.02810.0976-0.4767-0.29140.01610.10160.74030.01840.1472-47.8008-34.045445.044
140.14750.0582-0.09440.0318-0.05780.33970.0286-0.2739-0.0124-0.0472-0.044-0.0711-0.05610.3028-0.0157-0.1529-0.09480.21010.7587-0.0866-0.0814-44.7582-25.126539.9723
150.29670.1365-0.15850.469-0.12130.1113-0.0477-0.0268-0.0115-0.24330.13960.5636-0.0295-0.1026-0.124-0.01570.3615-0.10320.8068-0.1130.424-50.3029-23.225147.49
160.1559-0.0621-0.13480.03440.04790.1010.0666-0.06180.15940.00150.1579-0.2516-0.05650.10160.3833-0.150.39660.31891.0716-0.21260.2787-44.7964-17.344539.9969
170.23210.08260.01850.3983-0.11810.16970.01050.03460.1522-0.11390.12360.4092-0.0439-0.02920.13930.31650.4831-0.1541.0577-0.03310.5202-49.137-11.772546.2246
180.0982-0.09-0.09030.10470.07690.06170.10960.1395-0.039-0.1136-0.12840.064-0.0898-0.07150.06640.42450.7641-0.02160.9969-0.44340.2041-41.3733-10.450738.6837
190.04460.00760.01510.057-0.00120.1162-0.0507-0.08960.04030.06990.1299-0.10250.04140.01740.20191.03680.433-0.44890.572-0.14060.3261-43.721-2.384942.3882
200.0193-0.11950.04210.10670.0257-0.00880.1054-0.06680.11260.0680.0703-0.1479-0.07370.10950.63540.19840.528-0.0438-0.3106-0.7259-0.0389-36.2536-5.624635.4105
210.1131-0.0106-0.06990.09750.00330.03080.0789-0.16050.0891-0.04330.09260.0345-0.0076-0.08690.3180.58580.5411-0.52320.47670.20880.2916-34.76683.270737.8787
220.0734-0.0902-0.04020.28750.05630.02840.0423-0.12830.08670.27320.1541-0.27990.02410.1010.81730.91130.1463-0.53880.0313-0.31920.3455-29.9391-3.915231.3949
230.19640.02140.03220.3240.04090.0354-0.1413-0.1331-0.0433-0.0163-0.0982-0.0722-0.09990.0538-0.18750.6814-0.0287-0.03330.3510.2310.2714-25.58574.222731.0528
240.0890.1084-0.00960.1763-0.02960.07230.1553-0.1189-0.0274-0.0597-0.0403-0.02070.01030.04870.33730.8256-0.7947-0.58160.210.32680.5002-23.5855-5.707927.3994
250.0823-0.0131-0.06020.0913-0.04920.0595-0.01740.02450.0262-0.288-0.0896-0.02750.00630.0525-0.23770.5803-0.4037-0.0930.61750.76020.0595-16.1278-0.058326.2473
260.09150.0469-0.04950.0709-0.04080.02480.016-0.0898-0.04950.053-0.0556-0.2535-0.02950.20380.1277-0.056-0.54190.06980.33580.42950.1077-18.4926-10.577424.1805
270.1009-0.0123-0.11580.117-0.00820.12430.0595-0.0077-0.08620.0096-0.16840.01660.00420.0978-0.20730.31640.11220.20910.89380.17070.1072-10.1027-8.432621.1332
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 3:41)A3 - 41
2X-RAY DIFFRACTION2chain 'A' and (resseq 42:81)A42 - 81
3X-RAY DIFFRACTION3chain 'B' and (resseq 3:41)B3 - 41
4X-RAY DIFFRACTION4chain 'B' and (resseq 42:81)B42 - 81
5X-RAY DIFFRACTION5chain 'C' and (resseq 3:41)C3 - 41
6X-RAY DIFFRACTION6chain 'C' and (resseq 42:81)C42 - 81
7X-RAY DIFFRACTION7chain 'D' and (resseq 3:41)D3 - 41
8X-RAY DIFFRACTION8chain 'D' and (resseq 42:81)D42 - 81
9X-RAY DIFFRACTION9chain 'E' and (resseq 3:41)E3 - 41
10X-RAY DIFFRACTION10chain 'E' and (resseq 42:81)E42 - 81
11X-RAY DIFFRACTION11chain 'F'F3 - 79
12X-RAY DIFFRACTION12chain 'G' and (resseq 3:41)G3 - 41
13X-RAY DIFFRACTION13chain 'G' and (resseq 42:81)G42 - 81
14X-RAY DIFFRACTION14chain 'H' and (resseq 3:41)H3 - 41
15X-RAY DIFFRACTION15chain 'H' and (resseq 42:81)H42 - 81
16X-RAY DIFFRACTION16chain 'I' and (resseq 3:41)I3 - 41
17X-RAY DIFFRACTION17chain 'I' and (resseq 42:81)I42 - 81
18X-RAY DIFFRACTION18chain 'J' and (resseq 3:41)J3 - 41
19X-RAY DIFFRACTION19chain 'J' and (resseq 42:81)J42 - 81
20X-RAY DIFFRACTION20chain 'K' and (resseq 3:41)K3 - 41
21X-RAY DIFFRACTION21chain 'K' and (resseq 42:81)K42 - 81
22X-RAY DIFFRACTION22chain 'L' and (resseq 3:41)L3 - 41
23X-RAY DIFFRACTION23chain 'L' and (resseq 42:81)L42 - 81
24X-RAY DIFFRACTION24chain 'M' and (resseq 3:41)M3 - 41
25X-RAY DIFFRACTION25chain 'M' and (resseq 42:81)M42 - 81
26X-RAY DIFFRACTION26chain 'N' and (resseq 3:41)N3 - 41
27X-RAY DIFFRACTION27chain 'N' and (resseq 42:81)N42 - 81

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  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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