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- PDB-3v6i: Crystal structure of the peripheral stalk of Thermus thermophilus... -

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Basic information

Entry
Database: PDB / ID: 3v6i
TitleCrystal structure of the peripheral stalk of Thermus thermophilus H+-ATPase/synthase at 2.25 A resolution
Components
  • V-type ATP synthase subunit E
  • V-type ATP synthase, subunit (VAPC-THERM)
KeywordsHYDROLASE / peripheral stator stalk / right handed coiled-coil / ATPase/synthase / ATP Binding / Membrane
Function / homology
Function and homology information


proton-transporting two-sector ATPase complex, catalytic domain / proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ATP binding / metal ion binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2950 / F1F0 ATP synthase subunit B, membrane domain / ATP synthase, E subunit, C-terminal / hypothetical protein PF0899 fold / Vacuolar (H+)-ATPase G subunit / V-type ATPase subunit E / V-type ATPase subunit E, C-terminal domain superfamily / ATP synthase (E/31 kDa) subunit / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2950 / F1F0 ATP synthase subunit B, membrane domain / ATP synthase, E subunit, C-terminal / hypothetical protein PF0899 fold / Vacuolar (H+)-ATPase G subunit / V-type ATPase subunit E / V-type ATPase subunit E, C-terminal domain superfamily / ATP synthase (E/31 kDa) subunit / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
V-type ATP synthase subunit E / V-type ATP synthase, subunit (VAPC-THERM)
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.25 Å
AuthorsStewart, A.G. / Lee, L.K. / Donohoe, M. / Chaston, J.J. / Stock, D.
CitationJournal: Nat Commun / Year: 2012
Title: The dynamic stator stalk of rotary ATPases
Authors: Stewart, A.G. / Lee, L.K. / Donohoe, M. / Chaston, J.J. / Stock, D.
History
DepositionDec 19, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2012Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_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_ref_seq_dif.details / _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: V-type ATP synthase subunit E
B: V-type ATP synthase, subunit (VAPC-THERM)
X: V-type ATP synthase, subunit (VAPC-THERM)
Y: V-type ATP synthase subunit E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,80312
Polymers64,5344
Non-polymers2698
Water1,69394
1
A: V-type ATP synthase subunit E
B: V-type ATP synthase, subunit (VAPC-THERM)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4677
Polymers32,2672
Non-polymers2005
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-87 kcal/mol
Surface area17840 Å2
MethodPISA
2
X: V-type ATP synthase, subunit (VAPC-THERM)
Y: V-type ATP synthase subunit E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3365
Polymers32,2672
Non-polymers693
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-68 kcal/mol
Surface area17450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.510, 208.690, 36.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein V-type ATP synthase subunit E / V-ATPase subunit E


Mass: 20514.387 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: atpE, TTHA1276, vatE / Plasmid: pET Duet-1 MCS2 / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: P74901
#2: Protein V-type ATP synthase, subunit (VAPC-THERM)


Mass: 11752.551 Da / Num. of mol.: 2 / Fragment: N-terminally truncated, UNP residues 17-120
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA1279 / Plasmid: pET Duet-1 MCS1 / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: Q5SIT5
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O

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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: 3.06 Å3/Da / Density % sol: 59.78 % / Mosaicity: 0.6 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM HEPES (pH 7.5), 200mM Calcium acetate, 40% (v/v) PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 3, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionRedundancy: 4.9 % / Av σ(I) over netI: 4.6 / Number: 48607 / Rsym value: 0.137 / D res high: 3.416 Å / D res low: 104.24 Å / Num. obs: 9990 / % possible obs: 91.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
7.85104.9288.110.0570.0574.3
5.557.8590.210.1250.1254.8
4.535.5592.710.1020.1024.9
3.934.539210.1590.1595
3.513.9393.210.3760.3765
3.213.5172.410.5820.5824.7
ReflectionResolution: 2.24→19.67 Å / Num. all: 37768 / Num. obs: 37768 / % possible obs: 97.2 % / Redundancy: 2.5 % / Rsym value: 0.057 / Net I/σ(I): 10.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.25-2.372.50.6690.5331.41391155330.3960.6690.5332.198.7
2.37-2.522.50.4760.3821315852090.2820.4760.382.998.6
2.52-2.692.50.310.2483.11250549140.1820.310.2484.198.4
2.69-2.92.50.2070.1664.61161145840.1210.2070.1665.998.3
2.9-3.182.50.1230.0997.71064242170.0720.1230.099998.2
3.18-3.562.50.0740.0612.5964138390.0430.0740.0614.197.9
3.56-4.112.50.0480.03916.7853633880.0280.0480.03921.796.9
4.11-5.032.40.0360.02920.5674927810.0210.0360.02926.494.6
5.03-7.122.50.0330.02724.2532621700.0190.0330.02724.693.2
7.12-19.6662.40.0190.01539.9277411330.0110.0190.01533.984.4

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Phasing

PhasingMethod: MIRAS
Phasing set
ID
1
2
Phasing MIRResolution: 2.4→72.98 Å / FOM acentric: 0.046 / FOM centric: 0.07 / Reflection acentric: 26979 / Reflection centric: 4176
Phasing MIR der

Native set-ID: 1 / Resolution: 2.4→72.98 Å

IDR cullis acentricR cullis centricDer set-IDReflection acentricReflection centric
ISO_1001267333814
ISO_20.9180.86277791413
Phasing MIR der shell
Highest resolution (Å)Lowest resolution (Å)Der-IDR cullis acentricR cullis centricReflection acentricReflection centric
10.6272.98ISO_100202132
7.5510.62ISO_100465154
6.187.55ISO_100648165
5.366.18ISO_100791182
4.795.36ISO_100879186
4.384.79ISO_1001004186
4.054.38ISO_1001078175
3.794.05ISO_1001249167
3.583.79ISO_1001302177
3.393.58ISO_1001380176
3.233.39ISO_1001487209
3.13.23ISO_1001519198
2.983.1ISO_1001630223
2.872.98ISO_1001657193
2.772.87ISO_1001749223
2.682.77ISO_1001804209
2.62.68ISO_1001868222
2.532.6ISO_1001950213
2.462.53ISO_1001975202
2.42.46ISO_1002096222
10.6272.98ISO_20.4760.455181113
7.5510.62ISO_20.6740.692431134
6.187.55ISO_20.8310.852602145
5.366.18ISO_20.8940.929725158
4.795.36ISO_20.9210.966792161
4.384.79ISO_20.9390.951924159
4.054.38ISO_20.9720.9691044157
3.794.05ISO_20.9710.9811151150
3.583.79ISO_20.9730.9551227154
3.393.58ISO_21.0280.93370282
3.233.39ISO_20000
3.13.23ISO_20000
2.983.1ISO_20000
2.872.98ISO_20000
2.772.87ISO_20000
2.682.77ISO_20000
2.62.68ISO_20000
2.532.6ISO_20000
2.462.53ISO_20000
2.42.46ISO_20000
Phasing MIR shell
Resolution (Å)FOM acentricFOM centricReflection acentricReflection centric
10.62-72.980.7280.474217182
7.55-10.620.5950.348480201
6.18-7.550.4150.263658206
5.36-6.180.2410.181808213
4.79-5.360.1380.101952217
4.38-4.790.0820.0441050211
4.05-4.380.0450.0311110214
3.79-4.050.0240.0181263203
3.58-3.790.0110.0131313216
3.39-3.580.0030.0041393199
3.23-3.39001487209
3.1-3.23001519198
2.98-3.1001630223
2.87-2.98001657193
2.77-2.87001749223
2.68-2.77001804209
2.6-2.68001868222
2.53-2.6001950213
2.46-2.53001975202
2.4-2.46002096222

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
SHARPphasing
SOLOMONphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MIRAS / Resolution: 2.25→19.67 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.901 / WRfactor Rfree: 0.2496 / WRfactor Rwork: 0.2123 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8523 / SU B: 15.09 / SU ML: 0.147 / SU R Cruickshank DPI: 0.0407 / SU Rfree: 0.0477 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2629 1685 5 %RANDOM
Rwork0.2232 ---
obs0.2252 32182 87.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 71.06 Å2 / Biso mean: 13.0229 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-1.92 Å2-0 Å2-0 Å2
2---3.04 Å2-0 Å2
3---1.12 Å2
Refinement stepCycle: LAST / Resolution: 2.25→19.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4015 0 8 94 4117
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224051
X-RAY DIFFRACTIONr_angle_refined_deg1.2241.9875492
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6065572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.24723.934122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.91515668
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6181533
X-RAY DIFFRACTIONr_chiral_restr0.0810.2682
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212926
X-RAY DIFFRACTIONr_mcbond_it1.7721.52864
X-RAY DIFFRACTIONr_mcangle_it3.22924460
X-RAY DIFFRACTIONr_scbond_it5.21631187
X-RAY DIFFRACTIONr_scangle_it8.7724.51031
X-RAY DIFFRACTIONr_rigid_bond_restr2.47234051
LS refinement shellResolution: 2.249→2.307 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 44 -
Rwork0.252 997 -
all-1041 -
obs--36.5 %
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)
10.4659-0.14440.23980.35561.03394.25310.0642-0.11370.1648-0.18160.0487-0.1388-0.4356-0.0898-0.11290.2861-0.00020.08030.26020.01040.261715.6233136.838542.0309
20.0633-0.6571-0.12148.1651.47640.30780.09790.0155-0.0131-0.4798-0.1683-0.0539-0.0712-0.03170.07050.35890.0414-0.00510.2345-0.01670.273420.668274.819420.7856
31.1546-0.1671.36511.4355-1.0824.6740.0464-0.0168-0.0314-0.0766-0.0497-0.02410.0704-0.15890.00330.23880.00030.00310.2601-0.00390.161525.11610.4924.8005
43.214-0.09010.90672.7729-0.57763.73830.0552-0.0314-0.3441-0.07890.15730.21290.2709-0.5375-0.21250.2431-0.0698-0.0340.32560.02550.188320.74024.859126.7736
50.0763-0.0044-0.26915.3909-2.17152.47860.0833-0.0573-0.00230.3011-0.17080.0555-0.1444-0.04620.08750.2638-0.05220.00820.33970.00260.236224.274925.206926.4814
67.0967-8.8369-5.001611.98534.59836.27540.36880.08750.0796-0.4324-0.07930.0366-0.47-0.2685-0.28950.30620.0662-0.02580.302-0.04420.3495-0.5216139.74942.7037
70.6009-2.9513-1.394814.586.98763.53060.07140.0972-0.1687-0.1772-0.44370.8620.1568-0.26630.37220.37760.0172-0.00520.2372-0.04470.31649.8676106.371426.1308
80.9506-3.168-0.725814.65631.88721.2910.23590.20090.0369-0.904-0.58030.2414-0.1217-0.14420.34450.48280.1182-0.07780.2312-0.03170.319519.133861.74839.669
90.80750.0376-0.38634.7534-4.83467.24410.09340.0017-0.0342-0.1552-0.2251-0.4548-0.20460.05720.13170.36420.03540.07520.24370.01260.243229.696328.939713.3015
100.2916-1.744-1.528413.92029.99298.66230.11070.152-0.0955-0.2629-0.45170.8351-0.0721-0.64130.34090.36720.0892-0.15290.252-0.13650.411111.203763.653419.9421
113.2606-6.5627-5.497316.433613.869611.73460.01730.1105-0.6715-0.1905-0.54170.7584-0.1139-0.37420.52450.33040.0376-0.06190.2602-0.09510.39447.153290.917235.014
120.2603-0.1426-0.202611.62932.56020.70070.14210.01060.05280.3223-0.23830.38230.0243-0.08060.09620.2374-0.01120.04510.2431-0.00930.28722.0738127.367149.0117
138.30718.6253-4.624514.6545-3.41182.93230.2427-0.09120.37111.3124-0.21950.86110.13260.0696-0.02320.4673-0.06090.1030.2509-0.01470.415210.4632166.155257.2016
140.301-0.9725-0.34854.73311.57360.62880.04340.0455-0.05770.2343-0.13840.1750.1388-0.02410.09490.2320.0264-0.00350.2381-0.0130.252115.430195.387138.4752
150.58622.6981-0.119217.35980.62670.3228-0.0370.10370.297-0.16320.17391.12140.026-0.0401-0.13690.274-0.00470.07020.19780.03290.52845.3924163.375450.1019
163.28420.1753-1.77784.0179-1.35612.78380.0793-0.09350.0770.3287-0.03690.5904-0.19380.1346-0.04230.24990.00650.01430.2044-0.02570.323215.7874187.698745.9696
170.7351-1.39150.28562.6974-0.33264.09160.0648-0.0339-0.4195-0.15090.12720.9461-0.31970.0309-0.1920.30380.0065-0.10260.23470.10840.720715.8155191.201441.1144
180.93552.3156-0.91266.2108-2.39851.6880.03790.02070.0487-0.1674-0.15790.14940.01910.25630.120.2515-0.0158-0.02380.28280.03370.285516.2599170.486444.4779
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 17
2X-RAY DIFFRACTION2A18 - 90
3X-RAY DIFFRACTION3A91 - 123
4X-RAY DIFFRACTION4A124 - 155
5X-RAY DIFFRACTION5A156 - 188
6X-RAY DIFFRACTION6B20 - 36
7X-RAY DIFFRACTION7B37 - 71
8X-RAY DIFFRACTION8B72 - 101
9X-RAY DIFFRACTION9B102 - 120
10X-RAY DIFFRACTION10X22 - 47
11X-RAY DIFFRACTION11X48 - 63
12X-RAY DIFFRACTION12X64 - 100
13X-RAY DIFFRACTION13X101 - 120
14X-RAY DIFFRACTION14Y2 - 70
15X-RAY DIFFRACTION15Y71 - 94
16X-RAY DIFFRACTION16Y95 - 131
17X-RAY DIFFRACTION17Y132 - 156
18X-RAY DIFFRACTION18Y157 - 188

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  • 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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