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- PDB-2xqu: Microscopic rotary mechanism of ion translocation in the Fo compl... -

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Basic information

Entry
Database: PDB / ID: 2xqu
TitleMicroscopic rotary mechanism of ion translocation in the Fo complex of ATP synthases
ComponentsATP SYNTHASE C CHAIN
KeywordsMEMBRANE PROTEIN / F1FO-ATP SYNTHASE ROTOR / C-RING / ION (PROTON / H+)-TRANSLOCATION / N / N'- DICYCLOHEXYLCARBODIIMIDE (DCCD) INHIBITOR
Function / homology
Function and homology information


plasma membrane-derived thylakoid membrane / proton-transporting ATP synthase complex, coupling factor F(o) / membrane => GO:0016020 / proton-transporting ATP synthase activity, rotational mechanism / 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
CYMAL-4 / ATP synthase subunit c
Similarity search - Component
Biological speciesARTHROSPIRA PLATENSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsPogoryelov, D. / Krah, A. / Langer, J. / Yildiz, O. / Faraldo-Gomez, J.D. / Meier, T.
CitationJournal: Nat.Chem.Biol. / Year: 2010
Title: Microscopic Rotary Mechanism of Ion Translocation in the Fo Complex of ATP Synthases
Authors: Pogoryelov, D. / Krah, A. / Langer, J. / Yildiz, O. / Faraldo-Gomez, J.D. / Meier, T.
History
DepositionSep 7, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP SYNTHASE C CHAIN
B: ATP SYNTHASE C CHAIN
C: ATP SYNTHASE C CHAIN
D: ATP SYNTHASE C CHAIN
E: ATP SYNTHASE C CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,48860
Polymers41,0585
Non-polymers26,43055
Water2,162120
1
A: ATP SYNTHASE C CHAIN
B: ATP SYNTHASE C CHAIN
C: ATP SYNTHASE C CHAIN
D: ATP SYNTHASE C CHAIN
E: ATP SYNTHASE C CHAIN
hetero molecules

A: ATP SYNTHASE C CHAIN
B: ATP SYNTHASE C CHAIN
C: ATP SYNTHASE C CHAIN
D: ATP SYNTHASE C CHAIN
E: ATP SYNTHASE C CHAIN
hetero molecules

A: ATP SYNTHASE C CHAIN
B: ATP SYNTHASE C CHAIN
C: ATP SYNTHASE C CHAIN
D: ATP SYNTHASE C CHAIN
E: ATP SYNTHASE C CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,463180
Polymers123,17315
Non-polymers79,290165
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area66550 Å2
ΔGint-568.2 kcal/mol
Surface area37710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.890, 93.890, 257.320
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11C-2001-

HOH

21C-2017-

HOH

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Components

#1: Protein
ATP SYNTHASE C CHAIN / C15_RING


Mass: 8211.530 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) ARTHROSPIRA PLATENSIS (bacteria) / References: UniProt: D5A0Q7
#2: Chemical...
ChemComp-CVM / CYMAL-4 / 4-CYCLOHEXYLBUTYL 4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE


Mass: 480.546 Da / Num. of mol.: 55 / Source method: obtained synthetically / Formula: C22H40O11
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.99 Å3/Da / Density % sol: 69.15 % / Description: NONE
Crystal growpH: 4.3 / Details: pH 4.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8551
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 3, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8551 Å / Relative weight: 1
ReflectionResolution: 1.84→40 Å / Num. obs: 58617 / % possible obs: 99.1 % / Observed criterion σ(I): 1.8 / Redundancy: 12.9 % / Biso Wilson estimate: 24.97 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 13.5
Reflection shellResolution: 1.84→2 Å / Redundancy: 10.9 % / Rmerge(I) obs: 1.32 / Mean I/σ(I) obs: 1.8 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WIE

2wie


Resolution: 1.84→43.486 Å / SU ML: 0.19 / σ(F): 1.99 / Phase error: 23.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2235 2930 5 %
Rwork0.1892 --
obs0.1909 58555 98.99 %
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.448 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 40.21 Å2
Baniso -1Baniso -2Baniso -3
1-7.0892 Å20 Å20 Å2
2--7.0892 Å20 Å2
3----14.1783 Å2
Refinement stepCycle: LAST / Resolution: 1.84→43.486 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2885 0 560 120 3565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063555
X-RAY DIFFRACTIONf_angle_d0.8924722
X-RAY DIFFRACTIONf_dihedral_angle_d20.1981550
X-RAY DIFFRACTIONf_chiral_restr0.055601
X-RAY DIFFRACTIONf_plane_restr0.005517
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.87010.38481270.3812421X-RAY DIFFRACTION93
1.8701-1.90240.34991320.32122501X-RAY DIFFRACTION96
1.9024-1.9370.34321360.32782586X-RAY DIFFRACTION99
1.937-1.97420.28821370.2832607X-RAY DIFFRACTION100
1.9742-2.01450.31961380.26772614X-RAY DIFFRACTION100
2.0145-2.05830.31390.25262645X-RAY DIFFRACTION100
2.0583-2.10620.26121380.2272618X-RAY DIFFRACTION100
2.1062-2.15890.2241390.19872629X-RAY DIFFRACTION100
2.1589-2.21730.22591380.19042623X-RAY DIFFRACTION100
2.2173-2.28250.25541370.19272606X-RAY DIFFRACTION99
2.2825-2.35620.18681400.16212665X-RAY DIFFRACTION100
2.3562-2.44040.20691390.14882626X-RAY DIFFRACTION100
2.4404-2.53810.18081410.14492687X-RAY DIFFRACTION100
2.5381-2.65360.17621390.13872645X-RAY DIFFRACTION100
2.6536-2.79350.19431410.14822671X-RAY DIFFRACTION100
2.7935-2.96840.20441410.15882679X-RAY DIFFRACTION100
2.9684-3.19760.18431420.15942693X-RAY DIFFRACTION100
3.1976-3.51920.18671420.15982710X-RAY DIFFRACTION100
3.5192-4.02810.18271450.15292754X-RAY DIFFRACTION100
4.0281-5.07380.21231460.15822774X-RAY DIFFRACTION99
5.0738-43.49790.26371530.25962871X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: -45.613 Å / Origin y: 7.0081 Å / Origin z: 30.7214 Å
111213212223313233
T0.2434 Å20.0043 Å20.0187 Å2-0.0963 Å2-0.0155 Å2--0.1857 Å2
L0.5951 °20.0386 °2-0.0237 °2-0.5217 °20.0736 °2--0.6954 °2
S0 Å °-0.0188 Å °-0.1113 Å °-0.0586 Å °-0.0272 Å °0.0018 Å °0.2209 Å °0.0192 Å °0.0243 Å °
Refinement TLS groupSelection details: ALL

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