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- PDB-2wie: High-resolution structure of the rotor ring from a proton depende... -

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Basic information

Entry
Database: PDB / ID: 2wie
TitleHigh-resolution structure of the rotor ring from a proton dependent ATP synthase
ComponentsATP SYNTHASE C CHAIN
KeywordsHYDROLASE / F1FO ATP SYNTHASE ROTOR / ION PROTON-TRANSLOCATION / ION TRANSPORT / TRANSMEMBRANE / C-RING STRUCTURE / SPIRULINA PLATENSIS / HYDROGEN ION TRANSPORT / MEMBRANE PROTEIN COMPLEX / CF(0) / MEMBRANE / LIPID-BINDING
Function / homology
Function and homology information


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
CYMAL-4 / ATP synthase subunit c
Similarity search - Component
Biological speciesARTHROSPIRA PLATENSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsPogoryelov, D. / Yildiz, O. / Faraldo-Gomez, J.D. / Meier, T.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: High-Resolution Structure of the Rotor Ring of a Proton-Dependent ATP Synthase.
Authors: Pogoryelov, D. / Yildiz, O. / Faraldo-Gomez, J.D. / Meier, T.
History
DepositionMay 11, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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

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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)60,27945
Polymers41,0585
Non-polymers19,22240
Water2,270126
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)180,838135
Polymers123,17315
Non-polymers57,666120
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 area63580 Å2
ΔGint-595.5 kcal/mol
Surface area36400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.360, 93.360, 257.400
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
11D-2001-

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: A5HEI4, H+-transporting two-sector ATPase
#2: Chemical...
ChemComp-CVM / CYMAL-4 / 4-CYCLOHEXYLBUTYL 4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE


Mass: 480.546 Da / Num. of mol.: 40 / Source method: obtained synthetically / Formula: C22H40O11
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 3.41 Å3/Da / Density % sol: 68 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9202
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9202 Å / Relative weight: 1
ReflectionResolution: 2.13→20 Å / Num. obs: 37848 / % possible obs: 99.2 % / Observed criterion σ(I): 1.74 / Redundancy: 4.7 % / Biso Wilson estimate: 26.49 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 9.6
Reflection shellResolution: 2.13→20 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 1.7 / % possible all: 96.7

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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 1YCE

1yce


Resolution: 2.13→45.931 Å / SU ML: 0 / σ(F): 1.99 / Phase error: 22.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2349 1892 5 %
Rwork0.1965 --
obs0.1984 37792 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 103.494 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.485 Å20 Å2-0 Å2
2--1.485 Å20 Å2
3----13.9754 Å2
Refinement stepCycle: LAST / Resolution: 2.13→45.931 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2885 0 375 126 3386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063307
X-RAY DIFFRACTIONf_angle_d0.9444421
X-RAY DIFFRACTIONf_dihedral_angle_d20.7241299
X-RAY DIFFRACTIONf_chiral_restr0.053557
X-RAY DIFFRACTIONf_plane_restr0.005510
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.18320.351240.29912349X-RAY DIFFRACTION94
2.1832-2.24220.291320.26172517X-RAY DIFFRACTION99
2.2422-2.30820.30871320.23562504X-RAY DIFFRACTION100
2.3082-2.38270.25181330.21652532X-RAY DIFFRACTION100
2.3827-2.46790.26041340.20012543X-RAY DIFFRACTION100
2.4679-2.56670.22111330.17242530X-RAY DIFFRACTION100
2.5667-2.68350.22971350.16622548X-RAY DIFFRACTION100
2.6835-2.82490.21131340.16472553X-RAY DIFFRACTION100
2.8249-3.00190.17521350.16552570X-RAY DIFFRACTION100
3.0019-3.23360.20161360.15972574X-RAY DIFFRACTION100
3.2336-3.55890.16481360.16072580X-RAY DIFFRACTION100
3.5589-4.07360.20471380.15572636X-RAY DIFFRACTION100
4.0736-5.13130.21261390.17972655X-RAY DIFFRACTION99
5.1313-45.94150.31341510.27152809X-RAY DIFFRACTION98
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)
10.5013-0.11170.00390.5320.13060.49960.10410.0217-0.1023-0.02650.01770.06280.2141-0.0838-0.07720.2254-0.041-0.02060.1822-0.02410.2296-63.1059.915432.0774
20.5869-0.0754-0.22150.10280.03610.93670.0481-0.0515-0.1102-0.0291-0.05430.08930.2989-0.15960.01650.2791-0.0441-0.00770.1124-0.020.1866-54.72444.758531.7332
30.5065-0.04310.13120.2426-0.47280.46170.0453-0.0172-0.1046-0.02930.02080.07190.48810.1125-0.03010.33210.00590.0160.1414-0.01670.206-44.99753.384431.7024
40.46370.2237-0.02380.56350.04870.08910.0403-0.039-0.1119-0.0330.0935-0.04560.19560.0385-0.07880.26240.04310.0270.1345-0.01140.1995-35.56046.148531.7579
50.69780.15760.03170.939-0.40020.20080-0.0504-0.0912-0.04520.036-0.08320.25190.0814-0.01370.17730.03950.04160.195-0.0030.2184-28.058512.448931.7342
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E

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