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- PDB-5bn4: Structure of a unique ATP synthase NeqA-NeqB in complex with ANP ... -

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Basic information

Entry
Database: PDB / ID: 5bn4
TitleStructure of a unique ATP synthase NeqA-NeqB in complex with ANP from Nanoarcheaum equitans
Components
  • NEQ263
  • V-type ATP synthase alpha chain
KeywordsHYDROLASE / ATP Synthase / Nanoarcheaum equitans / Catalytic core
Function / homology
Function and homology information


ATP biosynthetic process / proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATPase activity, rotational mechanism / H+-transporting two-sector ATPase / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / ATP binding / plasma membrane
Similarity search - Function
NeqB N-terminal domain / Rossmann fold - #12240 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / V-type ATP synthase regulatory subunit B/beta / V-type ATP synthase catalytic alpha chain / ATPsynthase alpha/beta subunit, N-terminal extension / ATPsynthase alpha/beta subunit barrel-sandwich domain / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / : ...NeqB N-terminal domain / Rossmann fold - #12240 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / V-type ATP synthase regulatory subunit B/beta / V-type ATP synthase catalytic alpha chain / ATPsynthase alpha/beta subunit, N-terminal extension / ATPsynthase alpha/beta subunit barrel-sandwich domain / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / A-type ATP synthase subunit A / NEQ263
Similarity search - Component
Biological speciesNanoarchaeum equitans Kin4-M (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.699 Å
AuthorsMohanty, S. / Jobichen, C. / Chichili, V.P.R. / Sivaraman, J.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural Basis for a Unique ATP Synthase Core Complex from Nanoarcheaum equitans
Authors: Mohanty, S. / Jobichen, C. / Chichili, V.P.R. / Velazquez-Campoy, A. / Low, B.C. / Hogue, C.W.V. / Sivaraman, J.
History
DepositionMay 25, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Nov 18, 2015Group: Database references
Revision 1.3Nov 8, 2023Group: 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: V-type ATP synthase alpha chain
B: NEQ263
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,9744
Polymers111,4432
Non-polymers5312
Water5,855325
1
A: V-type ATP synthase alpha chain
B: NEQ263
hetero molecules

A: V-type ATP synthase alpha chain
B: NEQ263
hetero molecules

A: V-type ATP synthase alpha chain
B: NEQ263
hetero molecules


Theoretical massNumber of molelcules
Total (without water)335,92112
Polymers334,3296
Non-polymers1,5926
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area29900 Å2
ΔGint-129 kcal/mol
Surface area98140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.484, 193.484, 108.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
DetailsThe biological assembly is hetero-hexameric

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Components

#1: Protein V-type ATP synthase alpha chain / V-ATPase subunit A


Mass: 64768.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nanoarchaeum equitans Kin4-M (archaea) / Strain: Kin4-M / Gene: atpA, NEQ103
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG
References: UniProt: Q74MJ7, H+-transporting two-sector ATPase
#2: Protein NEQ263 / NeqB


Mass: 46674.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nanoarchaeum equitans Kin4-M (archaea) / Strain: Kin4-M / Gene: NEQ263
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: Q74MS5
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.52 Å3/Da / Density % sol: 65.04 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M MES, 1.6M Ammonium Sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.63→50 Å / Num. obs: 39977 / % possible obs: 99.8 % / Redundancy: 5.7 % / Net I/σ(I): 5.7
Reflection shellResolution: 2.63→2.68 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.8 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GQB

3gqb


Resolution: 2.699→27.37 Å / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 31.05 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2617 2090 5.23 %
Rwork0.2154 --
obs0.2177 39977 95.81 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.204 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--13.1493 Å20 Å20 Å2
2---13.1493 Å20 Å2
3---26.2987 Å2
Refinement stepCycle: LAST / Resolution: 2.699→27.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7674 0 32 325 8031
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027867
X-RAY DIFFRACTIONf_angle_d0.63210648
X-RAY DIFFRACTIONf_dihedral_angle_d11.2322972
X-RAY DIFFRACTIONf_chiral_restr0.0451182
X-RAY DIFFRACTIONf_plane_restr0.0031361
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6999-2.76740.38411310.32632694X-RAY DIFFRACTION89
2.7674-2.84210.37551400.31122628X-RAY DIFFRACTION89
2.8421-2.92570.43831520.3032581X-RAY DIFFRACTION87
2.9257-3.020.39111410.3012674X-RAY DIFFRACTION89
3.02-3.12770.32971400.27582643X-RAY DIFFRACTION90
3.1277-3.25280.34191380.26452678X-RAY DIFFRACTION90
3.2528-3.40050.32591520.24442751X-RAY DIFFRACTION92
3.4005-3.57940.27021330.22172829X-RAY DIFFRACTION94
3.5794-3.80310.25861590.21182790X-RAY DIFFRACTION94
3.8031-4.09580.25141400.19742677X-RAY DIFFRACTION90
4.0958-4.50630.18831480.16662735X-RAY DIFFRACTION91
4.5063-5.15430.22071510.17082704X-RAY DIFFRACTION91
5.1543-6.47880.25331410.2152764X-RAY DIFFRACTION93
6.4788-26.86190.18141470.16452799X-RAY DIFFRACTION94

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