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- PDB-5bn3: Structure of a unique ATP synthase NeqA-NeqB in complex with ADP ... -

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Basic information

Entry
Database: PDB / ID: 5bn3
TitleStructure of a unique ATP synthase NeqA-NeqB in complex with ADP 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 / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / ATP binding
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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / 1,4-DIETHYLENE DIOXIDE / V-type ATP synthase alpha chain / V-type ATP synthase beta chain
Similarity search - Component
Biological speciesNanoarchaeum equitans Kin4-M (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_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 alpha chain
B: NEQ263
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,43724
Polymers111,4432
Non-polymers1,99422
Water7,710428
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)340,31272
Polymers334,3296
Non-polymers5,98366
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 area43570 Å2
ΔGint-166 kcal/mol
Surface area94560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.459, 192.459, 110.241
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
DetailsThe biological assembly provided by author is hetero-hexameric

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Components

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Protein , 2 types, 2 molecules AB

#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

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Non-polymers , 6 types, 450 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H8O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 3.53 Å3/Da / Density % sol: 65.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M MES, 1.6M Ammonium Phosphate

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9897 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: 0.9897 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 102518 / % possible obs: 99.8 % / Redundancy: 5.5 % / Net I/σ(I): 37.12
Reflection shellResolution: 2→2.03 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.87 / % possible all: 98.5

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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→30.649 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 21.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2096 1767 1.72 %
Rwork0.1842 --
obs0.1846 102518 99.64 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.197 Å2 / ksol: 0.358 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.8777 Å20 Å20 Å2
2---3.8777 Å20 Å2
3---7.7555 Å2
Refinement stepCycle: LAST / Resolution: 2→30.649 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7586 0 127 428 8141
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097866
X-RAY DIFFRACTIONf_angle_d0.8610651
X-RAY DIFFRACTIONf_dihedral_angle_d13.6822983
X-RAY DIFFRACTIONf_chiral_restr0.0571187
X-RAY DIFFRACTIONf_plane_restr0.0031339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05410.25091360.23587624X-RAY DIFFRACTION97
2.0541-2.11450.2461210.23827736X-RAY DIFFRACTION100
2.1145-2.18280.27761380.23157753X-RAY DIFFRACTION100
2.1828-2.26070.21751400.22317798X-RAY DIFFRACTION100
2.2607-2.35120.22451320.20987746X-RAY DIFFRACTION100
2.3512-2.45820.23381430.21017781X-RAY DIFFRACTION100
2.4582-2.58770.22871310.20737756X-RAY DIFFRACTION100
2.5877-2.74980.23761460.2057771X-RAY DIFFRACTION100
2.7498-2.96190.23361410.20087785X-RAY DIFFRACTION100
2.9619-3.25970.19731300.19447788X-RAY DIFFRACTION100
3.2597-3.73070.24891330.16997746X-RAY DIFFRACTION100
3.7307-4.69750.15731400.14747791X-RAY DIFFRACTION100
4.6975-30.6530.19871360.17667676X-RAY DIFFRACTION99

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