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- PDB-4ix9: Crystal structure of subunit F of V-ATPase from S. cerevisiae -

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Basic information

Entry
Database: PDB / ID: 4ix9
TitleCrystal structure of subunit F of V-ATPase from S. cerevisiae
ComponentsV-type proton ATPase subunit F
KeywordsHYDROLASE / V-ATPase / stalk subunit / subunit F / Rossmann fold / Regulatory / coupling
Function / homology
Function and homology information


Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / vacuolar proton-transporting V-type ATPase, V1 domain / endosomal lumen acidification / proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification ...Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / vacuolar proton-transporting V-type ATPase, V1 domain / endosomal lumen acidification / proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification / fungal-type vacuole membrane / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / Golgi membrane / membrane
Similarity search - Function
ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F, eukaryotic / ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F superfamily / ATP synthase (F/14-kDa) subunit / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
V-type proton ATPase subunit F
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.33 Å
AuthorsBasak, S. / Balakrishna, A.M. / Manimekalai, M.S.S. / Gruber, G.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Crystal and NMR structures give insights into the role and dynamics of subunit F of the eukaryotic V-ATPase from Saccharomyces cerevisiae
Authors: Basak, S. / Lim, J. / Manimekalai, M.S.S. / Balakrishna, A.M. / Gruber, G.
History
DepositionJan 24, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: V-type proton ATPase subunit F
B: V-type proton ATPase subunit F
C: V-type proton ATPase subunit F
D: V-type proton ATPase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,99213
Polymers43,0434
Non-polymers9499
Water4,414245
1
A: V-type proton ATPase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0053
Polymers10,7611
Non-polymers2442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: V-type proton ATPase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2516
Polymers10,7611
Non-polymers4915
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: V-type proton ATPase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8532
Polymers10,7611
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: V-type proton ATPase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8832
Polymers10,7611
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.146, 160.312, 102.429
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-102-

TRS

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.99986, 0.007839, 0.014761), (-0.015752, -0.14671, -0.989054), (-0.005588, -0.989148, 0.146813)0.58776, 54.46471, 58.04155
3given(0.999532, -0.025697, 0.016624), (0.015245, -0.052959, -0.99848), (0.026538, 0.998266, -0.052543)-0.92782, 51.24261, -11.3832
4given(-0.990311, -0.095805, -0.100523), (-0.079824, 0.985081, -0.152457), (0.113629, -0.142956, -0.983185)31.98954, 8.99947, 99.83098

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Components

#1: Protein
V-type proton ATPase subunit F / V-ATPase subunit F / V-ATPase 14 kDa subunit / Vacuolar proton pump subunit F


Mass: 10760.775 Da / Num. of mol.: 4
Fragment: Coupling and Regulatory Subunit F, UNP residues 1-94
Mutation: I69M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: VMA7, YGR020C / Plasmid: pET9d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3
References: UniProt: P39111, H+-transporting two-sector ATPase
#2: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.25 Å3/Da / Density % sol: 45.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 30% PEG 4000, 0.05M MgCl2,6H2O, 0.1M Tris HCl pH 8.8, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.978836, 0.978683, 0.963626
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 31, 2012
Details: Vertically Collimating Premirror, Toroidal Focusing Mirror
RadiationMonochromator: Double Crystal Si(111) Monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9788361
20.9786831
30.9636261
ReflectionResolution: 2.33→50 Å / Num. all: 17114 / Num. obs: 17018 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Biso Wilson estimate: 37.6 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 18.8
Reflection shellResolution: 2.33→2.41 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1612 / % possible all: 96.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXCmodel building
SHELXDphasing
SHELXEmodel building
REFMAC5.7.0025refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXCphasing
RefinementMethod to determine structure: MAD / Resolution: 2.33→26.53 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.446 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.402 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21154 862 5.1 %RANDOM
Rwork0.1522 ---
obs0.15523 16138 99.44 %-
all-15276 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.034 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å20 Å20 Å2
2---0.28 Å20 Å2
3---0.93 Å2
Refinement stepCycle: LAST / Resolution: 2.33→26.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2934 0 62 245 3241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.023155
X-RAY DIFFRACTIONr_angle_refined_deg1.7921.974279
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2315388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.68425.749167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.62515548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7531517
X-RAY DIFFRACTIONr_chiral_restr0.1170.2501
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022392
LS refinement shellResolution: 2.328→2.389 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 59 -
Rwork0.197 1128 -
obs--95.49 %

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