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- PDB-4efa: Crystal Structure of the Heterotrimeric EGChead Peripheral Stalk ... -

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Basic information

Entry
Database: PDB / ID: 4efa
TitleCrystal Structure of the Heterotrimeric EGChead Peripheral Stalk Complex of the Yeast Vacuolar ATPase - second conformation
Components
  • V-type proton ATPase subunit C
  • V-type proton ATPase subunit E
  • V-type proton ATPase subunit G
KeywordsHYDROLASE / heterotrimer / peripheral stalk / vacuolar ATPase
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 / membrane raft / Golgi membrane / ATP hydrolysis activity / ATP binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2950 / ATP synthase, E subunit, C-terminal / hypothetical protein PF0899 fold / ATPase, V1 complex, subunit C / Vacuolar ATP synthase subunit C superfamily / V-ATPase subunit C / Vacuolar (H+)-ATPase G subunit / Vacuolar (H+)-ATPase G subunit / V-type ATPase subunit E / V-type ATPase subunit E, C-terminal domain superfamily ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2950 / ATP synthase, E subunit, C-terminal / hypothetical protein PF0899 fold / ATPase, V1 complex, subunit C / Vacuolar ATP synthase subunit C superfamily / V-ATPase subunit C / Vacuolar (H+)-ATPase G subunit / Vacuolar (H+)-ATPase G subunit / V-type ATPase subunit E / V-type ATPase subunit E, C-terminal domain superfamily / ATP synthase (E/31 kDa) subunit / Alpha-Beta Plaits - #100 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
V-type proton ATPase subunit E / V-type proton ATPase subunit C / V-type proton ATPase subunit G
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8163 Å
AuthorsOot, R.A. / Huang, L.S. / Berry, E.A. / Wilkens, S.
CitationJournal: Structure / Year: 2012
Title: Crystal Structure of the Yeast Vacuolar ATPase Heterotrimeric EGC(head) Peripheral Stalk Complex.
Authors: Oot, R.A. / Huang, L.S. / Berry, E.A. / Wilkens, S.
History
DepositionMar 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 13, 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 / database_2 / pdbx_initial_refinement_model / 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_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

Downloads & links

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Assembly

Deposited unit
C: V-type proton ATPase subunit C
G: V-type proton ATPase subunit G
E: V-type proton ATPase subunit E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6977
Polymers54,3133
Non-polymers3844
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7370 Å2
ΔGint-113 kcal/mol
Surface area27150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.537, 93.648, 116.891
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein V-type proton ATPase subunit C / V-ATPase subunit C / V-ATPase 42 kDa subunit / Vacuolar proton pump subunit C


Mass: 14586.475 Da / Num. of mol.: 1 / Fragment: UNP Residues 158-277
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: VAT3, VATC, VMA5, YKL080W, YKL410 / Plasmid: pMALc2e / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2
References: UniProt: P31412, H+-transporting two-sector ATPase
#2: Protein V-type proton ATPase subunit G / V-ATPase subunit G / V-ATPase 13 kDa subunit / Vacuolar proton pump subunit G


Mass: 13218.298 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: VMA10, YHR039BC, YHR039C-A, YHR039C-B / Plasmid: pMALc2e / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2
References: UniProt: P48836, H+-transporting two-sector ATPase
#3: Protein V-type proton ATPase subunit E / V-ATPase subunit E / V-ATPase 27 kDa subunit / Vacuolar proton pump subunit E


Mass: 26508.393 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: O6241, VAT5, VMA4, YOR332W / Plasmid: pMALc2e / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2
References: UniProt: P22203, H+-transporting two-sector ATPase
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.6 Å3/Da / Density % sol: 52.63 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M lithium sulfate, 0.1 M MES, 20% PEG mme 2000, 0.15 M glycine , pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 22, 2011
Diffraction measurementDetails: 1.00 degrees, 15.0 sec, detector distance 380.00 mm
Method: omega scans
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionAv R equivalents: 0.143 / Number: 198487
ReflectionResolution: 2.8→40 Å / Num. all: 14238 / Num. obs: 14187 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.9 % / Rmerge(I) obs: 0.132 / Rsym value: 0.132 / Net I/σ(I): 35.089
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0 / Mean I/σ(I) obs: 2.306 / Rsym value: 0 / % possible all: 100
Cell measurementReflection used: 198487

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.82 Å38.66 Å
Translation2.82 Å38.66 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.0phasing
PHENIXdev_1012refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4DL0

4dl0


Resolution: 2.8163→38.655 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.38 / σ(F): 1.34 / Phase error: 30.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2767 1418 10 %random using lattice symmetry
Rwork0.2295 ---
obs0.2345 14187 99.3 %-
all-14238 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.287 Å2 / ksol: 0.327 e/Å3
Displacement parametersBiso max: 222.28 Å2 / Biso mean: 93.5261 Å2 / Biso min: 22.53 Å2
Baniso -1Baniso -2Baniso -3
1--6.3956 Å20 Å20 Å2
2--1.4884 Å2-0 Å2
3---4.9071 Å2
Refinement stepCycle: LAST / Resolution: 2.8163→38.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3385 0 20 24 3429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023433
X-RAY DIFFRACTIONf_angle_d0.4994606
X-RAY DIFFRACTIONf_chiral_restr0.035535
X-RAY DIFFRACTIONf_plane_restr0.002588
X-RAY DIFFRACTIONf_dihedral_angle_d7.8511353
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8163-2.91690.37151350.33581209134497
2.9169-3.03370.34341420.299712801422100
3.0337-3.17170.35921380.294212401378100
3.1717-3.33880.33971410.275512761417100
3.3388-3.54790.29641400.266512571397100
3.5479-3.82160.27991390.23411255139499
3.8216-4.20570.28971400.22231273141399
4.2057-4.81330.23671440.182912931437100
4.8133-6.06050.25271460.216813121458100
6.0605-38.65870.24731530.2061374152799
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)
15.6385-0.08140.17376.2732.95752.22640.07310.07760.8719-0.58090.4371-0.3993-0.54030.7007-0.51510.3554-0.13730.06470.8351-0.21510.5409-107.073112.0629156.929
24.1943-1.3203-2.18855.67740.76182.34240.47950.2443-0.1795-0.4895-0.2378-0.38860.05220.4799-0.21590.43710.01710.00060.6996-0.16080.3726-94.385693.1442158.5256
33.5113-0.6646-2.39113.78362.24179.51460.3839-0.10220.09810.27130.5024-0.1802-0.12870.30880.62110.48-0.19730.08250.2648-0.06020.2761-97.0799103.9559161.5372
47.7832-1.1011-2.28769.18472.34437.37550.0717-0.1257-0.560.25410.2879-0.59890.340.4446-0.24390.2122-0.0206-0.07170.4095-0.04330.2632-97.364388.4772162.8563
57.55330.4285-1.72827.4716-2.33882.00010.10421.5409-0.4933-0.95380.10750.84130.9183-0.428-0.66010.5827-0.1489-0.41271.15-0.09370.8406-103.405890.2892151.7954
61.06150.0220.27095.28926.6038.240.1349-0.1573-0.1098-0.81820.2542-0.7028-0.33250.5039-0.2340.4539-0.02410.03690.7731-0.21150.5782-84.160158.69131.2477
70.11050.0637-0.06570.5885-1.0671.9453-0.00950.2170.06750.52010.8007-0.60180.84981.5896-0.85490.79080.3043-0.36070.998-0.22111.0301-83.2142-17.0127100.5418
80.50450.0336-0.04574.67463.68142.83410.18620.1253-0.20271.59450.2772-0.38421.23030.2963-0.43950.92870.1679-0.27710.8053-0.19410.5954-87.131536.4746125.9122
92.13271.3832-0.01341.2121-0.89813.4620.04040.7469-0.3634-0.21450.5276-0.53720.77450.4626-0.55750.940.3108-0.16760.7459-0.21840.7934-96.1882-28.588875.1828
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 158:172 )C0
2X-RAY DIFFRACTION2chain 'C' and (resid 173:222 )C0
3X-RAY DIFFRACTION3chain 'C' and (resid 223:230 )C0
4X-RAY DIFFRACTION4chain 'C' and (resid 231:258 )C0
5X-RAY DIFFRACTION5chain 'C' and (resid 259:263 )C0
6X-RAY DIFFRACTION6chain 'G' and (resid 2:60 )G0
7X-RAY DIFFRACTION7chain 'G' and (resid 61:105 )G0
8X-RAY DIFFRACTION8chain 'E' and (resid 2:111 )E0
9X-RAY DIFFRACTION9chain 'E' and (resid 112:226 )E0

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