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- PDB-4rnd: Crystal Structure of the subunit DF-assembly of the eukaryotic V-... -

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Basic information

Entry
Database: PDB / ID: 4rnd
TitleCrystal Structure of the subunit DF-assembly of the eukaryotic V-ATPase.
Components
  • V-type proton ATPase subunit D
  • V-type proton ATPase subunit F
KeywordsHYDROLASE / alpha helical / 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 / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification / proton-transporting V-type ATPase complex ...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 / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification / proton-transporting V-type ATPase complex / fungal-type vacuole membrane / Neutrophil degranulation / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / membrane raft / Golgi membrane / membrane
Similarity search - Function
ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F, eukaryotic / ATPase, V1 complex, subunit D / ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F superfamily / ATP synthase subunit D / ATP synthase (F/14-kDa) subunit / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
V-type proton ATPase subunit D / V-type proton ATPase subunit F
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.18 Å
AuthorsBalakrishna, A.M. / Basak, S. / Gruber, G.
Citation
Journal: J.Biol.Chem. / Year: 2015
Title: Crystal Structure of Subunits D and F in Complex Gives Insight into Energy Transmission of the Eukaryotic V-ATPase from Saccharomyces cerevisiae.
Authors: Balakrishna, A.M. / Basak, S. / Manimekalai, M.S. / Gruber, G.
#1: Journal: 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. / Balakrishna, A.M. / Gruber, G.
History
DepositionOct 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: 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 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: V-type proton ATPase subunit D
B: V-type proton ATPase subunit F
C: V-type proton ATPase subunit D
D: V-type proton ATPase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,7057
Polymers85,4284
Non-polymers2763
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15200 Å2
ΔGint-110 kcal/mol
Surface area28100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.063, 168.063, 128.629
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUARGARGAA37 - 20237 - 202
21GLUGLUARGARGCC37 - 20237 - 202
12ALAALALEULEUBB2 - 1152 - 115
22ALAALALEULEUDD2 - 1152 - 115

NCS ensembles :
ID
1
2

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Components

#1: Protein V-type proton ATPase subunit D / V-ATPase subunit D / Vacuolar proton pump subunit D


Mass: 29235.023 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: SYGP-ORF11, VMA8, YEL051W / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P32610
#2: Protein V-type proton ATPase subunit F / V-ATPase subunit F / V-ATPase 14 kDa subunit / Vacuolar proton pump subunit F


Mass: 13479.170 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: VMA7, YGR020C / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P39111
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 6.14 Å3/Da / Density % sol: 79.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M sodium citrate tribasic dehydrate, 1.2 M Ammonium citrate monobasic, ph 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 22, 2014
Details: Vertically Collimating Premirror, Toroidal Focusing Mirror
RadiationMonochromator: Double Crystal Si(111) Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3.18→30 Å / Num. all: 38345 / Num. obs: 33061 / % possible obs: 80.08 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 11.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.1
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 1.2 / % possible all: 98.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3.18→29.63 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.895 / SU B: 20.993 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23201 1010 3 %RANDOM
Rwork0.20365 ---
obs0.20448 33061 97.83 %-
all-38345 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.757 Å2
Baniso -1Baniso -2Baniso -3
1--7.23 Å2-0 Å2-0 Å2
2---7.23 Å2-0 Å2
3---14.46 Å2
Refinement stepCycle: LAST / Resolution: 3.18→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4664 0 18 59 4741
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194753
X-RAY DIFFRACTIONr_bond_other_d0.0040.024637
X-RAY DIFFRACTIONr_angle_refined_deg1.1251.9636405
X-RAY DIFFRACTIONr_angle_other_deg0.946310636
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8545576
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.69324.049247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.94615884
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9861546
X-RAY DIFFRACTIONr_chiral_restr0.060.2734
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025355
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021099
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A80250.17
12C80250.17
21B60480.15
22D60480.15
LS refinement shellResolution: 3.177→3.259 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 46 -
Rwork0.3 1879 -
obs--75.52 %
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)
12.28661.40910.04450.91620.04670.0219-0.0240.0311-0.21320.05180.0295-0.11890.0153-0.0056-0.00560.1634-0.0687-0.04660.23630.03630.1454-19.880267.58759.7277
21.27330.91990.83422.47581.07421.06290.1536-0.2535-0.07620.4124-0.11030.0610.1542-0.0761-0.04340.2927-0.1465-0.00340.2370.06490.0305-11.258176.933321.8969
33.13850.967-0.15690.3486-0.09510.1116-0.03530.249-0.02160.05240.0721-0.0318-0.007-0.0599-0.03680.17-0.0511-0.01920.17180.03310.1382-54.827453.27889.5829
42.2117-0.58840.07071.5551-0.10631.0174-0.08860.22810.2562-0.07210.1323-0.0431-0.1812-0.0541-0.04370.1658-0.094-0.04470.18780.11830.1099-69.624457.13982.6872
500000000000000-00.16000.1600.16000
600000000000000-00.16000.1600.16000
700000000000000-00.16000.1600.16000
800000000000000-00.16000.1600.16000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 204
2X-RAY DIFFRACTION2B1 - 118
3X-RAY DIFFRACTION3C37 - 203
4X-RAY DIFFRACTION4D2 - 116
5X-RAY DIFFRACTION5A401 - 423
6X-RAY DIFFRACTION5B301 - 312
7X-RAY DIFFRACTION5C401 - 417
8X-RAY DIFFRACTION5D201 - 210
9X-RAY DIFFRACTION6A301
10X-RAY DIFFRACTION7C301
11X-RAY DIFFRACTION8B201

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