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- PDB-2o98: Structure of the 14-3-3 / H+-ATPase plant complex -

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Basic information

Entry
Database: PDB / ID: 2o98
TitleStructure of the 14-3-3 / H+-ATPase plant complex
Components
  • 14-3-3-like protein C
  • Plasma membrane H+ ATPase
KeywordsPROTEIN BINDING / H / ATPase / 14-3-3 / plasma membrane / electrochemical proton gradient / cell turgor / regulation
Function / homology
Function and homology information


P-type H+-exporting transporter / proton export across plasma membrane / P-type proton-exporting transporter activity / membrane => GO:0016020 / signal transduction / ATP hydrolysis activity / ATP binding / membrane / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Helix Hairpins - #890 / P-type ATPase, subfamily IIIA / 14-3-3 domain / Delta-Endotoxin; domain 1 / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / Helix Hairpins / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site ...Helix Hairpins - #890 / P-type ATPase, subfamily IIIA / 14-3-3 domain / Delta-Endotoxin; domain 1 / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / Helix Hairpins / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / Helix non-globular / Special / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
FUSICOCCIN / 14-3-3-like protein C / Plasma membrane ATPase 3 / Plasma membrane H+ ATPase
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco)
Nicotiana plumbaginifolia (curled-leaved tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsOttmann, C. / Weyand, M. / Wittinghofer, A. / Oecking, C.
CitationJournal: Mol.Cell / Year: 2007
Title: Structure of a 14-3-3 coordinated hexamer of the plant plasma membrane H+ -ATPase by combining X-ray crystallography and electron cryomicroscopy
Authors: Ottmann, C. / Marco, S. / Jaspert, N. / Marcon, C. / Schauer, N. / Weyand, M. / Vandermeeren, C. / Duby, G. / Boutry, M. / Wittinghofer, A. / Rigaud, J.L. / Oecking, C.
History
DepositionDec 13, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Nov 10, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / 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
Revision 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 14-3-3-like protein C
B: 14-3-3-like protein C
P: Plasma membrane H+ ATPase
Q: Plasma membrane H+ ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4998
Polymers66,9464
Non-polymers1,5544
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10660 Å2
ΔGint-73 kcal/mol
Surface area27590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.370, 114.370, 236.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein 14-3-3-like protein C / 14-3-3 isoform C / 14-3-3-like protein B


Mass: 27428.959 Da / Num. of mol.: 2 / Fragment: residues 1-242
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: P93343
#2: Protein Plasma membrane H+ ATPase / H-ATPASE PMA2


Mass: 6043.797 Da / Num. of mol.: 2 / Fragment: C-terminal region / Mutation: T439D,V440I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana plumbaginifolia (curled-leaved tobacco)
Gene: pma2 / Plasmid: pTYB12 / Production host: Escherichia coli (E. coli) / References: UniProt: Q40409, UniProt: Q08436*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-FSC / FUSICOCCIN / Fusicoccin


Mass: 680.823 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C36H56O12
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.73 Å3/Da / Density % sol: 54.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 14, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.7→103.14 Å / Num. all: 21892 / Num. obs: 21892 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 6.53 % / Biso Wilson estimate: 54.4 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.086 / Net I/σ(I): 16.48
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 4.05 / Num. unique all: 2216 / Rsym value: 0.504 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345CCDdata collection
XDSdata reduction
XSCALEdata scaling
AMoREphasing
RefinementResolution: 2.7→15 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.901 / SU B: 21.918 / SU ML: 0.231 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.851 / ESU R Free: 0.347 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26276 1095 5 %RANDOM
Rwork0.17846 ---
obs0.18247 20797 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.612 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2---0.09 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4580 0 106 127 4813
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224738
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.681.9996407
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.575572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.97224.632231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.14615864
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6891536
X-RAY DIFFRACTIONr_chiral_restr0.110.2734
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023508
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2390.22396
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.23274
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3570.2220
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3190.272
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2340.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6861.52918
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.22224571
X-RAY DIFFRACTIONr_scbond_it2.06832012
X-RAY DIFFRACTIONr_scangle_it3.4714.51834
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 79 -
Rwork0.205 1504 -
obs--100 %
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)
12.58730.79680.41953.4341-0.69582.61350.0569-0.0787-0.3074-0.00020.0318-0.08650.10170.1345-0.0887-0.21360.07670.03-0.3761-0.0173-0.18376.171974.0506115.9065
22.9983-0.85961.01813.1568-0.44162.7517-0.01660.7170.0743-0.556-0.0709-0.12940.01330.33910.08750.0302-0.09770.03280.01740.0466-0.2481-5.000191.416286.2053
34.4069-2.0345-0.80172.2826-0.63710.901-0.1207-0.2174-0.18890.12040.05560.31260.2321-0.19910.0652-0.13520.0337-0.0354-0.26190.0241-0.1766-12.454783.8805115.1604
46.5705-0.43960.29833.91760.84616.3626-0.0289-0.0306-0.1034-0.0838-0.10810.1827-0.1785-0.13860.1369-0.1501-0.0057-0.104-0.31430.0828-0.3278-14.008292.8949104.5243
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 2412 - 241
2X-RAY DIFFRACTION2BB4 - 2404 - 240
3X-RAY DIFFRACTION3PC905 - 9561 - 52
4X-RAY DIFFRACTION4QD907 - 9563 - 52

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