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- PDB-1mhs: Model of Neurospora crassa proton ATPase -

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Basic information

Entry
Database: PDB / ID: 1mhs
TitleModel of Neurospora crassa proton ATPase
ComponentsPlasma Membrane ATPase
KeywordsMEMBRANE PROTEIN / PROTON TRANSPORT / ion transport / proton pump / P-type ATPase / active transport
Function / homology
Function and homology information


P-type H+-exporting transporter / proton export across plasma membrane / P-type proton-exporting transporter activity / proton transmembrane transport / regulation of intracellular pH / ATP hydrolysis activity / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
P-type ATPase, subfamily IIIA / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain / 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, subfamily IIIA / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain / 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
Similarity search - Domain/homology
Plasma membrane ATPase
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 8 Å
AuthorsKuhlbrandt, W.
Citation
Journal: Science / Year: 2002
Title: Structure, mechanism, and regulation of the Neurospora plasma membrane H+-ATPase.
Authors: Werner Kühlbrandt / Johan Zeelen / Jens Dietrich /
Abstract: Proton pumps in the plasma membrane of plants and yeasts maintain the intracellular pH and membrane potential. To gain insight into the molecular mechanisms of proton pumping, we built an atomic ...Proton pumps in the plasma membrane of plants and yeasts maintain the intracellular pH and membrane potential. To gain insight into the molecular mechanisms of proton pumping, we built an atomic homology model of the proton pump based on the 2.6 angstrom x-ray structure of the related Ca2+ pump from rabbit sarcoplasmic reticulum. The model, when fitted to an 8 angstrom map of the Neurospora proton pump determined by electron microscopy, reveals the likely path of the proton through the membrane and shows that the nucleotide-binding domain rotates by approximately 70 degrees to deliver adenosine triphosphate (ATP) to the phosphorylation site. A synthetic peptide corresponding to the carboxyl-terminal regulatory domain stimulates ATPase activity, suggesting a mechanism for proton transport regulation.
#1: Journal: Nature / Year: 1998
Title: Three-dimensional map of the plasma membrane H+-ATPase in the open conformation
Authors: AUER, M. / SCARBOROUGH, G.A. / KUHLBRANDT, W.
History
DepositionAug 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 18, 2018Group: Author supporting evidence / Data collection / Category: em_single_particle_entity / em_software / Item: _em_software.image_processing_id
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation.pdbx_scattering_type
Remark 295 NON-CRYSTALLOGRAPHIC SYMMETRY THE TRANSFORMATIONS PRESENTED ON THE MTRIX RECORDS BELOW DESCRIBE ... NON-CRYSTALLOGRAPHIC SYMMETRY THE TRANSFORMATIONS PRESENTED ON THE MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG ATOMS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. CHAIN IDENTIFIERS GIVEN AS "?" REFER TO CHAINS FOR WHICH ATOMS ARE NOT FOUND IN THE ENTRY. APPLIED TO TRANSFORMED TO TRANSFORM CHAIN RESIDUES CHAIN RESIDUES RMSD SSS M 1 A 1 .. 920 B 1 .. 920 ? WHERE SSS -> COLUMNS 8-10 OF MTRIX RECORDS
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS A PORTION OF THE BIOLOGICALLY SIGNIFICANT MULTIMER. SEE REMARK ...BIOMOLECULE: 1 THIS ENTRY CONTAINS A PORTION OF THE BIOLOGICALLY SIGNIFICANT MULTIMER. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S) ASSEMBLY COMPONENTS COM_ID: 1 NAME:PLASMA MEMBRANE PROTON ATPASE HEXAMERIC ASSEMBLY

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Assembly

Deposited unit
A: Plasma Membrane ATPase
B: Plasma Membrane ATPase


Theoretical massNumber of molelcules
Total (without water)199,9692
Polymers199,9692
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)167.000, 167.000, 250.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (0.5, 0.866), (-0.866, 0.5), (1) / Vector: 84.5, 48.2)

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Components

#1: Protein Plasma Membrane ATPase / Proton pump


Mass: 99984.359 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: isolated from plasma membrane of cultured Neurospora cells
Source: (natural) Neurospora crassa (fungus) / Strain: FGSC 4761 / References: UniProt: P07038, EC: 3.6.3.6

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

Component
IDNameTypeDetailsParent-ID
1Neurospora ATPase hexamer crystalCOMPLEX2D crystals were grown as described in Auer et al, J. Mol. Biol. 287, 961-968 (1999)0
2plasma membrane proton ATPase hexameric assemblyCOMPLEX1
Buffer solutionName: 100 mM ammonium sulphate, Tris-HCl, 30% glycerol, 10.5% PEG 4000
pH: 6.8
Details: 100 mM ammonium sulphate, Tris-HCl, 30% glycerol, 10.5% PEG 4000
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: hydrophobic carbon support film on 400 mesh gold-plated Cu EM grid
VitrificationDetails: 2D crystals were vitrified by immersion in liquid nitrogen
Crystal grow
*PLUS
Method: other / Details: MRC ELECTRON CRYSTALLOGRAPHY

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Data collection

MicroscopyModel: JEOL 3000SFF
Details: Images were also recorded on JEOL 2000 EX and Philips CM200 FEG electron microscopes at 80 K at a dose of 1000 e/nm**2
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 50000 X / Nominal defocus max: 1200 nm / Nominal defocus min: 600 nm / Cs: 1.6 mm
Specimen holderTemperature: 4 K / Tilt angle max: 60 ° / Tilt angle min: 0 °
Image recordingElectron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 60
RadiationScattering type: electron
Radiation wavelengthRelative weight: 1

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Processing

EM softwareName: MRC / Category: 3D reconstruction
CTF correctionDetails: crystallographic
3D reconstructionResolution: 8 Å / Nominal pixel size: 1.4 Å / Actual pixel size: 1.4 Å
Magnification calibration: electron diffraction of standard specimen
Symmetry type: 2D CRYSTAL
Atomic model buildingProtocol: OTHER / Space: REAL / Target criteria: best visual fit using the program o / Details: METHOD--manual REFINEMENT PROTOCOL--manual fit
Atomic model buildingDetails: this entry
RefinementHighest resolution: 8 Å
Refinement stepCycle: LAST / Highest resolution: 8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14082 0 0 0 14082

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