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- PDB-7z5j: The molybdenum storage protein loaded with tungstate -

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Basic information

Entry
Database: PDB / ID: 7z5j
TitleThe molybdenum storage protein loaded with tungstate
Components(Molybdenum storage protein subunit ...) x 2
KeywordsMETAL BINDING PROTEIN / Metal storage protein / polytungstate / Keggin ion / EM
Function / homology
Function and homology information


nutrient reservoir activity / molybdenum ion binding / cytoplasm
Similarity search - Function
Molybdenum storage protein subunit alpha/beta / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / tungstate cluster / Chem-IV9 / W11-O35 cluster / W8-O26 cluster / W10-O37 cluster / W3-O10 cluster / MOLYBDATE ION / Molybdenum storage protein subunit beta / Molybdenum storage protein subunit alpha
Similarity search - Component
Biological speciesAzotobacter vinelandii DJ (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.58 Å
AuthorsErmler, U. / Aziz, I. / Kaltwasser, S. / Kayastha, K. / Vonck, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
Alexander von Humboldt Foundation Germany
CitationJournal: J Inorg Biochem / Year: 2022
Title: The molybdenum storage protein forms and deposits distinct polynuclear tungsten oxygen aggregates.
Authors: Iram Aziz / Susann Kaltwasser / Kanwal Kayastha / Radhika Khera / Janet Vonck / Ulrich Ermler /
Abstract: Some N-fixing bacteria store Mo to maintain the formation of the vital FeMo-cofactor dependent nitrogenase under Mo depleting conditions. The Mo storage protein (MoSto), developed for this purpose, ...Some N-fixing bacteria store Mo to maintain the formation of the vital FeMo-cofactor dependent nitrogenase under Mo depleting conditions. The Mo storage protein (MoSto), developed for this purpose, has the unique capability to compactly deposit molybdate as polyoxometalate (POM) clusters in a (αβ) hexameric cage; the same occurs with the physicochemically related tungstate. To explore the structural diversity of W-based POM clusters, MoSto loaded under different conditions with tungstate and two site-specifically modified MoSto variants were structurally characterized by X-ray crystallography or single-particle cryo-EM. The MoSto cage contains five major locations for POM clusters occupied among others by heptanuclear, Keggin ion and even Dawson-like species also found in bulk solvent under defined conditions. We found both lacunary derivatives of these archetypical POM clusters with missing WO units at positions exposed to bulk solvent and expanded derivatives with additional WO units next to protecting polypeptide segments or other POM clusters. The cryo-EM map, unexpectedly, reveals a POM cluster in the cage center anchored to the wall by a WO linker. Interestingly, distinct POM cluster structures can originate from identical, highly occupied core fragments of three to seven WO units that partly correspond to those found in MoSto loaded with molybdate. These core fragments are firmly bound to the complementary protein template in contrast to the more variable, less occupied residual parts of the visible POM clusters. Due to their higher stability, W-based POM clusters are, on average, larger and more diverse than their Mo-based counterparts.
History
DepositionMar 9, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_initial_refinement_model
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Molybdenum storage protein subunit beta
A: Molybdenum storage protein subunit alpha
D: Molybdenum storage protein subunit beta
C: Molybdenum storage protein subunit alpha
F: Molybdenum storage protein subunit beta
E: Molybdenum storage protein subunit alpha
H: Molybdenum storage protein subunit beta
I: Molybdenum storage protein subunit alpha
J: Molybdenum storage protein subunit beta
G: Molybdenum storage protein subunit alpha
L: Molybdenum storage protein subunit beta
K: Molybdenum storage protein subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)404,45366
Polymers344,95912
Non-polymers59,49454
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area90150 Å2
ΔGint-608 kcal/mol
Surface area86930 Å2
MethodPISA

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Components

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Molybdenum storage protein subunit ... , 2 types, 12 molecules BDFHJLACEIGK

#1: Protein
Molybdenum storage protein subunit beta / MoSto subunit beta


Mass: 28247.582 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii DJ (bacteria) / Gene: mosB, Avin_43210
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P84253
#2: Protein
Molybdenum storage protein subunit alpha / Mo storage protein subunit alpha / MoSto subunit alpha


Mass: 29245.582 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii DJ (bacteria) / Strain: DJ / ATCC BAA-1303 / Gene: mosA, Avin_43200
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P84308

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Non-polymers , 9 types, 54 molecules

#3: Chemical
ChemComp-MOO / MOLYBDATE ION / MOLYBDATE


Mass: 159.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: MoO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-IWL / W11-O35 cluster


Mass: 2582.219 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: O35W11 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-IV9 / 1,1,3,3,5,7,7,9,11,15,15-undecakis($l^{1}-oxidanyl)-2$l^{4},4$l^{3},6$l^{5},8,10,12,14,16,17,18,19$l^{3},20,21,22,23-pentadecaoxa-1$l^{6},3$l^{6},5$l^{6},7$l^{6},9$l^{6},11$l^{6},13$l^{6},15$l^{6}-octatungstapentadecacyclo[7.7.1.1^{1,13}.1^{3,5}.1^{3,15}.1^{5,7}.1^{5,11}.1^{7,11}.0^{2,13}.0^{2,15}.0^{4,13}.0^{6,9}.0^{6,11}.0^{6,13}.0^{9,19}]tricosane


Mass: 1886.704 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: O26W8 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-IWO / W8-O26 cluster


Mass: 1886.704 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: O26W8 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-IWZ / W10-O37 cluster


Mass: 2430.378 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O37W10 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-IHW / tungstate cluster


Mass: 3869.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O58W16 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-IX3 / W3-O10 cluster


Mass: 711.514 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O10W3 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: MoSto dodecamer 2 x (AB)3 / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.345 MDa / Experimental value: NO
Source (natural)Organism: Azotobacter vinelandii DJ (bacteria)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2100 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 42.6 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
2EPUimage acquisition
7RELIONmodel fitting
13RELIONmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D3 (2x3 fold dihedral)
3D reconstructionResolution: 2.58 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 674283 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Atomic model buildingPDB-ID: 6RKE

6rke


Accession code: 6RKE / Source name: PDB / Type: experimental model

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