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- EMDB-14522: The molybdenum storage protein loaded with tungstate -

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Basic information

Entry
Database: EMDB / ID: EMD-14522
TitleThe molybdenum storage protein loaded with tungstate
Map data
Sample
  • Complex: MoSto dodecamer 2 x (AB)3
    • Protein or peptide: x 2 types
  • Ligand: x 9 types
Function / homologyMolybdenum storage protein subunit alpha/beta / nutrient reservoir activity / molybdenum ion binding / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / cytoplasm / Molybdenum storage protein subunit beta / Molybdenum storage protein subunit alpha
Function and homology information
Biological speciesAzotobacter vinelandii DJ (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.58 Å
AuthorsErmler U / Aziz I / Kaltwasser S / Kayastha K / Vonck J
Funding support Germany, 1 items
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, 2022-
Header (metadata) releaseJul 13, 2022-
Map releaseJul 13, 2022-
UpdateJul 13, 2022-
Current statusJul 13, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14522.png

Downloads & links

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Map

FileDownload / File: emd_14522.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 280 pix.
= 232.68 Å		0.83 Å/pix.
x 280 pix.
= 232.68 Å		0.83 Å/pix.
x 280 pix.
= 232.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.831 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0082
Minimum - Maximum-0.011543922 - 0.065977976
Average (Standard dev.)3.0743115e-05 (±0.0017187805)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 232.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14522_msk_1.map
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AxesZYX

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Half map: #2

Fileemd_14522_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_14522_half_map_2.map
Projections & Slices
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Sample components

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Entire : MoSto dodecamer 2 x (AB)3

EntireName: MoSto dodecamer 2 x (AB)3
Components
  • Complex: MoSto dodecamer 2 x (AB)3
    • Protein or peptide: Molybdenum storage protein subunit beta
    • Protein or peptide: Molybdenum storage protein subunit alpha
  • Ligand: MOLYBDATE ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: W11-O35 cluster
  • Ligand: 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
  • Ligand: W8-O26 cluster
  • Ligand: W10-O37 cluster
  • Ligand: tungstate cluster
  • Ligand: W3-O10 cluster

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Supramolecule #1: MoSto dodecamer 2 x (AB)3

SupramoleculeName: MoSto dodecamer 2 x (AB)3 / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Azotobacter vinelandii DJ (bacteria)
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Molecular weightTheoretical: 345 KDa

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Macromolecule #1: Molybdenum storage protein subunit beta

MacromoleculeName: Molybdenum storage protein subunit beta / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Azotobacter vinelandii DJ (bacteria)
Molecular weightTheoretical: 28.247582 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: ANSTAELEEL LMQRSLTDPQ LQAAAAAAAD FRILPDATVI KIGGQSVIDR GRAAVYPLVD EIVAARKNHK LLIGTGAGTR ARHLYSIAA GLGLPAGVLA QLGSSVADQN AAMLGQLLAK HGIPVVGGAG LSAVPLSLAE VNAVVFSGMP PYKLWMRPAA E GVIPPYRT ...String:
ANSTAELEEL LMQRSLTDPQ LQAAAAAAAD FRILPDATVI KIGGQSVIDR GRAAVYPLVD EIVAARKNHK LLIGTGAGTR ARHLYSIAA GLGLPAGVLA QLGSSVADQN AAMLGQLLAK HGIPVVGGAG LSAVPLSLAE VNAVVFSGMP PYKLWMRPAA E GVIPPYRT DAGCFLLAEQ FGCKQMIFVK DEDGLYTANP KTSKDATFIP RISVDEMKAK GLHDSILEFP VLDLLQSAQH VR EVQVVNG LVPGNLTRAL AGEHVGTIIT AS

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Macromolecule #2: Molybdenum storage protein subunit alpha

MacromoleculeName: Molybdenum storage protein subunit alpha / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Azotobacter vinelandii DJ (bacteria) / Strain: DJ / ATCC BAA-1303
Molecular weightTheoretical: 29.245582 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: TDTTNSIKHV ISPLARQTLQ DRDLTRPVAG KRPIRLLPWL QVVKIGGRVM DRGADAILPL VEELRKLLPE HRLLILTGAG VRARHVFSV GLDLGLPVGS LAPLAASEAG QNGHILAAML ASEGVSYVEH PTVADQLAIH LSATRAVVGS AFPPYHHHEF P GSRIPPHR ...String:
TDTTNSIKHV ISPLARQTLQ DRDLTRPVAG KRPIRLLPWL QVVKIGGRVM DRGADAILPL VEELRKLLPE HRLLILTGAG VRARHVFSV GLDLGLPVGS LAPLAASEAG QNGHILAAML ASEGVSYVEH PTVADQLAIH LSATRAVVGS AFPPYHHHEF P GSRIPPHR ADTGAFLLAD AFGAAGLTIV ENVDGIYTAD PNGPDRGQAR FLPETSATDL AKSEGPLPVD RALLDVMATA RH IERVQVV NGLVPGRLTA ALRGEHVGTL IRTGVRPA

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Macromolecule #3: MOLYBDATE ION

MacromoleculeName: MOLYBDATE ION / type: ligand / ID: 3 / Number of copies: 6 / Formula: MOO
Molecular weightTheoretical: 159.938 Da
Chemical component information

ChemComp-MOO:
MOLYBDATE ION / Molybdate

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Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 12 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 12 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: W11-O35 cluster

MacromoleculeName: W11-O35 cluster / type: ligand / ID: 6 / Number of copies: 6 / Formula: IWL
Molecular weightTheoretical: 2.582219 KDa
Chemical component information

ChemComp-IWL:
W11-O35 cluster

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Macromolecule #7: 1,1,3,3,5,7,7,9,11,15,15-undecakis($l^{1}-oxidanyl)-2$l^{4},4$l^{...

MacromoleculeName: 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$l^{3},20,21,22,23-pentadecaoxa- ...Name: 1,1,3,3,5,7,7,9,11,15,15-undecakis($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
type: ligand / ID: 7 / Number of copies: 6 / Formula: IV9
Molecular weightTheoretical: 1.886704 KDa
Chemical component information

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

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Macromolecule #8: W8-O26 cluster

MacromoleculeName: W8-O26 cluster / type: ligand / ID: 8 / Number of copies: 6 / Formula: IWO
Molecular weightTheoretical: 1.886704 KDa
Chemical component information

ChemComp-IWO:
W8-O26 cluster

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Macromolecule #9: W10-O37 cluster

MacromoleculeName: W10-O37 cluster / type: ligand / ID: 9 / Number of copies: 2 / Formula: IWZ
Molecular weightTheoretical: 2.430378 KDa
Chemical component information

ChemComp-IWZ:
W10-O37 cluster

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Macromolecule #10: tungstate cluster

MacromoleculeName: tungstate cluster / type: ligand / ID: 10 / Number of copies: 2 / Formula: IHW
Molecular weightTheoretical: 3.869405 KDa
Chemical component information

ChemComp-IHW:
tungstate cluster

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Macromolecule #11: W3-O10 cluster

MacromoleculeName: W3-O10 cluster / type: ligand / ID: 11 / Number of copies: 2 / Formula: IX3
Molecular weightTheoretical: 711.514 Da
Chemical component information

ChemComp-IX3:
W3-O10 cluster

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 42.6 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6rke

Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Point group: D3 (2x3 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.58 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 674283
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6rke

RefinementProtocol: AB INITIO MODEL
Output model

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

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