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- EMDB-16863: Molecular Mechanism of trypanosomal AQP2 -

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Basic information

Entry
Database: EMDB / ID: EMD-16863
TitleMolecular Mechanism of trypanosomal AQP2
Map data
Sample
  • Complex: Aquaporin 2 tetramer wildtype
    • Protein or peptide: Aquaglyceroporin 2
  • Ligand: 1,5-BIS(4-AMIDINOPHENOXY)PENTANE
KeywordsAquaporin / Tetramer / Drug Uptake / Glycerol / MEMBRANE PROTEIN
Function / homology
Function and homology information


glycerol channel activity / urea transmembrane transporter activity / urea transmembrane transport / glycerol transmembrane transport / water channel activity / water transport / membrane
Similarity search - Function
: / Major intrinsic protein / Major intrinsic protein / Aquaporin-like
Similarity search - Domain/homology
Biological speciesTrypanosoma brucei (eukaryote) / Trypanosoma brucei brucei (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsWeyand SN / Matusevicius M / Yamashita K
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust101234/Z/13/Z United Kingdom
CitationJournal: To Be Published
Title: Molecular Mechanism of trypanosomal AQP2
Authors: Weyand SN
History
DepositionMar 17, 2023-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateOct 2, 2024-
Current statusOct 2, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16863.png

Downloads & links

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Map

FileDownload / File: emd_16863.map.gz / Format: CCP4 / Size: 9.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 134 pix.
= 139.628 Å		1.04 Å/pix.
x 134 pix.
= 139.628 Å		1.04 Å/pix.
x 134 pix.
= 139.628 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.042 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.8
Minimum - Maximum-6.0193944 - 7.6156206
Average (Standard dev.)-0.023292592 (±0.42445332)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin939393
Dimensions134134134
Spacing134134134
CellA=B=C: 139.628 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16863_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_16863_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_16863_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Aquaporin 2 tetramer wildtype

EntireName: Aquaporin 2 tetramer wildtype
Components
  • Complex: Aquaporin 2 tetramer wildtype
    • Protein or peptide: Aquaglyceroporin 2
  • Ligand: 1,5-BIS(4-AMIDINOPHENOXY)PENTANE

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Supramolecule #1: Aquaporin 2 tetramer wildtype

SupramoleculeName: Aquaporin 2 tetramer wildtype / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Trypanosoma brucei (eukaryote)
Molecular weightTheoretical: 220 KDa

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Macromolecule #1: Aquaglyceroporin 2

MacromoleculeName: Aquaglyceroporin 2 / type: protein_or_peptide / ID: 1 / Details: Pentamidine / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote)
Molecular weightTheoretical: 33.614645 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MQSQPDNVAY PMELQAVNKD GTVEVRVQGN VDNSSNERWD ADVQKHEVAE AQEKPVGGIN FWAPRELRLN YRDYVAEFLG NFVLIYIAK GAVITSLLVP DFGLLGLTIG IGVAVTMALY VSLGISGGHL NSAVTVGNAV FGDFPWRKVP GYIAAQMLGT F LGAACAYG ...String:
MQSQPDNVAY PMELQAVNKD GTVEVRVQGN VDNSSNERWD ADVQKHEVAE AQEKPVGGIN FWAPRELRLN YRDYVAEFLG NFVLIYIAK GAVITSLLVP DFGLLGLTIG IGVAVTMALY VSLGISGGHL NSAVTVGNAV FGDFPWRKVP GYIAAQMLGT F LGAACAYG VFADLLKAHG GGELIAFGEK GIAWVFAMYP AEGNGIFYPI FAELISTAVL LLCVCGIFDP NNSPAKGYET VA IGALVFV MVNNFGLASP LAMNPSLDFG PRVFGAILLG GEVFSHANYY FWVPLVVPFF GAILGLFLYK YFLPH

UniProtKB: Aquaglyceroporin-2

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Macromolecule #2: 1,5-BIS(4-AMIDINOPHENOXY)PENTANE

MacromoleculeName: 1,5-BIS(4-AMIDINOPHENOXY)PENTANE / type: ligand / ID: 2 / Number of copies: 1 / Formula: PNT
Molecular weightTheoretical: 340.419 Da
Chemical component information

ChemComp-PNT:
1,5-BIS(4-AMIDINOPHENOXY)PENTANE / medication, Antimicrobial*YM

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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

Concentration0.8 mg/mL
BufferpH: 7.2
Component:
ConcentrationFormulaName
100.0 mMNaClSodium Chloride
20.0 mMC8H18N2O4SHEPES

Details: 20 mM HEPES 100 mM NaCl
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsMonodisperse

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 56.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 100075
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 6 / Applied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 83845
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Details: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Details: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: RECIPROCAL
Output model

PDB-8ofy:
Molecular Mechanism of trypanosomal AQP2

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