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- PDB-8ofy: Molecular Mechanism of trypanosomal AQP2 -

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Basic information

Entry
Database: PDB / ID: 8ofy
TitleMolecular Mechanism of trypanosomal AQP2
ComponentsAquaglyceroporin 2
KeywordsMEMBRANE PROTEIN / Aquaporin / Tetramer / Drug Uptake / Glycerol
Function / homology
Function and homology information


glycerol channel activity / urea transmembrane transporter activity / urea transmembrane transport / glycerol transmembrane transport / water transport / water channel activity / membrane / plasma membrane
Similarity search - Function
: / Major intrinsic protein / Major intrinsic protein / Aquaporin-like
Similarity search - Domain/homology
1,5-BIS(4-AMIDINOPHENOXY)PENTANE / Aquaglyceroporin-2
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsWeyand, S.N. / Matusevicius, M. / Yamashita, K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust101234/Z/13/Z United Kingdom
CitationJournal: To Be Published
Title: Molecular Mechanism of trypanosomal AQP2
Authors: Weyand, S.N.
History
DepositionMar 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aquaglyceroporin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9552
Polymers33,6151
Non-polymers3401
Water00
1
A: Aquaglyceroporin 2
hetero molecules

A: Aquaglyceroporin 2
hetero molecules

A: Aquaglyceroporin 2
hetero molecules

A: Aquaglyceroporin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,8208
Polymers134,4594
Non-polymers1,3624
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
point symmetry operation3
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(-1), (1), (1)333.44
3generate(-1), (-1), (1)333.44, 333.44
4generate(1), (-1), (1)333.44

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Components

#1: Protein Aquaglyceroporin 2


Mass: 33614.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Pentamidine / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: aqp2 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6ZXT3
#2: Chemical ChemComp-PNT / 1,5-BIS(4-AMIDINOPHENOXY)PENTANE


Mass: 340.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H24N4O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, Antimicrobial*YM
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: Aquaporin 2 tetramer wildtype / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.22 MDa / Experimental value: YES
Source (natural)Organism: Trypanosoma brucei (eukaryote)
Source (recombinant)Organism: Spodoptera (butterflies/moths)
Buffer solutionpH: 7.2 / Details: 20 mM HEPES 100 mM NaCl
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMSodium ChlorideNaCl1
220 mMHEPESC8H18N2O4S1
SpecimenConc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Monodisperse
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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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 defocus max: 3000 nm / Nominal defocus min: 1000 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 56 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: REFMAC / Version: 5.8.0403 / Classification: refinement
EM software
IDNameCategory
2EPUimage acquisition
4GctfCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 100075
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 83845 / Num. of class averages: 6 / Symmetry type: POINT
Atomic model buildingSpace: RECIPROCAL
RefinementResolution: 3.7→3.7 Å / Cor.coef. Fo:Fc: 0.905 / SU B: 23.466 / SU ML: 0.354 / ESU R: 0.371
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.35826 --
obs0.35826 28598 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 167.337 Å2
Refinement stepCycle: 1 / Total: 1855
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0060.0111913
ELECTRON MICROSCOPYr_bond_other_d00.0161820
ELECTRON MICROSCOPYr_angle_refined_deg1.5251.6182610
ELECTRON MICROSCOPYr_angle_other_deg0.5851.5644154
ELECTRON MICROSCOPYr_dihedral_angle_1_deg6.435243
ELECTRON MICROSCOPYr_dihedral_angle_2_deg5.853
ELECTRON MICROSCOPYr_dihedral_angle_3_deg16.07610255
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.0690.2289
ELECTRON MICROSCOPYr_gen_planes_refined0.0070.022201
ELECTRON MICROSCOPYr_gen_planes_other0.0030.02469
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it16.8915.709975
ELECTRON MICROSCOPYr_mcbond_other16.88115.718976
ELECTRON MICROSCOPYr_mcangle_it25.75528.3881217
ELECTRON MICROSCOPYr_mcangle_other25.7928.4071218
ELECTRON MICROSCOPYr_scbond_it19.79917.972938
ELECTRON MICROSCOPYr_scbond_other19.78817.983939
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other31.18432.1481394
ELECTRON MICROSCOPYr_long_range_B_refined43.804380.5731766
ELECTRON MICROSCOPYr_long_range_B_other43.803380.5731767
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.5→3.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork2.463 2120 -
obs--100 %

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