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- PDB-6poj: STRUCTURAL REFINEMENT OF AQUAPORIN 1 VIA SSNMR -

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Basic information

Entry
Database: PDB / ID: 6poj
TitleSTRUCTURAL REFINEMENT OF AQUAPORIN 1 VIA SSNMR
ComponentsAquaporin-1
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


metanephric descending thin limb development / metanephric proximal straight tubule development / metanephric proximal convoluted tubule segment 2 development / metanephric glomerulus vasculature development / hydrogen peroxide channel activity / nitric oxide transmembrane transporter activity / cerebrospinal fluid secretion / lipid digestion / cellular response to salt stress / renal water transport ...metanephric descending thin limb development / metanephric proximal straight tubule development / metanephric proximal convoluted tubule segment 2 development / metanephric glomerulus vasculature development / hydrogen peroxide channel activity / nitric oxide transmembrane transporter activity / cerebrospinal fluid secretion / lipid digestion / cellular response to salt stress / renal water transport / corticotropin secretion / secretory granule organization / carbon dioxide transmembrane transport / carbon dioxide transmembrane transporter activity / glycerol transmembrane transporter activity / water transmembrane transporter activity / renal water absorption / Passive transport by Aquaporins / positive regulation of saliva secretion / establishment or maintenance of actin cytoskeleton polarity / pancreatic juice secretion / lateral ventricle development / glycerol transmembrane transport / cellular response to mercury ion / intracellular water homeostasis / intracellularly cGMP-activated cation channel activity / potassium ion transmembrane transporter activity / transepithelial water transport / water transport / water channel activity / ammonium transmembrane transport / ankyrin-1 complex / ammonium channel activity / glomerular filtration / camera-type eye morphogenesis / fibroblast migration / multicellular organismal-level water homeostasis / cellular homeostasis / cellular hyperosmotic response / hyperosmotic response / cell volume homeostasis / positive regulation of fibroblast migration / odontogenesis / cGMP-mediated signaling / nitric oxide transport / brush border / transmembrane transporter activity / potassium channel activity / renal water homeostasis / cellular response to retinoic acid / cellular response to copper ion / cellular response to cAMP / ephrin receptor binding / sensory perception of pain / cellular response to nitric oxide / cellular response to dexamethasone stimulus / basal plasma membrane / establishment of localization in cell / carbon dioxide transport / wound healing / brush border membrane / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / potassium ion transport / sarcolemma / cellular response to hydrogen peroxide / cellular response to mechanical stimulus / positive regulation of fibroblast proliferation / positive regulation of angiogenesis / Vasopressin regulates renal water homeostasis via Aquaporins / cellular response to UV / apical part of cell / defense response to Gram-negative bacterium / basolateral plasma membrane / cellular response to hypoxia / nuclear membrane / apical plasma membrane / axon / negative regulation of apoptotic process / extracellular exosome / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Aquaporin 1 / Glycerol uptake facilitator protein / Glycerol uptake facilitator protein. / Aquaporin transporter / Major intrinsic protein, conserved site / MIP family signature. / Major intrinsic protein / Major intrinsic protein / Aquaporin-like / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLID-STATE NMR / simulated annealing
AuthorsDingwell, D.A. / Brown, L.S. / Ladizhansky, V.
Funding support Canada, 2items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2014-04547 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2018-04397 Canada
CitationJournal: J.Phys.Chem.B / Year: 2019
Title: Structure of the Functionally Important Extracellular Loop C of Human Aquaporin 1 Obtained by Solid-State NMR under Nearly Physiological Conditions.
Authors: Dingwell, D.A. / Brown, L.S. / Ladizhansky, V.
History
DepositionJul 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aquaporin-1


Theoretical massNumber of molelcules
Total (without water)31,2361
Polymers31,2361
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Aquaporin-1 / AQP-1 / Aquaporin-CHIP / Urine water channel / Water channel protein for red blood cells and kidney ...AQP-1 / Aquaporin-CHIP / Urine water channel / Water channel protein for red blood cells and kidney proximal tubule


Mass: 31235.779 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AQP1, CHIP28 / Plasmid: PPICZB / Production host: Komagataella pastoris (fungus) / Strain (production host): SMD1168H / References: UniProt: P29972

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic1HBR2 3D NCOCX
121anisotropic2HBR2 3D NCOCX

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Sample preparation

DetailsType: solid / Contents: 2 w/v [U-13C; U-15N] AQUAPORIN 1, NMR buffer / Label: UCN_sample / Solvent system: NMR buffer
SampleConc.: 2 w/v / Component: AQUAPORIN 1 / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 10 mM NaCl Not defined / Label: conditions_all / pH: 7 / Pressure: 1 atm / Temperature: 278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.48Schwieters, Kuszewski, Tjandra and Clorerefinement
TopSpinBrukercollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CARAKellerpeak picking
X-PLOR NIH2.48Schwieters, Kuszewski, Tjandra and Clorestructure calculation
CARAKeller and Wuthrichchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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