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- PDB-2d57: Double layered 2D crystal structure of AQUAPORIN-4 (AQP4M23) at 3... -

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Basic information

Entry
Database: PDB / ID: 2d57
TitleDouble layered 2D crystal structure of AQUAPORIN-4 (AQP4M23) at 3.2 a resolution by electron crystallography
ComponentsAquaporin-4
KeywordsTRANSPORT PROTEIN / WATER TRANSPORT / WATER CHANNEL / AQUAPORIN / TWO-DIMENSIONAL CRYSTAL / MEMBRANE PROTEIN / BACULOVIRUS EXPRESSION SYSTEM
Function / homology
Function and homology information


Passive transport by Aquaporins / cerebrospinal fluid secretion / renal water absorption / regulation of vascular endothelial growth factor production / cerebrospinal fluid circulation / astrocyte end-foot / water channel activity / intracellular water homeostasis / water transport / negative regulation of cell adhesion molecule production ...Passive transport by Aquaporins / cerebrospinal fluid secretion / renal water absorption / regulation of vascular endothelial growth factor production / cerebrospinal fluid circulation / astrocyte end-foot / water channel activity / intracellular water homeostasis / water transport / negative regulation of cell adhesion molecule production / cell projection membrane / multicellular organismal-level water homeostasis / Vasopressin regulates renal water homeostasis via Aquaporins / cellular response to interleukin-6 / negative regulation of interleukin-1 beta production / negative regulation of interleukin-6 production / cellular response to interleukin-1 / response to glucocorticoid / T-tubule / basal plasma membrane / establishment of localization in cell / cellular response to estradiol stimulus / female pregnancy / sensory perception of sound / cellular response to glucose stimulus / sarcolemma / carbon dioxide transport / cellular response to type II interferon / cell-cell adhesion / cell-cell junction / protein homotetramerization / basolateral plasma membrane / endosome membrane / external side of plasma membrane / protein-containing complex / extracellular region / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
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 speciesRattus norvegicus (Norway rat)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / MOLECULAR REPLACEMENT / cryo EM / Resolution: 3.2 Å
AuthorsHiroaki, Y. / Tani, K. / Kamegawa, A. / Gyobu, N. / Nishikawa, K. / Suzuki, H. / Walz, T. / Sasaki, S. / Mitsuoka, K. / Kimura, K. ...Hiroaki, Y. / Tani, K. / Kamegawa, A. / Gyobu, N. / Nishikawa, K. / Suzuki, H. / Walz, T. / Sasaki, S. / Mitsuoka, K. / Kimura, K. / Mizoguchi, A. / Fujiyoshi, Y.
CitationJournal: J Mol Biol / Year: 2006
Title: Implications of the aquaporin-4 structure on array formation and cell adhesion.
Authors: Yoko Hiroaki / Kazutoshi Tani / Akiko Kamegawa / Nobuhiko Gyobu / Kouki Nishikawa / Hiroshi Suzuki / Thomas Walz / Sei Sasaki / Kaoru Mitsuoka / Kazushi Kimura / Akira Mizoguchi / Yoshinori Fujiyoshi /
Abstract: Aquaporin-4 (AQP4) is the predominant water channel in the mammalian brain and an important drug target for treatment of cerebral edema, bipolar disorder and mesial temporal lobe epilepsy. We ...Aquaporin-4 (AQP4) is the predominant water channel in the mammalian brain and an important drug target for treatment of cerebral edema, bipolar disorder and mesial temporal lobe epilepsy. We determined the AQP4 structure by electron crystallography of double-layered, two-dimensional (2D) crystals. The structure allows us to discuss how the expression ratio between the long and short AQP4 splicing variant can determine the size of in vivo orthogonal arrays. Furthermore, AQP4 contains a short 3(10) helix in an extracellular loop, which mediates weak but specific interactions between AQP4 molecules in adjoining membranes. This finding suggests a previously unexpected role for AQP4 in cell adhesion. This notion was corroborated by expression of AQP4 in L-cells, which resulted in clustering of the cells. Our AQP4 structure thus enables us to propose models for the size regulation of orthogonal arrays and channel-mediated cell adhesion.
History
DepositionOct 29, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 18, 2018Group: Author supporting evidence / Data collection / Database references
Category: database_2 / diffrn_source ...database_2 / diffrn_source / em_image_scans / em_imaging / em_single_particle_entity
Item: _diffrn_source.type / _em_imaging.details
Revision 1.4Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_vitrification / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 240 EXPERIMENT TYPE : ELECTRON DIFFRACTION DATE OF DATA COLLECTION : 01-APR-2002 TEMPERATURE (KELVIN) : ... EXPERIMENT TYPE : ELECTRON DIFFRACTION DATE OF DATA COLLECTION : 01-APR-2002 TEMPERATURE (KELVIN) : 4.2 PH : 6.00 NUMBER OF CRYSTALS USED : 135 RADIATION SOURCE : JEM3000SFF OPTICS : CRYSTALS TILTED TO MAX 60 DEGREES DETECTOR TYPE : CCD DETECTOR MANUFACTURER : GATAN ULTRASCAN INTENSITY INTEGRATION SOFTWARE : PICKYCOR, AN MRC ELECTRON DIFFRACTION PROGRAM DATA SCALING SOFTWARE : MERGEDIFF,AN MRC ELECTRON DIFFRACTION PROGRAM ACCELERATION VOLTAGE (KV) : 300 NUMBER OF UNIQUE REFLECTIONS : 5992 RESOLUTION RANGE HIGH (A) : 3.20 RESOLUTION RANGE LOW (A) : 22.21 OVERALL. COMPLETENESS FOR RANGE (%) : 87.0 DATA REDUNDANCY : NULL R MERGE (I) : 0.223 R SYM (I) : NULL FOR THE DATA SET : NULL IN THE HIGHEST RESOLUTION SHELL. HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.20 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.40 COMPLETENESS FOR SHELL (%) : 85.8 DATA REDUNDANCY IN SHELL : NULL R MERGE FOR SHELL (I) : 0.445 R SYM FOR SHELL (I) : NULL FOR SHELL : NULL METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT SOFTWARE USED: CNS STARTING MODEL: PDB ENTRY 1J4N

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Assembly

Deposited unit
A: Aquaporin-4


Theoretical massNumber of molelcules
Total (without water)32,1891
Polymers32,1891
Non-polymers00
Water0
1
A: Aquaporin-4

A: Aquaporin-4

A: Aquaporin-4

A: Aquaporin-4


Theoretical massNumber of molelcules
Total (without water)128,7584
Polymers128,7584
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area13010 Å2
ΔGint-133 kcal/mol
Surface area30580 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)69.000, 69.000, 160.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein Aquaporin-4 / / AQP-4 / WCH4 / Mercurial-insensitive water channel / MIWC


Mass: 32189.381 Da / Num. of mol.: 1 / Fragment: residues 23-323
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Aqp4 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P47863

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY / Number of used crystals: 1
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: AQUAPORIN 4 CRYSTAL / Type: COMPLEX
SpecimenEmbedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
EM embeddingDetails: 7% trehalose / Material: trehalose
CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.41 %
Crystal growTemperature: 293 K / Method: dialysys / pH: 6
Details: 10mM MES(pH 6.0), 100mM NaCl, 50mM MgCl2, 2mM DTT, 1% glycerol, dialysys, temperature 293K

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Data collection

MicroscopyModel: JEOL 3000SFF / Details: diffraction and images
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION
Specimen holderCryogen: HELIUM
DiffractionMean temperature: 4.2 K
Ambient temp details: data was collected by electron microscope equipped with a helium stage
Diffraction sourceSource: ELECTRON MICROSCOPE / Wavelength: 0.01968 Å
DetectorType: GATAN ULTRASCAN / Detector: CCD / Date: Apr 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: electron
Radiation wavelengthWavelength: 0.01968 Å / Relative weight: 1
ReflectionResolution: 3.2→22.21 Å / Num. all: 6888 / Num. obs: 5992 / % possible obs: 87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.223
Reflection shellResolution: 3.2→3.4 Å / Rmerge(I) obs: 0.445 / % possible all: 85.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
MRCdata reduction
MRCdata scaling
CNSphasing
3D reconstructionSymmetry type: 2D CRYSTAL
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J4N
Resolution: 3.2→22.21 Å / Rfactor Rfree error: 0.018 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.338 337 5.6 %RANDOM
Rwork0.283 ---
all0.286 6888 --
obs0.283 5992 87 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 83.0511 Å2 / ksol: 0.147131 e/Å3
Displacement parametersBiso mean: 53.7 Å2
Baniso -1Baniso -2Baniso -3
1--25.43 Å20 Å20 Å2
2---25.43 Å20 Å2
3---50.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.63 Å0.48 Å
Luzzati d res low-5 Å
Luzzati sigma a0.77 Å0.65 Å
Refinement stepCycle: LAST / Resolution: 3.2→22.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1659 0 0 0 1659
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
ELECTRON CRYSTALLOGRAPHYc_bond_d0.011
ELECTRON CRYSTALLOGRAPHYc_angle_deg1.6
ELECTRON CRYSTALLOGRAPHYc_dihedral_angle_d19.1
ELECTRON CRYSTALLOGRAPHYc_improper_angle_d1.1
ELECTRON CRYSTALLOGRAPHYc_mcbond_it10.91.5
ELECTRON CRYSTALLOGRAPHYc_mcangle_it16.92
ELECTRON CRYSTALLOGRAPHYc_scbond_it13.552
ELECTRON CRYSTALLOGRAPHYc_scangle_it19.192.5
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.387 63 6.6 %
Rwork0.34 891 -
obs-891 85.8 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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