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- PDB-4csk: human Aquaporin -

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Basic information

Entry
Database: PDB / ID: 4csk
Titlehuman Aquaporin
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.28 Å
AuthorsRuiz-Carrillo, D. / To-Yiu-Ying, J. / Darwis, D. / Soon, C.H. / Cornvik, T. / Torres, J. / Lescar, J.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Crystallization and Preliminary Crystallographic Analysis of Human Aquaporin 1 at a Resolution of 3.28 A.
Authors: Ruiz Carrillo, D. / To Yiu Ying, J. / Darwis, D. / Soon, C.H. / Cornvik, T. / Torres, J. / Lescar, J.
History
DepositionMar 8, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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)31,1661
Polymers31,1661
Non-polymers00
Water1086
1
A: AQUAPORIN-1

A: AQUAPORIN-1

A: AQUAPORIN-1

A: AQUAPORIN-1


Theoretical massNumber of molelcules
Total (without water)124,6634
Polymers124,6634
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465y-1,-x+1,z1
crystal symmetry operation3_665-y+1,x+1,z1
crystal symmetry operation2_575-x,-y+2,z1
Buried area13460 Å2
ΔGint-110.1 kcal/mol
Surface area33210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.280, 89.280, 174.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein AQUAPORIN-1 / AQUAPORIN-CHIP / URINE WATER CHANNEL / WATER CHANNEL PROTEIN FOR RED BLOOD CELLS AND KIDNEY ...AQUAPORIN-CHIP / URINE WATER CHANNEL / WATER CHANNEL PROTEIN FOR RED BLOOD CELLS AND KIDNEY PROXIMAL TUBULE / AQUAPORIN 1 / AQP-1


Mass: 31165.697 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P29972
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.99 % / Description: NONE
Crystal growpH: 9 / Details: pH 9

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Feb 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.28→12.5 Å / Num. obs: 5560 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 25.3 % / Biso Wilson estimate: 103.06 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 22.1
Reflection shellResolution: 3.28→3.67 Å / Redundancy: 16.9 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 3.9 / % possible all: 96.9

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J4N

1j4n


Resolution: 3.28→12.49 Å / Cor.coef. Fo:Fc: 0.9455 / Cor.coef. Fo:Fc free: 0.9538 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.538
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2978 259 4.66 %RANDOM
Rwork0.2338 ---
obs0.2368 5555 99.05 %-
Displacement parametersBiso mean: 197.09 Å2
Baniso -1Baniso -2Baniso -3
1--2.2939 Å20 Å20 Å2
2---2.2939 Å20 Å2
3---4.5877 Å2
Refine analyzeLuzzati coordinate error obs: 1.653 Å
Refinement stepCycle: LAST / Resolution: 3.28→12.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1722 0 0 6 1728
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011755HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.362388HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d575SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes27HARMONIC2
X-RAY DIFFRACTIONt_gen_planes266HARMONIC5
X-RAY DIFFRACTIONt_it1755HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.46
X-RAY DIFFRACTIONt_other_torsion26.19
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion241SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2284SEMIHARMONIC4
LS refinement shellResolution: 3.28→3.67 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2413 77 5.06 %
Rwork0.2392 1445 -
all0.2393 1522 -
obs--99.05 %

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