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- PDB-1h6i: A REFINED STRUCTURE OF HUMAN AQUAPORIN 1 -

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Basic information

Entry
Database: PDB / ID: 1h6i
TitleA REFINED STRUCTURE OF HUMAN AQUAPORIN 1
ComponentsAQUAPORIN-1
KeywordsMEMBRANE PROTEIN / WATER CHANNEL / TWO-DIMENSIONAL CRYSTAL
Function / homology
Function and homology information


nitric oxide transmembrane transporter activity / metanephric descending thin limb development / metanephric proximal straight tubule development / metanephric proximal convoluted tubule segment 2 development / metanephric glomerulus vasculature development / cerebrospinal fluid secretion / lipid digestion / cellular response to salt stress / renal water transport / glycerol transmembrane transporter activity ...nitric oxide transmembrane transporter activity / metanephric descending thin limb development / metanephric proximal straight tubule development / metanephric proximal convoluted tubule segment 2 development / metanephric glomerulus vasculature development / cerebrospinal fluid secretion / lipid digestion / cellular response to salt stress / renal water transport / glycerol transmembrane transporter activity / corticotropin secretion / secretory granule organization / carbon dioxide transmembrane transport / carbon dioxide transmembrane transporter activity / renal water absorption / positive regulation of saliva secretion / Passive transport by Aquaporins / glycerol transmembrane transport / water transmembrane transporter activity / establishment or maintenance of actin cytoskeleton polarity / pancreatic juice secretion / lateral ventricle development / cellular response to mercury ion / potassium ion transmembrane transporter activity / water channel activity / intracellular water homeostasis / cellular response to inorganic substance / intracellularly cGMP-activated cation channel activity / ammonium transmembrane transport / water transport / transepithelial water transport / glomerular filtration / ankyrin-1 complex / ammonium transmembrane transporter activity / camera-type eye morphogenesis / multicellular organismal-level water homeostasis / fibroblast migration / cellular homeostasis / cellular hyperosmotic response / hyperosmotic response / renal water homeostasis / cell volume homeostasis / positive regulation of fibroblast migration / odontogenesis / nitric oxide transport / cGMP-mediated signaling / potassium channel activity / brush border / transmembrane transporter activity / cellular response to nitric oxide / cellular response to retinoic acid / cellular response to cAMP / sensory perception of pain / cellular response to copper ion / ephrin receptor binding / cellular response to dexamethasone stimulus / basal plasma membrane / establishment of localization in cell / brush border membrane / sarcolemma / carbon dioxide transport / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / wound healing / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / potassium ion transport / cellular response to hydrogen peroxide / Vasopressin regulates renal water homeostasis via Aquaporins / cellular response to mechanical stimulus / cellular response to UV / positive regulation of angiogenesis / positive regulation of fibroblast proliferation / apical part of cell / cellular response to hypoxia / basolateral plasma membrane / nuclear membrane / defense response to Gram-negative bacterium / 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)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 3.54 Å
AuthorsDe Groot, B.L. / Engel, A. / Grubmuller, H.
Citation
Journal: FEBS Lett / Year: 2001
Title: A refined structure of human aquaporin-1.
Authors: B L de Groot / A Engel / H Grubmüller /
Abstract: A refined structure of the human water channel aquaporin-1 is presented. The model rests on the high resolution X-ray structure of the homologous bacterial glycerol transporter GlpF, electron ...A refined structure of the human water channel aquaporin-1 is presented. The model rests on the high resolution X-ray structure of the homologous bacterial glycerol transporter GlpF, electron crystallographic data at 3.8 A resolution and a multiple sequence alignment of the aquaporin superfamily. The crystallographic R and free R values (36.7% and 37.8%) for the refined structure are significantly lower than for previous models. Improved geometry and enhanced stability in molecular dynamics simulations demonstrate a significant improvement of the aquaporin-1 structure. Comparison with previous aquaporin-1 models shows significant differences, not only in the loop regions, but also in the core of the water channel.
#1: Journal: J Mol Biol / Year: 2000
Title: The fold of human aquaporin 1.
Authors: B L de Groot / J B Heymann / A Engel / K Mitsuoka / Y Fujiyoshi / H Grubmüller /
Abstract: The fold of human aquaporin 1 is determined from cryo-electron microscopic data at 4.5 A resolution. The monomeric structure consists of two transmembrane triple helices arranged around a pseudo-2- ...The fold of human aquaporin 1 is determined from cryo-electron microscopic data at 4.5 A resolution. The monomeric structure consists of two transmembrane triple helices arranged around a pseudo-2-fold axis connected by a long flexible extracellular loop. Each triplet contains between its second and third helix a functional loop containing the highly conserved fingerprint NPA motif. These functional loops are assumed to fold inwards between the two triplets, thereby forming the heart of the water channel. The helix topology was determined from the directionality pattern of each of the six transmembrane helices with respect to the membrane, together with constraints defined by the sequence and atomic force microscopy data. The directionality of the helices was determined by collecting the best-fitting orientations resulting from a search through the three-dimensional experimental map for a large number of alpha-helical fragments. Tests on cryo-electron crystallographic bacteriorhodopsin data suggest that our method is generally applicable to determine the topology of helical proteins for which only medium-resolution electron microscopy data are available.
History
DepositionJun 15, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

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Assembly

Deposited unit
A: AQUAPORIN-1


Theoretical massNumber of molelcules
Total (without water)28,5501
Polymers28,5501
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)99.580, 99.580, 100.000
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-1 /


Mass: 28549.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell: ERYTHROCYTE / References: UniProt: P29972

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: HUMAN AQUAPORIN 1Aquaporin-1 / Type: COMPLEX
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES

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Data collection

MicroscopyModel: JEOL 3000SFF
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION
DetectorDate: Jun 7, 1996
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: CNS / Version: 1 / Classification: refinement
3D reconstructionSymmetry type: 2D CRYSTAL
RefinementStarting model: THE MODEL WAS DERIVED USING ELECTRON DIFFRACTION DATA ON 2D CRYSTALS

Resolution: 3.54→30.04 Å / Rfactor Rfree error: 0.017 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.376 514 9.5 %RANDOM
Rwork0.364 ---
obs0.364 5408 82.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 18.5467 Å2 / ksol: 0.09599202 e/Å3
Displacement parametersBiso mean: 44.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.79 Å0.79 Å
Luzzati d res low-6 Å
Luzzati sigma a0.89 Å1 Å
Refinement stepCycle: LAST / Resolution: 3.54→30.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1653 0 0 0 1653
Refine LS restraints
Refine-IDTypeDev ideal
ELECTRON CRYSTALLOGRAPHYc_bond_d0.008
ELECTRON CRYSTALLOGRAPHYc_bond_d_na
ELECTRON CRYSTALLOGRAPHYc_bond_d_prot
ELECTRON CRYSTALLOGRAPHYc_angle_d
ELECTRON CRYSTALLOGRAPHYc_angle_d_na
ELECTRON CRYSTALLOGRAPHYc_angle_d_prot
ELECTRON CRYSTALLOGRAPHYc_angle_deg1.6
ELECTRON CRYSTALLOGRAPHYc_angle_deg_na
ELECTRON CRYSTALLOGRAPHYc_angle_deg_prot
ELECTRON CRYSTALLOGRAPHYc_dihedral_angle_d20.4
ELECTRON CRYSTALLOGRAPHYc_dihedral_angle_d_na
ELECTRON CRYSTALLOGRAPHYc_dihedral_angle_d_prot
ELECTRON CRYSTALLOGRAPHYc_improper_angle_d1.65
ELECTRON CRYSTALLOGRAPHYc_improper_angle_d_na
ELECTRON CRYSTALLOGRAPHYc_improper_angle_d_prot
ELECTRON CRYSTALLOGRAPHYc_mcbond_it
ELECTRON CRYSTALLOGRAPHYc_mcangle_it
ELECTRON CRYSTALLOGRAPHYc_scbond_it
ELECTRON CRYSTALLOGRAPHYc_scangle_it
LS refinement shellResolution: 3.5→3.72 Å / Rfactor Rfree error: 0.058 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.428 54 10.9 %
Rwork0.431 443 -
obs--44.9 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

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