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- PDB-3gd8: Crystal Structure of Human Aquaporin 4 at 1.8 and its Mechanism o... -

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Basic information

Entry
Database: PDB / ID: 3gd8
TitleCrystal Structure of Human Aquaporin 4 at 1.8 and its Mechanism of Conductance
ComponentsAquaporin-4
KeywordsMEMBRANE PROTEIN / brain edema / aquaporin / proton exclusion / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for Structures of Membrane Proteins / CSMP / Glycoprotein / Membrane / Phosphoprotein / Transmembrane / Transport
Function / homology
Function and homology information


: / Passive transport by Aquaporins / cerebrospinal fluid circulation / astrocyte end-foot / intracellular water homeostasis / water transport / water channel activity / multicellular organismal-level water homeostasis / renal water homeostasis / plasma membrane => GO:0005886 ...: / Passive transport by Aquaporins / cerebrospinal fluid circulation / astrocyte end-foot / intracellular water homeostasis / water transport / water channel activity / multicellular organismal-level water homeostasis / renal water homeostasis / plasma membrane => GO:0005886 / sarcolemma / Vasopressin regulates renal water homeostasis via Aquaporins / cellular response to type II interferon / basolateral plasma membrane / protein homotetramerization / membrane => GO:0016020 / endosome membrane / external side of plasma membrane / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHo, J.D. / Yeh, R. / Sandstrom, A. / Chorny, I. / Harries, W.E.C. / Robbins, R.A. / Miercke, L.J.W. / Stroud, R.M. / Center for Structures of Membrane Proteins (CSMP)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Crystal structure of human aquaporin 4 at 1.8 A and its mechanism of conductance.
Authors: Ho, J.D. / Yeh, R. / Sandstrom, A. / Chorny, I. / Harries, W.E. / Robbins, R.A. / Miercke, L.J. / Stroud, R.M.
History
DepositionFeb 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aquaporin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2807
Polymers23,5271
Non-polymers7536
Water1,11762
1
A: Aquaporin-4
hetero molecules

A: Aquaporin-4
hetero molecules

A: Aquaporin-4
hetero molecules

A: Aquaporin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,11828
Polymers94,1074
Non-polymers3,01124
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_445-y-1/2,x-1/2,z1
crystal symmetry operation4_545y+1/2,-x-1/2,z1
Buried area19000 Å2
ΔGint-134 kcal/mol
Surface area28730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.058, 82.058, 76.353
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-18-

HOH

DetailsTetramer is generated by the 4 fold axis.

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Components

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


Mass: 23526.744 Da / Num. of mol.: 1 / Fragment: hAQP4 trypsinized (residue 32-254)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AQP4 / Production host: Pichia pastoris (fungus) / Strain (production host): X-33 / References: UniProt: P55087
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 25% PEG-2K-MME, 50mM Citrate, pH 6.0, 40mM OG, 5% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11 Å / Relative weight: 1
ReflectionHighest resolution: 1.6 Å / Num. all: 23583 / Num. obs: 23583 / Redundancy: 12 %

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→36.13 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.241 / SU ML: 0.047 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16453 1265 5.1 %RANDOM
Rwork0.15966 ---
obs0.1599 23583 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.212 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20 Å2
2---0.21 Å20 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.8→36.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1654 0 50 62 1766
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221757
X-RAY DIFFRACTIONr_bond_other_d0.0010.021136
X-RAY DIFFRACTIONr_angle_refined_deg1.0471.9672390
X-RAY DIFFRACTIONr_angle_other_deg0.932794
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1795226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.49823.07752
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.97815259
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.784153
X-RAY DIFFRACTIONr_chiral_restr0.0660.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211900
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02354
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.257
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.090.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1970.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3921.51106
X-RAY DIFFRACTIONr_mcbond_other0.1211.5465
X-RAY DIFFRACTIONr_mcangle_it0.70921784
X-RAY DIFFRACTIONr_scbond_it1.3143651
X-RAY DIFFRACTIONr_scangle_it2.0544.5605
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.798→1.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.182 86 -
Rwork0.179 1706 -
obs--98.9 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
158.61220051.21097.58970.58391.15932.920.52410.98041.2543-2.0218-1.2571-1.56430.16780.05480.00560.07090.13170.1616-0.588-10.7354.143
21.52680.1417-0.66264.8769-1.01334.9459-0.04480.17960.2734-0.15320.1599-0.0523-0.2907-0.2835-0.11520.03030.0023-0.0094-0.03160.0374-0.0206-1.136-16.37914.817
33.6824-0.8426-1.85842.67570.81977.0618-0.0473-0.21990.09260.0896-0.02120.032-0.0205-0.05280.0686-0.0722-0.00860.0015-0.0874-0.0221-0.0657-1.827-24.4130.1
451.05062.7984-8.431773.39135.23282.79381.2514-5.90292.32185.06720.077-2.056-2.13992.6216-1.32850.75760.0460.11650.7699-0.21190.3729-0.767-25.70846.283
528.2222-4.72616.26321.23157.610582.8711-1.0308-3.59120.33021.98750.37430.2244-1.7779-2.82410.65660.16140.13570.02640.3762-0.032-0.01642.217-34.27836.193
61.5625-0.78061.05172.9065-2.19875.8975-0.03240.13050.1054-0.1651-0.0102-0.0079-0.15390.01990.0426-0.0674-0.00580.0082-0.08650.0107-0.08570.002-27.73816.59
77.0583-0.55952.44421.6588-1.24976.43850.07090.1779-0.0162-0.31880.09220.0412-0.008-0.109-0.16320.0166-0.01930.0247-0.03960.0446-0.05159.141-20.20513.558
88.666-6.92962.53912.7926-0.186610.80120.3860.77220.3942-0.4293-0.5419-0.0662-0.19660.25360.15590.0716-0.0440.08560.1360.09890.006914.769-16.295.709
94.1071-0.7054-5.16691.16620.46839.85760.14990.24520.378-0.1973-0.0157-0.0392-0.5947-0.2003-0.13410.0582-0.00260.0116-0.07250.04050.00953.238-12.4918.486
104.56230.6574-0.47690.90710.03871.5217-0.0078-0.30270.34310.1276-0.02510.0765-0.2569-0.1190.0329-0.01680.01260.0273-0.036-0.0358-0.0087-2.299-18.16835.394
1120.420610.9028-6.319115.960800-0.362-0.66430.47520.57840.4641-0.4215-0.241-0.3279-0.1021-0.0267-0.0307-0.0171-0.049-0.0596-0.019117.307-25.47337.56
122.10350.69542.6712.04351.95038.7454-0.02820.0720.11980.0244-0.0063-0.2452-0.14610.45280.0345-0.0829-0.04210.0083-0.03990.0071-0.054519.448-27.12223.708
138.275-1.12223.70754.49031.81627.49150.050.49250.238-0.5423-0.02170.0433-0.14720.2443-0.0283-0.0148-0.03770.0324-0.02330.0354-0.083113.801-30.829.379
1417.24947.0784-0.487111.05472.81379.8179-0.92751.8249-0.3756-1.33920.7064-0.2802-0.1462-0.15160.22120.1955-0.11760.02010.3089-0.008-0.040711.952-35.3890.729
152.04231.16450.71931.5782.47737.7878-0.00220.1852-0.0179-0.1522-0.11070.02690.2489-0.10750.1129-0.0611-0.00070.008-0.0688-0.0028-0.08135.259-34.83413.196
164.34911.04692.52412.57041.59383.9295-0.004-0.13220.07140.1749-0.02610.06460.05380.03280.0302-0.0972-0.020.0048-0.09740.0034-0.097912.04-31.53428.741
172.6332-0.3347-0.82591.35710.69412.22830.0139-0.15480.24530.0944-0.0001-0.0453-0.20430.163-0.0139-0.0002-0.03340.0055-0.0718-0.0049-0.02310.614-16.28728.563
181.1957-0.7363-1.25452.92833.4626.31760.01060.12230.1422-0.34240.0628-0.1981-0.29870.3243-0.0734-0.019-0.05110.0376-0.00210.0258-0.040719.248-22.6716.692
1929.13474.57913.517615.9691-6.376926.3279-0.68271.48050.4427-0.74710.5361-0.0241-0.95420.61210.14670.1332-0.060.13060.2353-0.01830.072323.067-29.6333.749
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A32 - 36
2X-RAY DIFFRACTION2A37 - 47
3X-RAY DIFFRACTION3A48 - 59
4X-RAY DIFFRACTION4A60 - 65
5X-RAY DIFFRACTION5A66 - 71
6X-RAY DIFFRACTION6A72 - 92
7X-RAY DIFFRACTION7A93 - 102
8X-RAY DIFFRACTION8A103 - 115
9X-RAY DIFFRACTION9A116 - 132
10X-RAY DIFFRACTION10A133 - 148
11X-RAY DIFFRACTION11A149 - 154
12X-RAY DIFFRACTION12A155 - 171
13X-RAY DIFFRACTION13A172 - 177
14X-RAY DIFFRACTION14A178 - 185
15X-RAY DIFFRACTION15A186 - 197
16X-RAY DIFFRACTION16A198 - 210
17X-RAY DIFFRACTION17A211 - 232
18X-RAY DIFFRACTION18A233 - 248
19X-RAY DIFFRACTION19A249 - 254

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