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- PDB-6kxw: Crystal structure of human aquaporin AQP7 in bound to glycerol -

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Basic information

Entry
Database: PDB / ID: 6kxw
TitleCrystal structure of human aquaporin AQP7 in bound to glycerol
ComponentsAquaporin-7
KeywordsMEMBRANE PROTEIN / aquaporin / transporter / lipid metabolism
Function / homology
Function and homology information


Transport of glycerol from adipocytes to the liver by Aquaporins / glycerol channel activity / urea transmembrane transporter activity / Passive transport by Aquaporins / glycerol transmembrane transport / water transport / water channel activity / lipid droplet / cytoplasmic vesicle membrane / cell-cell junction ...Transport of glycerol from adipocytes to the liver by Aquaporins / glycerol channel activity / urea transmembrane transporter activity / Passive transport by Aquaporins / glycerol transmembrane transport / water transport / water channel activity / lipid droplet / cytoplasmic vesicle membrane / cell-cell junction / cell cortex / basolateral plasma membrane / plasma membrane / cytoplasm
Similarity search - Function
Glycerol uptake facilitator protein / Glycerol uptake facilitator protein. / 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: 3.7 Å
AuthorsZhang, L. / Yao, D. / Zhou, F. / Zhang, Q. / Zhou, L. / Cao, Y.
Funding support China, 4items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2017YFC1001303 China
Ministry of Science and Technology (China)2018YFC1004704 China
National Science Foundation (China)U1632132 China
National Science Foundation (China)31670849 China
CitationJournal: Sci Bull (Beijing) / Year: 2020
Title: The structural basis for glycerol permeation by human AQP7
Authors: Zhang, L. / Yao, D. / Xia, Y. / Zhang, Q. / Zhou, F. / Wang, Q. / Qin, A. / Zhao, J. / Li, D. / Li, Y. / Zhou, L. / Cao, Y.
History
DepositionSep 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Sep 8, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aquaporin-7
B: Aquaporin-7
C: Aquaporin-7
D: Aquaporin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,2426
Polymers149,0584
Non-polymers1842
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15300 Å2
ΔGint-147 kcal/mol
Surface area35670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.508, 106.286, 214.416
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Aquaporin-7 / AQP-7 / Aquaglyceroporin-7 / Aquaporin adipose / AQPap / Aquaporin-7-like


Mass: 37264.395 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AQP7, AQP7L, AQP9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O14520
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 3.57 Å3/Da / Density % sol: 65.59 %
Crystal growTemperature: 277 K / Method: evaporation
Details: 30% v/v PEG 400, 50mM CAPS, pH 10.0, 0.16% w/v 1,5-Naphthalenedisulfonic acid disodium, 0.16% w/v Naphthalene-1,3,6-trisulfonic acid trisodium, 0.16% 1,4-piperazinediethanesulfonic acid

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97775 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97775 Å / Relative weight: 1
ReflectionResolution: 3.7→47.614 Å / Num. obs: 16925 / % possible obs: 99.9 % / Redundancy: 20 % / CC1/2: 0.973 / Net I/σ(I): 9.05
Reflection shellResolution: 3.7→3.8333 Å / Num. unique obs: 311 / CC1/2: 0.608

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F7H

6f7h


Resolution: 3.7→47.614 Å / SU ML: 0.6 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 34.36
RfactorNum. reflection% reflection
Rfree0.3221 881 5.22 %
Rwork0.2679 --
obs0.2707 16881 71.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 268.64 Å2 / Biso mean: 109.2368 Å2 / Biso min: 7.27 Å2
Refinement stepCycle: final / Resolution: 3.7→47.614 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7574 0 12 0 7586
Biso mean--55.2 --
Num. residues----999
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.7004-3.93220.333637626
3.9322-4.23560.366482144940
4.2356-4.66150.32121350.2547270473
4.6615-5.33530.31882020.2461366699
5.3353-6.71890.38742270.3063712100
6.7189-47.610.2711980.2655384399
Refinement TLS params.Method: refined / Origin x: -13.1329 Å / Origin y: -44.6983 Å / Origin z: 21.6915 Å
111213212223313233
T0.2585 Å20.0071 Å2-0.0292 Å2-0.6448 Å20.5975 Å2--0.5005 Å2
L0.971 °2-0.0555 °2-0.1248 °2-0.9937 °20.0053 °2--1.0354 °2
S0.2753 Å °-1.72 Å °-1.1495 Å °0.1902 Å °-0.269 Å °0.0275 Å °0.0967 Å °0.1392 Å °0.0035 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA27 - 401
2X-RAY DIFFRACTION1allB30 - 278
3X-RAY DIFFRACTION1allC30 - 400
4X-RAY DIFFRACTION1allD30 - 278

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