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- PDB-8h1d: Solid-state NMR Structure of Aquaporin Z in its Native Cellular M... -

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Basic information

Entry
Database: PDB / ID: 8h1d
TitleSolid-state NMR Structure of Aquaporin Z in its Native Cellular Membranes
ComponentsAquaporin Z
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


water channel activity / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Aquaporin Z / Aquaporin transporter / Major intrinsic protein, conserved site / MIP family signature. / Major intrinsic protein / Major intrinsic protein / Aquaporin-like
Similarity search - Domain/homology
Biological speciesEscherichia coli BL21 (bacteria)
MethodSOLID-STATE NMR / distance geometry
AuthorsXie, H. / Zhao, Y. / Zhao, W. / Chen, Y. / Liu, M. / Yang, J.
Funding support China, 5items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21927801 China
National Natural Science Foundation of China (NSFC)21904136 China
National Natural Science Foundation of China (NSFC)21921004 China
National Natural Science Foundation of China (NSFC)22004124 China
Chinese Academy of SciencesYJKYYQ20190032 China
CitationJournal: Sci Adv / Year: 2023
Title: Solid-state NMR structure determination of a membrane protein in E. coli cellular inner membrane.
Authors: Xie, H. / Zhao, Y. / Zhao, W. / Chen, Y. / Liu, M. / Yang, J.
History
DepositionOct 2, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 15, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aquaporin Z


Theoretical massNumber of molelcules
Total (without water)25,1851
Polymers25,1851
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Aquaporin Z


Mass: 25185.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Gene: aqpZ, ECBD_2719 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A140NDF1

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D NCA
121isotropic12D DARR
131isotropic13D NCACX
141isotropic13D NCOCX
151isotropic13D CONCA
261isotropic12D 100ms CORD
281isotropic12D 500ms CORD

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Sample preparation

DetailsType: membrane
Contents: 29.4 % w/w [U-13C; U-15N] aquaporin Z, 5 mM Tris-Cl pH 8.0
Details: The cellular membranes for ssNMR experiments were collected directly after overexpression of AqpZ in E.coli, cell lysis, and isolation of cell components without protein purification.
Label: 13C,15N_sample / Solvent system: 5 mM Tris-Cl pH 8.0
SampleConc.: 29.4 % w/w / Component: aquaporin Z / Isotopic labeling: [U-13C; U-15N]
Sample conditions

Ionic strength: 1 M / Ionic strength err: 0.1 / pH: 8.0 / PH err: 0.1 / Pressure: 1 atm / Pressure err: 0.1 / Temperature: 298 K / Temperature err: 1

Conditions-IDDetailsLabel
1Inner membrane 1 (IM1) is the E. coli inner cell membrane obtained after removing outer membrane components by sucrose density gradient centrifugation of TM2.IM1
2IM2 is the same as IM1 except for the use of 100 uL rifampicin treatment before induction of AqpZ expression.IM2

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz
Details: A standard Bruker Advance 800 MHz spectrometer with a 3.2 mm E-free HCN MAS probe.

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Processing

NMR software
NameVersionDeveloperClassification
NMRFAM-SPARKY2.6T. D. Goddard and D. G. Knellerchemical shift assignment
X-PLOR NIH2.47Schwieters, Kuszewski, Tjandra and Clorestructure calculation
TopSpin3.6Bruker Biospincollection
NMRPipe3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: distance geometry / Software ordinal: 2
Details: We calculated 1000 monomer structures using 1007 distance restraints, 214 angle restraints predicted from TALOS+ using assigned 15N and 13C chemical shifts, and 132 intrahelical hydrogen ...Details: We calculated 1000 monomer structures using 1007 distance restraints, 214 angle restraints predicted from TALOS+ using assigned 15N and 13C chemical shifts, and 132 intrahelical hydrogen bonds predicted from both the chemical shift index and TALOS+.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 10

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