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- PDB-9vxw: Cryo-EM structure of hAQP11 in LMNG -

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Basic information

Entry
Database: PDB / ID: 9vxw
TitleCryo-EM structure of hAQP11 in LMNG
ComponentsAquaporin-11,sfGFP
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


hydrogen peroxide transmembrane transport / proximal tubule development / hydrogen peroxide channel activity / Passive transport by Aquaporins / negative regulation of response to endoplasmic reticulum stress / glycerol channel activity / negative regulation of ERAD pathway / glycerol transmembrane transport / intracellular water homeostasis / water transport ...hydrogen peroxide transmembrane transport / proximal tubule development / hydrogen peroxide channel activity / Passive transport by Aquaporins / negative regulation of response to endoplasmic reticulum stress / glycerol channel activity / negative regulation of ERAD pathway / glycerol transmembrane transport / intracellular water homeostasis / water transport / water channel activity / intracellular oxygen homeostasis / endosomal lumen acidification / protein targeting to membrane / : / cytoplasmic vesicle membrane / protein homooligomerization / negative regulation of epithelial cell proliferation / channel activity / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / endoplasmic reticulum membrane / cell surface / endoplasmic reticulum / plasma membrane / cytoplasm
Similarity search - Function
Aquaporin 11/12 / Aquaporin 11 / : / Major intrinsic protein / Major intrinsic protein / Aquaporin-like
Similarity search - Domain/homology
DECANE / Aquaporin-11
Similarity search - Component
Biological speciesHomo sapiens (human)
Aequorea victoria (jellyfish)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsSuzuki, S. / Nishikawa, K. / Kamegawa, A. / kozai, D. / Fujiyoshi, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20H00451 Japan
CitationJournal: To Be Published
Title: rimeric water channel human AQP11 with a large pore radius
Authors: Suzuki, S. / Kamegawa, A. / Nishikawa, K. / Kozai, D. / Fujiyoshi, Y.
History
DepositionJul 20, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 31, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: Aquaporin-11,sfGFP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1532
Polymers60,0111
Non-polymers1421
Water00
1
A: Aquaporin-11,sfGFP
hetero molecules

A: Aquaporin-11,sfGFP
hetero molecules

A: Aquaporin-11,sfGFP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,4606
Polymers180,0333
Non-polymers4273
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation2

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Components

#1: Protein Aquaporin-11,sfGFP / AQP-11


Mass: 60011.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-term 3c protease site and sfGFP (N272-S273 LINKER, L274-P281 3c protease cut site, T282-S287 Linker, S289-K523 super folder GFP (Uniprot ID could not be found. https://www.fpbase. ...Details: C-term 3c protease site and sfGFP (N272-S273 LINKER, L274-P281 3c protease cut site, T282-S287 Linker, S289-K523 super folder GFP (Uniprot ID could not be found. https://www.fpbase.org/protein/superfolder-gfp/), S254-G527 Linker, H528-H537 His tag)
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Aequorea victoria (jellyfish)
Gene: AQP11, AQPX1, PSEC0027, gfp / Production host: Homo sapiens (human) / References: UniProt: Q8NBQ7
#2: Chemical ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: homo trimer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Homo sapiens (human)9606
21Aequorea victoria (jellyfish)6100
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenConc.: 15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 71 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 202060 / Symmetry type: POINT

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