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- EMDB-65443: Cryo-EM structure of hAQP11 in LMNG -

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Basic information

Entry
Database: EMDB / ID: EMD-65443
TitleCryo-EM structure of hAQP11 in LMNG
Map datamap
Sample
  • Complex: homo trimer
    • Protein or peptide: Aquaporin-11,sfGFP
  • Ligand: DECANE
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
Biological speciesHomo sapiens (human) / Aequorea victoria (jellyfish)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsSuzuki S / Nishikawa K / Kamegawa A / kozai D / Fujiyoshi Y
Funding support Japan, 1 items
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, 2025-
Header (metadata) releaseDec 31, 2025-
Map releaseDec 31, 2025-
UpdateDec 31, 2025-
Current statusDec 31, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65443.png

Downloads & links

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Map

FileDownload / File: emd_65443.map.gz / Format: CCP4 / Size: 24.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.79 Å/pix.
x 186 pix.
= 146.94 Å		0.79 Å/pix.
x 186 pix.
= 146.94 Å		0.79 Å/pix.
x 186 pix.
= 146.94 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.79 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.286
Minimum - Maximum-1.0301001 - 1.6417347
Average (Standard dev.)0.0014543395 (±0.06852676)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions186186186
Spacing186186186
CellA=B=C: 146.94 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65443_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: b

Fileemd_65443_half_map_1.map
Annotationb
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: b

Fileemd_65443_half_map_2.map
Annotationb
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : homo trimer

EntireName: homo trimer
Components
  • Complex: homo trimer
    • Protein or peptide: Aquaporin-11,sfGFP
  • Ligand: DECANE

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Supramolecule #1: homo trimer

SupramoleculeName: homo trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Aquaporin-11,sfGFP

MacromoleculeName: Aquaporin-11,sfGFP / type: protein_or_peptide / ID: 1
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)
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Aequorea victoria (jellyfish)
Molecular weightTheoretical: 60.011047 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSPLLGLRSE LQDTCTSLGL MLSVVLLMGL ARVVARQQLH RPVAHAFVLE FLATFQLCCC THELQLLSEQ HPAHPTWTLT LVYFFSLVH GLTLVGTSSN PCGVMMQMML GGMSPETGAV RLLAQLVSAL CSRYCTSALW SLGLTQYHVS ERSFACKNPI R VDLLKAVI ...String:
MSPLLGLRSE LQDTCTSLGL MLSVVLLMGL ARVVARQQLH RPVAHAFVLE FLATFQLCCC THELQLLSEQ HPAHPTWTLT LVYFFSLVH GLTLVGTSSN PCGVMMQMML GGMSPETGAV RLLAQLVSAL CSRYCTSALW SLGLTQYHVS ERSFACKNPI R VDLLKAVI TEAVCSFLFH SALLHFQEVR TKLRIHLLAA LITFLVYAGG SLTGAVFNPA LALSLHFMCF DEAFPQFFIV YW LAPSLGI LLMILMFSFF LPWLHNNHTI NKKENSLEVL FQGPTAAAAS KGEELFTGVV PILVELDGDV NGHKFSVRGE GEG DATNGK LTLKFICTTG KLPVPWPTLV TTLTYGVQCF SRYPDHMKRH DFFKSAMPEG YVQERTISFK DDGTYKTRAE VKFE GDTLV NRIELKGIDF KEDGNILGHK LEYNFNSHNV YITADKQKNG IKANFKIRHN VEDGSVQLAD HYQQNTPIGD GPVLL PDNH YLSTQSVLSK DPNEKRDHMV LLEFVTAAGI THGMDELYKS GGGHHHHHHH HHH

UniProtKB: Aquaporin-11

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Macromolecule #2: DECANE

MacromoleculeName: DECANE / type: ligand / ID: 2 / Number of copies: 1 / Formula: D10
Molecular weightTheoretical: 142.282 Da
Chemical component information

ChemComp-D10:
DECANE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration15 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K
DetailsThis sample was monodisperse

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 71.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 202060
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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