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- EMDB-43044: Structure of human AQP4 in lipid nanodisc -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-43044
TitleStructure of human AQP4 in lipid nanodisc
Map dataSharpened map
Sample
  • Complex: Human AQP4 tetramer in nanodisc
    • Protein or peptide: Aquaporin-4
  • Ligand: water
KeywordsAquaporin / Water-channel / TRANSPORT PROTEIN
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 / sarcolemma / cellular response to type II interferon ...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 / sarcolemma / cellular response to type II interferon / Vasopressin regulates renal water homeostasis via Aquaporins / basolateral plasma membrane / protein homotetramerization / endosome membrane / external side of plasma membrane / extracellular region / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Aquaporin transporter / Major intrinsic protein, conserved site / MIP family signature. / Major intrinsic protein / Major intrinsic protein / Aquaporin-like
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsGupta M / Khandelwal NK / Stroud RM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Structure of human AQP4 in lipid nanodisc
Authors: Gupta M / Khandelwal NK / Stroud RM
History
DepositionDec 6, 2023-
Header (metadata) releaseDec 11, 2024-
Map releaseDec 11, 2024-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43044.png

Downloads & links

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Map

FileDownload / File: emd_43044.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 288 pix.
= 240.192 Å		0.83 Å/pix.
x 288 pix.
= 240.192 Å		0.83 Å/pix.
x 288 pix.
= 240.192 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.834 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.48
Minimum - Maximum-1.587509 - 2.8190832
Average (Standard dev.)-0.0016278204 (±0.06464755)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 240.192 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map

Fileemd_43044_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_43044_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_43044_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human AQP4 tetramer in nanodisc

EntireName: Human AQP4 tetramer in nanodisc
Components
  • Complex: Human AQP4 tetramer in nanodisc
    • Protein or peptide: Aquaporin-4
  • Ligand: water

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Supramolecule #1: Human AQP4 tetramer in nanodisc

SupramoleculeName: Human AQP4 tetramer in nanodisc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Aquaporin-4

MacromoleculeName: Aquaporin-4 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.982934 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: MHHHHHHHHD YKDDDDKLVP RGSEFMSDRP TARRWGKCGP LCTRENIMVA FKGVWTQAFW KAVTAEFLAM LIFVLLSLGS TINWGGTEK PLPVDMVLIS LCFGLSIATM VQCFGHISGG HINPAVTVAM VCTRKISIAK SVFYIAAQCL GAIIGAGILY L VTPPSVVG ...String:
MHHHHHHHHD YKDDDDKLVP RGSEFMSDRP TARRWGKCGP LCTRENIMVA FKGVWTQAFW KAVTAEFLAM LIFVLLSLGS TINWGGTEK PLPVDMVLIS LCFGLSIATM VQCFGHISGG HINPAVTVAM VCTRKISIAK SVFYIAAQCL GAIIGAGILY L VTPPSVVG GLGVTMVHGN LTAGHGLLVE LIITFQLVFT IFASCDSKRT DVTGSIALAI GFSVAIGHLF AINYTGASMN PA RSFGPAV IMGNWENHWI YWVGPIIGAV LAGGLYEYVF CPDVEFKRRF KEAFSKAAQQ TKGSYMEVED NRSQVETDDL ILK PGVVHV IDVDRGEEKK GKDQSGEVLS SV

UniProtKB: Aquaporin-4

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 101 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: OTHER / Average electron dose: 60.0 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: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3gd8

Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 371328
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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