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- EMDB-43071: Structure of human AQP4 with a pathogenic autoantibody - rAB 186 -

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Basic information

Entry
Database: EMDB / ID: EMD-43071
TitleStructure of human AQP4 with a pathogenic autoantibody - rAB 186
Map dataSharpened map
Sample
  • Complex: Human AQP4 tetramer bound to Fab fragment of the pathogenic autoantibody- rAB 186
    • Protein or peptide: Aquaporin-4
    • Protein or peptide: rAB 186 Heavy Chain
    • Protein or peptide: rAB 186 Light Chain
  • Ligand: water
KeywordsAquaporin / Water-channel / TRANSPORT PROTEIN-IMMUNE SYSTEM complex / Neuromyelitis Optica (NMO) / Autoimmnune disease
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 / protein homotetramerization / basolateral plasma membrane / 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: 2.9 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: Human AQP4 structure in lipid nanodisc using cryo-EM
Authors: Gupta M / Khandelwal NK / Stroud RM
History
DepositionDec 7, 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_43071.png

Downloads & links

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Map

FileDownload / File: emd_43071.map.gz / Format: CCP4 / Size: 229.8 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 392 pix.
= 326.928 Å		0.83 Å/pix.
x 392 pix.
= 326.928 Å		0.83 Å/pix.
x 392 pix.
= 326.928 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: 0.45
Minimum - Maximum-2.1645837 - 3.282229
Average (Standard dev.)0.0016021836 (±0.06985979)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions392392392
Spacing392392392
CellA=B=C: 326.928 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map

Fileemd_43071_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_43071_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_43071_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 bound to Fab fragment of the pathogenic autoa...

EntireName: Human AQP4 tetramer bound to Fab fragment of the pathogenic autoantibody- rAB 186
Components
  • Complex: Human AQP4 tetramer bound to Fab fragment of the pathogenic autoantibody- rAB 186
    • Protein or peptide: Aquaporin-4
    • Protein or peptide: rAB 186 Heavy Chain
    • Protein or peptide: rAB 186 Light Chain
  • Ligand: water

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Supramolecule #1: Human AQP4 tetramer bound to Fab fragment of the pathogenic autoa...

SupramoleculeName: Human AQP4 tetramer bound to Fab fragment of the pathogenic autoantibody- rAB 186
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
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: rAB 186 Heavy Chain

MacromoleculeName: rAB 186 Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.642572 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SQVQLQESGP GLVKPSQTLP LTCTVSGGYI SSGSHQWGWI RQPAGKGLEW IGRIYTSGST NYNPSLKSRV TISVDTSKNQ FSLKLSSVT AADTAVYYCA RVNYDLLTGR ANFFDPWGQG TPVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF P EPVTVSWN ...String:
SQVQLQESGP GLVKPSQTLP LTCTVSGGYI SSGSHQWGWI RQPAGKGLEW IGRIYTSGST NYNPSLKSRV TISVDTSKNQ FSLKLSSVT AADTAVYYCA RVNYDLLTGR ANFFDPWGQG TPVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF P EPVTVSWN SGALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KVDKKVEPKS CDKTH

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Macromolecule #3: rAB 186 Light Chain

MacromoleculeName: rAB 186 Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.321896 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVLTQSPGT LSLSPGERAT LSCRASQSVS SRSVAWYQQK PGQAPRLLIY GASNRATGIP DRFSGSGSGT DFTLTISRLE PEDFVVFYC QQYGSSPLTF GGGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
EIVLTQSPGT LSLSPGERAT LSCRASQSVS SRSVAWYQQK PGQAPRLLIY GASNRATGIP DRFSGSGSGT DFTLTISRLE PEDFVVFYC QQYGSSPLTF GGGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 80 / 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: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 220335
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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