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- PDB-9zd2: C1 local refinement of aquaporin 1 bound to endogenous human stomatin -

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Basic information

Entry
Database: PDB / ID: 9zd2
TitleC1 local refinement of aquaporin 1 bound to endogenous human stomatin
Components
  • Aquaporin-1
  • Stomatin
KeywordsMEMBRANE PROTEIN / Oligomer / C8 symmetry / scaffold
Function / homology
Function and homology information


metanephric descending thin limb development / metanephric proximal straight tubule development / metanephric proximal convoluted tubule segment 2 development / metanephric glomerulus vasculature development / nitric oxide transmembrane transporter activity / hydrogen peroxide channel activity / lipid digestion / renal water transport / corticotropin secretion / cellular response to salt stress ...metanephric descending thin limb development / metanephric proximal straight tubule development / metanephric proximal convoluted tubule segment 2 development / metanephric glomerulus vasculature development / nitric oxide transmembrane transporter activity / hydrogen peroxide channel activity / lipid digestion / renal water transport / corticotropin secretion / cellular response to salt stress / positive regulation of viral process / carbon dioxide transmembrane transport / carbon dioxide transmembrane transporter activity / glycerol transmembrane transporter activity / secretory granule organization / renal water absorption / water transmembrane transporter activity / cerebrospinal fluid secretion / positive regulation of saliva secretion / Passive transport by Aquaporins / pancreatic juice secretion / establishment or maintenance of actin cytoskeleton polarity / lateral ventricle development / glycerol transmembrane transport / cellular response to mercury ion / intracellular water homeostasis / intracellularly cGMP-activated cation channel activity / host-mediated activation of viral genome replication / potassium ion transmembrane transporter activity / transepithelial water transport / water transport / water channel activity / ammonium transmembrane transport / ammonium channel activity / ankyrin-1 complex / glomerular filtration / camera-type eye morphogenesis / fibroblast migration / multicellular organismal-level water homeostasis / regulation of monoatomic ion transmembrane transport / cellular hyperosmotic response / cellular homeostasis / RNA polymerase binding / cell volume homeostasis / hyperosmotic response / positive regulation of fibroblast migration / odontogenesis / : / nitric oxide transport / azurophil granule membrane / RHOB GTPase cycle / RHOC GTPase cycle / RHOJ GTPase cycle / ion channel inhibitor activity / RHOQ GTPase cycle / CDC42 GTPase cycle / brush border / tertiary granule membrane / RHOH GTPase cycle / RHOA GTPase cycle / cellular response to dexamethasone stimulus / transmembrane transporter activity / positive regulation of protein targeting to membrane / potassium channel activity / specific granule membrane / renal water homeostasis / ephrin receptor binding / cellular response to retinoic acid / cellular response to nitric oxide / sensory perception of pain / basal plasma membrane / cellular response to copper ion / cellular response to cAMP / establishment of localization in cell / carbon dioxide transport / potassium ion transport / wound healing / brush border membrane / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / cellular response to mechanical stimulus / sarcolemma / Stimuli-sensing channels / positive regulation of fibroblast proliferation / cellular response to hydrogen peroxide / apical part of cell / positive regulation of angiogenesis / cellular response to UV / Vasopressin regulates renal water homeostasis via Aquaporins / melanosome / blood microparticle / cellular response to hypoxia / nuclear membrane / basolateral plasma membrane / vesicle / defense response to Gram-negative bacterium / cytoskeleton / apical plasma membrane / membrane raft / axon
Similarity search - Function
Band-7 stomatin-like / Aquaporin 1 / Band 7/stomatin-like, conserved site / Band 7 protein family signature. / Stomatin/HflK/HflC family / Band 7 domain / SPFH domain / Band 7 family / prohibitin homologues / Aquaporin transporter / Band 7/SPFH domain superfamily ...Band-7 stomatin-like / Aquaporin 1 / Band 7/stomatin-like, conserved site / Band 7 protein family signature. / Stomatin/HflK/HflC family / Band 7 domain / SPFH domain / Band 7 family / prohibitin homologues / Aquaporin transporter / Band 7/SPFH domain superfamily / Major intrinsic protein, conserved site / MIP family signature. / Major intrinsic protein / Major intrinsic protein / Aquaporin-like
Similarity search - Domain/homology
CHOLESTEROL / PALMITIC ACID / Stomatin / Aquaporin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsVallese, F. / Clarke, O.B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Stomatin encapsulates aquaporin-1 and urea transporter-B in the erythrocyte membrane
Authors: Vallese, F. / Li, H. / Clarke, O.B.
History
DepositionNov 24, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Aquaporin-1
B: Aquaporin-1
C: Aquaporin-1
A: Aquaporin-1
F: Stomatin
G: Stomatin
E: Stomatin
I: Stomatin
H: Stomatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,20017
Polymers209,6289
Non-polymers2,5728
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Aquaporin-1 / AQP-1 / Aquaporin-CHIP / Channel-like integral membrane protein of 28 kDa / Urine water channel


Mass: 25996.072 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: Aquaporin-1 / Source: (natural) Homo sapiens (human) / References: UniProt: P29972
#2: Protein
Stomatin / Erythrocyte band 7 integral membrane protein / Erythrocyte membrane protein band 7.2 / Protein 7.2b


Mass: 21128.730 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Details: Stomatin region in contact with AQP-1,Stomatin region in contact with AQP-1
Source: (natural) Homo sapiens (human) / References: UniProt: P27105
#3: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C16H32O2 / Details: Aquaporin-1 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C27H46O / 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: The stomatin region in contact with two AQP-1 monomers
Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
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: 500 nm / Cs: 2.7 mm
Image recordingElectron dose: 58 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 135000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00415075
ELECTRON MICROSCOPYf_angle_d0.68220522
ELECTRON MICROSCOPYf_dihedral_angle_d6.7842400
ELECTRON MICROSCOPYf_chiral_restr0.0452508
ELECTRON MICROSCOPYf_plane_restr0.0042542

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