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- PDB-9zcz: C4 local refinement of stomatin-bound aquaporin (human) -

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Basic information

Entry
Database: PDB / ID: 9zcz
TitleC4 local refinement of stomatin-bound aquaporin (human)
ComponentsAquaporin-1
KeywordsTRANSPORT PROTEIN / MEMBRANE PROTEIN / aquaporin / SPFH
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 / 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 / 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 / cellular hyperosmotic response / cellular homeostasis / cell volume homeostasis / hyperosmotic response / positive regulation of fibroblast migration / odontogenesis / : / nitric oxide transport / brush border / cellular response to dexamethasone stimulus / transmembrane transporter activity / potassium channel activity / 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 / 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 / cellular response to hypoxia / nuclear membrane / basolateral plasma membrane / defense response to Gram-negative bacterium / apical plasma membrane / axon / negative regulation of apoptotic process / extracellular exosome / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Aquaporin 1 / Aquaporin transporter / Major intrinsic protein, conserved site / MIP family signature. / Major intrinsic protein / Major intrinsic protein / Aquaporin-like
Similarity search - Domain/homology
CHOLESTEROL / PALMITIC ACID / Aquaporin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.3 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: Mask / Part number: 1 / Data content type: Mask / 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

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Assembly

Deposited unit
D: Aquaporin-1
B: Aquaporin-1
C: Aquaporin-1
A: Aquaporin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,55712
Polymers103,9844
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 / Source: (natural) Homo sapiens (human) / References: UniProt: P29972
#2: 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
#3: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C16H32O2 / 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: Local C4 refinement of aquaporin 1 within the stomatin oligomer (16mer with approximate C8 symmetry).
Type: COMPLEX / Entity ID: #1 / 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: C4 (4 fold cyclic)
3D reconstructionResolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 631000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0037620
ELECTRON MICROSCOPYf_angle_d0.56710392
ELECTRON MICROSCOPYf_dihedral_angle_d7.6811148
ELECTRON MICROSCOPYf_chiral_restr0.0371268
ELECTRON MICROSCOPYf_plane_restr0.0031272

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