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- PDB-9oqq: Human pannexin 1 channel W74A mutant with 10mM ATP -

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Basic information

Entry
Database: PDB / ID: 9oqq
TitleHuman pannexin 1 channel W74A mutant with 10mM ATP
ComponentsPannexin-1,RNA-directed RNA polymerase L chimera
KeywordsTRANSPORT PROTEIN / PANX1 / Pannexin / Large pore channel
Function / homology
Function and homology information


ATP transmembrane transporter activity / NNS virus cap methyltransferase / ATP transport / Electric Transmission Across Gap Junctions / leak channel activity / GDP polyribonucleotidyltransferase / positive regulation of interleukin-1 alpha production / wide pore channel activity / bleb / monoatomic anion transmembrane transport ...ATP transmembrane transporter activity / NNS virus cap methyltransferase / ATP transport / Electric Transmission Across Gap Junctions / leak channel activity / GDP polyribonucleotidyltransferase / positive regulation of interleukin-1 alpha production / wide pore channel activity / bleb / monoatomic anion transmembrane transport / monoatomic anion channel activity / gap junction / gap junction channel activity / positive regulation of macrophage cytokine production / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / oogenesis / response to ATP / The NLRP3 inflammasome / monoatomic cation transport / bioluminescence / response to ischemia / positive regulation of interleukin-1 beta production / generation of precursor metabolites and energy / virion component / calcium channel activity / actin filament binding / calcium ion transport / cell-cell signaling / protease binding / scaffold protein binding / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / transmembrane transporter binding / host cell cytoplasm / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / hydrolase activity / signaling receptor binding / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / endoplasmic reticulum membrane / structural molecule activity / endoplasmic reticulum / protein-containing complex / ATP binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
RNA-directed RNA polymerase L methyltransferase domain, rhabdovirus / Virus-capping methyltransferase, MT domain / RNA-directed RNA polymerase, paramyxovirus / Pannexin / Mononegavirus L protein 2-O-ribose methyltransferase / RNA-directed RNA polymerase L, C-terminal / Mononegavirus L protein 2'-O-ribose methyltransferase domain profile. / Innexin / Innexin / Pannexin family profile. ...RNA-directed RNA polymerase L methyltransferase domain, rhabdovirus / Virus-capping methyltransferase, MT domain / RNA-directed RNA polymerase, paramyxovirus / Pannexin / Mononegavirus L protein 2-O-ribose methyltransferase / RNA-directed RNA polymerase L, C-terminal / Mononegavirus L protein 2'-O-ribose methyltransferase domain profile. / Innexin / Innexin / Pannexin family profile. / Mononegavirales RNA-directed RNA polymerase catalytic domain / Mononegavirales mRNA-capping domain V / Mononegavirales RNA dependent RNA polymerase / Mononegavirales mRNA-capping region V / RdRp of negative ssRNA viruses with non-segmented genomes catalytic domain profile. / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
RNA-directed RNA polymerase L / Pannexin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Human respiratory syncytial virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsRuan, Z. / Li, Y. / Du, J. / Lu, W.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R00NS128258 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL153219 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS112363 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM138321 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS111031 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS129804 United States
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis of PANX1 permeation and positive modulation by mefloquine.
Authors: Yangyang Li / Zheng Ruan / Junuk Lee / Ian J Orozco / Edward Zhou / Juan Du / Wei Lü /
Abstract: Purinergic signaling relies on ATP release through exocytosis and large-pore channels. Large-pore channels permeate both small anions like chloride and large signaling molecules like ATP, but how ...Purinergic signaling relies on ATP release through exocytosis and large-pore channels. Large-pore channels permeate both small anions like chloride and large signaling molecules like ATP, but how this broad cargo selectivity is structurally controlled remains elusive. Here we investigate PANX1, a prototypical large-pore channel, and uncover structural plasticity at the extracellular entrance formed by seven tryptophan (W74) residues. The W74 sidechains are flexible, sampling conformations that range from a constricted state permissive only to chloride to a dilated state compatible with ATP. These states are coupled to variable cation-π interactions between W74 and arginine 75 (R75), suggesting a mechanism for dynamic tuning of pore architecture and selective cargo permeation. We also identify mefloquine as a positive modulator of PANX1 that binds near the side tunnel to control ion flow through this pathway. Together, these findings define the structural principles underlying PANX1 permeation and modulation.
History
DepositionMay 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data 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
A: Pannexin-1,RNA-directed RNA polymerase L chimera
B: Pannexin-1,RNA-directed RNA polymerase L chimera
C: Pannexin-1,RNA-directed RNA polymerase L chimera
D: Pannexin-1,RNA-directed RNA polymerase L chimera
E: Pannexin-1,RNA-directed RNA polymerase L chimera
F: Pannexin-1,RNA-directed RNA polymerase L chimera
G: Pannexin-1,RNA-directed RNA polymerase L chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)546,75314
Polymers545,2057
Non-polymers1,5487
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
Pannexin-1,RNA-directed RNA polymerase L chimera / PANX1 / Large structural protein / Replicase / Transcriptase


Mass: 77886.406 Da / Num. of mol.: 7 / Mutation: W74A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Human respiratory syncytial virus
Gene: PANX1, MRS1, UNQ2529/PRO6028 / Production host: Homo sapiens (human)
References: UniProt: Q96RD7, UniProt: A0A5P9VSM8, NNS virus cap methyltransferase, RNA-directed RNA polymerase, GDP polyribonucleotidyltransferase
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
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: Human Pannexin 1 channel W74A mutant in GDN detergent with 10mM ATP
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1900 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 584553 / Symmetry type: POINT

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