[English] 日本語
Yorodumi
- EMDB-45177: Cryo-EM structure of the full-length human P2X4 receptor in the A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-45177
TitleCryo-EM structure of the full-length human P2X4 receptor in the ATP-bound desensitized state
Map dataLocally sharpened map for the human P2X4 receptor in the ATP-bound desensitized state
Sample
  • Complex: Membrane protein
    • Protein or peptide: P2X purinoceptor 4
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: MAGNESIUM ION
  • Ligand: water
KeywordsMembrane Protein / Ion Channel / Ligand-gated Ion Channel / P2X Receptor / Allosteric Antagonist
Function / homology
Function and homology information


sensory perception of touch / Platelet homeostasis / positive regulation of microglial cell migration / purinergic nucleotide receptor signaling pathway / extracellularly ATP-gated monoatomic cation channel activity / purinergic nucleotide receptor activity / ligand-gated calcium channel activity / negative regulation of cardiac muscle hypertrophy / Elevation of cytosolic Ca2+ levels / positive regulation of prostaglandin secretion ...sensory perception of touch / Platelet homeostasis / positive regulation of microglial cell migration / purinergic nucleotide receptor signaling pathway / extracellularly ATP-gated monoatomic cation channel activity / purinergic nucleotide receptor activity / ligand-gated calcium channel activity / negative regulation of cardiac muscle hypertrophy / Elevation of cytosolic Ca2+ levels / positive regulation of prostaglandin secretion / tissue homeostasis / regulation of chemotaxis / response to fluid shear stress / positive regulation of calcium ion transport / relaxation of cardiac muscle / endothelial cell activation / positive regulation of endothelial cell chemotaxis / response to ATP / cellular response to zinc ion / cellular response to ATP / behavioral response to pain / positive regulation of calcium ion transport into cytosol / membrane depolarization / positive regulation of blood vessel endothelial cell migration / regulation of cardiac muscle contraction / response to axon injury / Purinergic signaling in leishmaniasis infection / regulation of sodium ion transport / sensory perception of pain / positive regulation of calcium-mediated signaling / response to ischemia / apoptotic signaling pathway / calcium-mediated signaling / calcium ion transmembrane transport / regulation of blood pressure / positive regulation of nitric oxide biosynthetic process / cell junction / cell body / monoatomic ion transmembrane transport / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / postsynapse / cadherin binding / copper ion binding / signaling receptor binding / lysosomal membrane / perinuclear region of cytoplasm / signal transduction / extracellular exosome / zinc ion binding / ATP binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
P2X4 purinoceptor / : / ATP P2X receptors signature. / ATP P2X receptor / P2X purinoreceptor / P2X purinoreceptor extracellular domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsShi H / Ditter IA / Oken AC / Mansoor SE
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R00HL138129 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DP2GM149551 United States
CitationJournal: Sci Adv / Year: 2025
Title: Human P2X4 receptor gating is modulated by a stable cytoplasmic cap and a unique allosteric pocket.
Authors: Haoyuan Shi / Ismayn A Ditter / Adam C Oken / Steven E Mansoor /
Abstract: P2X receptors (P2XRs) are adenosine 5'-triphosphate (ATP)-gated ion channels comprising homomeric and heteromeric trimers of seven subtypes (P2X1-P2X7) that confer different rates of desensitization. ...P2X receptors (P2XRs) are adenosine 5'-triphosphate (ATP)-gated ion channels comprising homomeric and heteromeric trimers of seven subtypes (P2X1-P2X7) that confer different rates of desensitization. The helical recoil model of P2XR desensitization proposes stability of the cytoplasmic cap sets the rate of desensitization, but timing of its formation is unclear for slow-desensitizing P2XRs. We report cryo-electron microscopy structures of full-length wild-type human P2X4 receptor in apo closed, antagonist-bound inhibited, and ATP-bound desensitized states. Because the apo closed and antagonist-bound inhibited state structures of this slow-desensitizing P2XR include an intact cytoplasmic cap while the ATP-bound desensitized state structure does not, the cytoplasmic cap is formed before agonist binding. Furthermore, structural and functional data suggest the cytoplasmic cap is stabilized by lipids to modulate desensitization, and P2X4 is modified by glycosylation and palmitoylation. Last, our antagonist-bound inhibited state structure reveals features specific to the allosteric ligand-binding pocket in human receptors that facilitates development of small-molecule modulators.
History
DepositionJun 3, 2024-
Header (metadata) releaseJan 29, 2025-
Map releaseJan 29, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_45177.png

Downloads & links

-
Map

FileDownload / File: emd_45177.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocally sharpened map for the human P2X4 receptor in the ATP-bound desensitized state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 600 pix.
= 388.8 Å		0.65 Å/pix.
x 600 pix.
= 388.8 Å		0.65 Å/pix.
x 600 pix.
= 388.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.648 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.0028888816 - 0.6203105
Average (Standard dev.)0.00014269822 (±0.0050582485)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 388.8 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_45177_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Unsharpened map for the human P2X4 receptor in...

Fileemd_45177_additional_1.map
AnnotationUnsharpened map for the human P2X4 receptor in the ATP-bound desensitized state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Sharpened map for the human P2X4 receptor in...

Fileemd_45177_additional_2.map
AnnotationSharpened map for the human P2X4 receptor in the ATP-bound desensitized state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map A for the human P2X4 receptor...

Fileemd_45177_half_map_1.map
AnnotationHalf map A for the human P2X4 receptor in the ATP-bound desensitized state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map B for the human P2X4 receptor...

Fileemd_45177_half_map_2.map
AnnotationHalf map B for the human P2X4 receptor in the ATP-bound desensitized state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Membrane protein

EntireName: Membrane protein
Components
  • Complex: Membrane protein
    • Protein or peptide: P2X purinoceptor 4
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: MAGNESIUM ION
  • Ligand: water

-
Supramolecule #1: Membrane protein

SupramoleculeName: Membrane protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: P2X purinoceptor 4

MacromoleculeName: P2X purinoceptor 4 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.415 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAGCCAALAA FLFEYDTPRI VLIRSRKVGL MNRAVQLLIL AYVIGWVFVW EKGYQETDSV VSSVTTKVKG VAVTNTSKLG FRIWDVADY VIPAQEENSL FVMTNVILTM NQTQGLCPEI PDATTVCKSD ASCTAGSAGT HSNGVSTGRC VAFNGSVKTC E VAAWCPVE ...String:
MAGCCAALAA FLFEYDTPRI VLIRSRKVGL MNRAVQLLIL AYVIGWVFVW EKGYQETDSV VSSVTTKVKG VAVTNTSKLG FRIWDVADY VIPAQEENSL FVMTNVILTM NQTQGLCPEI PDATTVCKSD ASCTAGSAGT HSNGVSTGRC VAFNGSVKTC E VAAWCPVE DDTHVPQPAF LKAAENFTLL VKNNIWYPKF NFSKRNILPN ITTTYLKSCI YDAKTDPFCP IFRLGKIVEN AG HSFQDMA VEGGIMGIQV NWDCNLDRAA SLCLPRYSFR RLDTRDVEHN VSPGYNFRFA KYYRDLAGNE QRTLIKAYGI RFD IIVFGK AGKFDIIPTM INIGSGLALL GMATVLCDII VLYCMKKRLY YREKKYKYVE DYEQGLASEL DQ

UniProtKB: P2X purinoceptor 4

-
Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 3 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

-
Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 9 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 249 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 15582 / Average electron dose: 43.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5svl

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 122405
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more