[English] 日本語
Yorodumi
- EMDB-34376: Cryo-EM structure of human Pannexin-2 in pre-open state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-34376
TitleCryo-EM structure of human Pannexin-2 in pre-open state
Map data
Sample
  • Complex: Pannexin-2
    • Protein or peptide: Pannexin-2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsPannexin / ATP / Inner channel lipids / Cell-cell communication / MEMBRANE PROTEIN
Function / homology
Function and homology information


Electric Transmission Across Gap Junctions / wide pore channel activity / positive regulation of interleukin-1 production / gap junction / monoatomic cation transport / monoatomic ion transmembrane transport / response to ischemia / cell-cell signaling / structural molecule activity / plasma membrane / cytoplasm
Similarity search - Function
Pannexin / Innexin / Innexin / Pannexin family profile.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsCong Y / Jin X / Kong F / Yan C
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2020YFA0509301 China
CitationJournal: To Be Published
Title: Inner channel lipids regulated gating mechanism of human pannexins.
Authors: Cong Y / Jin X / Kong F / Yan C
History
DepositionSep 23, 2022-
Header (metadata) releaseApr 17, 2024-
Map releaseApr 17, 2024-
UpdateApr 17, 2024-
Current statusApr 17, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_34376.png

Downloads & links

-
Map

FileDownload / File: emd_34376.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.29
Minimum - Maximum-2.1639738 - 3.8989239
Average (Standard dev.)0.0064459452 (±0.08755336)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_34376_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_34376_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_34376_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Pannexin-2

EntireName: Pannexin-2
Components
  • Complex: Pannexin-2
    • Protein or peptide: Pannexin-2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: Pannexin-2

SupramoleculeName: Pannexin-2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 500 KDa

-
Macromolecule #1: Pannexin-2

MacromoleculeName: Pannexin-2 / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 74.54193 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHHLLEQSAD MATALLAGEK LRELILPGAQ DDKAGALAAL LLQLKLELPF DRVVTIGTVL VPILLVTLVF TKNFAEEPIY CYTPHNFTR DQALYARGYC WTELRDALPG VDASLWPSLF EHKFLPYALL AFAAIMYVPA LGWEFLASTR LTSELNFLLQ E IDNCYHRA ...String:
MHHLLEQSAD MATALLAGEK LRELILPGAQ DDKAGALAAL LLQLKLELPF DRVVTIGTVL VPILLVTLVF TKNFAEEPIY CYTPHNFTR DQALYARGYC WTELRDALPG VDASLWPSLF EHKFLPYALL AFAAIMYVPA LGWEFLASTR LTSELNFLLQ E IDNCYHRA AEGRAPKIEK QIQSKGPGIT EREKREIIEN AEKEKSPEQN LFEKYLERRG RSNFLAKLYL ARHVLILLLS AV PISYLCT YYATQKQNEF TCALGASPDG AAGAGPAVRV SCKLPSVQLQ RIIAGVDIVL LCVMNLIILV NLIHLFIFRK SNF IFDKLH KVGIKTRRQW RRSQFCDINI LAMFCNENRD HIKSLNRLDF ITNESDLMYD NVVRQLLAAL AQSNHDATPT VRDS GVQTV DPSANPAEPD GAAEPPVVKR PRKKMKWIPT SNPLPQPFKE PLAIMRVENS KAEKPKPARR KTATDTLIAP LLDRS AHHY KGGGGDPGPG PAPAPAPPPA PDKKHARHFS LDVHPYILGT KKAKAEAVPA ALPASRSQEG GFLSQAEDCG LGLAPA PIK DAPLPEKEIP YPTEPARAGL PSGGPFHVRS PPAAPAVAPL TPASLGKAEP LTILSRNATH PLLHINTLYE AREEEDG GP RLPQDVGDLI AIPAPQQILI ATFDEPRTVV STVEF

UniProtKB: Pannexin-2

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 7 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.8 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 131444

+
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