[English] 日本語
Yorodumi
- EMDB-62931: Cryo-EM structure of nanodisc (PE:PS:PC) reconstituted GLIC at pH... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-62931
TitleCryo-EM structure of nanodisc (PE:PS:PC) reconstituted GLIC at pH 4 in iiooo conformation
Map datapostprocess masked map of GLIC nanodisc at pH4 in iiooo conformation
Sample
  • Complex: pentameric ligand-gated ion channel
    • Protein or peptide: Proton-gated ion channel
  • Ligand: CHLORIDE ION
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
Keywordspentameric ligand-gated ion channels / cis-loop / cryo-EM / nanodisc / MEMBRANE PROTEIN
Function / homology
Function and homology information


sodium channel activity / potassium channel activity / extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / identical protein binding / plasma membrane
Similarity search - Function
Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain
Similarity search - Domain/homology
Proton-gated ion channel
Similarity search - Component
Biological speciesGloeobacter violaceus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsLi Z / Bharambe N / Basak S
Funding support Singapore, 1 items
OrganizationGrant numberCountry
Other private Singapore
CitationJournal: To Be Published
Title: Cryo-EM structure of nanodisc (PE:PS:PC) reconstituted GLIC at pH 4 in iiooo conformation
Authors: Li Z / Bharambe N / Basak S
History
DepositionJan 2, 2025-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_62931.png

Downloads & links

-
Map

FileDownload / File: emd_62931.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpostprocess masked map of GLIC nanodisc at pH4 in iiooo conformation
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.76 Å/pix.
x 300 pix.
= 228. Å		0.76 Å/pix.
x 300 pix.
= 228. Å		0.76 Å/pix.
x 300 pix.
= 228. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.76 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00212
Minimum - Maximum-0.01794588 - 0.027731093
Average (Standard dev.)0.00000839549 (±0.00090002053)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 228.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_62931_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: postprocessed unmasked map of GLIC nanodisc at pH4...

Fileemd_62931_additional_1.map
Annotationpostprocessed unmasked map of GLIC nanodisc at pH4 in iiooo conformation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: autorefined map of GLIC nanodisc at pH4 in iiooo conformation

Fileemd_62931_additional_2.map
Annotationautorefined map of GLIC nanodisc at pH4 in iiooo conformation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half1 map of GLIC nanodisc at pH4 in iiooo conformation

Fileemd_62931_half_map_1.map
Annotationhalf1 map of GLIC nanodisc at pH4 in iiooo conformation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half2 map of GLIC nanodisc at pH4 in iiooo conformation

Fileemd_62931_half_map_2.map
Annotationhalf2 map of GLIC nanodisc at pH4 in iiooo conformation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : pentameric ligand-gated ion channel

EntireName: pentameric ligand-gated ion channel
Components
  • Complex: pentameric ligand-gated ion channel
    • Protein or peptide: Proton-gated ion channel
  • Ligand: CHLORIDE ION
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine

-
Supramolecule #1: pentameric ligand-gated ion channel

SupramoleculeName: pentameric ligand-gated ion channel / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Gloeobacter violaceus (bacteria)

-
Macromolecule #1: Proton-gated ion channel

MacromoleculeName: Proton-gated ion channel / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Gloeobacter violaceus (bacteria)
Molecular weightTheoretical: 35.699094 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: VSPPPPIADE PLTVNTGIYL IECYSLDDKA ETFKVNAFLS LSWKDRRLAF DPVRSGVRVK TYEPEAIWIP EIRFVNVENA RDADVVDIS VSPDGTVQYL ERFSARVLSP LDFRRYPFDS QTLHIYLIVR SVDTRNIVLA VDLEKVGKND DVFLTGWDIE S FTAVVKPA ...String:
VSPPPPIADE PLTVNTGIYL IECYSLDDKA ETFKVNAFLS LSWKDRRLAF DPVRSGVRVK TYEPEAIWIP EIRFVNVENA RDADVVDIS VSPDGTVQYL ERFSARVLSP LDFRRYPFDS QTLHIYLIVR SVDTRNIVLA VDLEKVGKND DVFLTGWDIE S FTAVVKPA NFALEDRLES KLDYQLRISR QYFSYIPNII LPMLFILFIS WTAFWSTSYE ANVTLVVSTL IAHIAFNILV ET NLPKTPY MTYTGAIIFM IYLFYFVAVI EVTVQHYLKV ESQPARAASI TRASRIAFPV VFLLANIILA FLFFG

UniProtKB: Proton-gated ion channel

-
Macromolecule #2: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 2 / Number of copies: 3 / Formula: CL
Molecular weightTheoretical: 35.453 Da

-
Macromolecule #3: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine

MacromoleculeName: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / type: ligand / ID: 3 / Number of copies: 19 / Formula: PEE
Molecular weightTheoretical: 744.034 Da
Chemical component information

ChemComp-PEE:
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE, phospholipid*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.5 mg/mL
BufferpH: 4
Component:
ConcentrationNameFormula
10.0 mMsodium citrate
150.0 mMsodium chlorideNaCl
1.0 mMEthylenediaminetetraacetic acidEDTA
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Detector mode: COUNTING / Number real images: 14076 / Average exposure time: 6.35 sec. / Average electron dose: 71.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.6 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 641067
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8wcr

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.1) / Number images used: 16336
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.1)
Final 3D classificationSoftware - Name: RELION (ver. 4.0.1)
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