[English] 日本語
Yorodumi
- EMDB-4441: MloK1 map from single particle analysis of 2D crystals, class 1 (... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-4441
TitleMloK1 map from single particle analysis of 2D crystals, class 1 (extended conformation)
Map dataMloK1 map from single particle analysis of 2D crystals, class 1 (extended conformation)
Sample
  • Complex: MloK1 potassium channel in lipidic bilayer of 2D crystals
    • Protein or peptide: Cyclic nucleotide-gated potassium channel mll3241
  • Ligand: POTASSIUM ION
KeywordsVoltage-gated potassium channel / Cyclic nucleotide-binding domain / ion channel / ion transport / MEMBRANE PROTEIN
Function / homology
Function and homology information


potassium channel activity / cAMP binding / protein-containing complex binding / identical protein binding / plasma membrane
Similarity search - Function
Cyclic nucleotide-regulated ion channel, N-terminal / : / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily ...Cyclic nucleotide-regulated ion channel, N-terminal / : / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Cyclic nucleotide-gated potassium channel mll3241
Similarity search - Component
Biological speciesMesorhizobium loti MAFF303099 (bacteria) / Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.2 Å
AuthorsRighetto R / Biyani N
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation205320_166164 Switzerland
CitationJournal: Nat Commun / Year: 2019
Title: Retrieving high-resolution information from disordered 2D crystals by single-particle cryo-EM.
Authors: Ricardo D Righetto / Nikhil Biyani / Julia Kowal / Mohamed Chami / Henning Stahlberg /
Abstract: Electron crystallography can reveal the structure of membrane proteins within 2D crystals under close-to-native conditions. High-resolution structural information can only be reached if crystals are ...Electron crystallography can reveal the structure of membrane proteins within 2D crystals under close-to-native conditions. High-resolution structural information can only be reached if crystals are perfectly flat and highly ordered. In practice, such crystals are difficult to obtain. Available image unbending algorithms correct for disorder, but only perform well on images of non-tilted, flat crystals, while out-of-plane distortions are not addressed. Here, we present an approach that employs single-particle refinement procedures to locally unbend crystals in 3D. With this method, density maps of the MloK1 potassium channel with a resolution of 4 Å were obtained from images of 2D crystals that do not diffract beyond 10 Å. Furthermore, 3D classification allowed multiple structures to be resolved, revealing a series of MloK1 conformations within a single 2D crystal. This conformational heterogeneity explains the poor diffraction observed and is related to channel function. The approach is implemented in the FOCUS package.
History
DepositionNov 27, 2018-
Header (metadata) releaseApr 24, 2019-
Map releaseApr 24, 2019-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6iax
  • Surface level: 2.5
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6iax
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4441.png

Downloads & links

-
Map

FileDownload / File: emd_4441.map.gz / Format: CCP4 / Size: 4.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMloK1 map from single particle analysis of 2D crystals, class 1 (extended conformation)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 104 pix.
= 135.2 Å		1.3 Å/pix.
x 104 pix.
= 135.2 Å		1.3 Å/pix.
x 104 pix.
= 135.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.5 / Movie #1: 2.5
Minimum - Maximum-5.9093347 - 7.596996
Average (Standard dev.)0.000000000015317 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions104104104
Spacing104104104
CellA=B=C: 135.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z104104104
origin x/y/z0.0000.0000.000
length x/y/z135.200135.200135.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS104104104
D min/max/mean-5.9097.5970.000

-
Supplemental data

-
Mask #1

Fileemd_4441_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_4441_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_4441_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : MloK1 potassium channel in lipidic bilayer of 2D crystals

EntireName: MloK1 potassium channel in lipidic bilayer of 2D crystals
Components
  • Complex: MloK1 potassium channel in lipidic bilayer of 2D crystals
    • Protein or peptide: Cyclic nucleotide-gated potassium channel mll3241
  • Ligand: POTASSIUM ION

-
Supramolecule #1: MloK1 potassium channel in lipidic bilayer of 2D crystals

SupramoleculeName: MloK1 potassium channel in lipidic bilayer of 2D crystals
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mesorhizobium loti MAFF303099 (bacteria)
Molecular weightTheoretical: 160 KDa

-
Macromolecule #1: Cyclic nucleotide-gated potassium channel mll3241

MacromoleculeName: Cyclic nucleotide-gated potassium channel mll3241 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099) (bacteria)
Strain: LMG 29417 / CECT 9101 / MAFF 303099
Molecular weightTheoretical: 37.766297 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSVLPFLRIY APLNAVLAAP GLLAVAALTI PDMSGRSRLA LAALLAVIWG AYLLQLAATL LKRRAGVVRD RTPKIAIDVL AVLVPLAAF LLDGSPDWSL YCAVWLLKPL RDSTFFPVLG RVLANEARNL IGVTTLFGVV LFAVALAAYV IERDIQPEKF G SIPQAMWW ...String:
MSVLPFLRIY APLNAVLAAP GLLAVAALTI PDMSGRSRLA LAALLAVIWG AYLLQLAATL LKRRAGVVRD RTPKIAIDVL AVLVPLAAF LLDGSPDWSL YCAVWLLKPL RDSTFFPVLG RVLANEARNL IGVTTLFGVV LFAVALAAYV IERDIQPEKF G SIPQAMWW AVVTLSTTGY GDTIPQSFAG RVLAGAVMMS GIGIFGLWAG ILATGFYQEV RRGDFVRNWQ LVAAVPLFQK LG PAVLVEI VRALRARTVP AGAVICRIGE PGDRMFFVVE GSVSVATPNP VELGPGAFFG EMALISGEPR SATVSAATTV SLL SLHSAD FQMLCSSSPE IAEIFRKTAL ERRGAAASA

UniProtKB: Cyclic nucleotide-gated potassium channel mll3241

-
Macromolecule #2: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: K
Molecular weightTheoretical: 39.098 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state2D array

-
Sample preparation

BufferpH: 7.6
Details: 20 mM KCl, 20 mM Tris-HCl pH 7.6, 1 mM BaCl2, 1 mM EDTA, 0.2 mM cAMP
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 270 / Average exposure time: 16.0 sec. / Average electron dose: 45.0 e/Å2
Details: The dataset of 346 movies recorded and processed for Kowal et al. (2018) 2 was employed. As reported, the data were collected on an FEI Titan Krios TEM equipped with a Gatan K2 DED. Total ...Details: The dataset of 346 movies recorded and processed for Kowal et al. (2018) 2 was employed. As reported, the data were collected on an FEI Titan Krios TEM equipped with a Gatan K2 DED. Total dose: 40 e-/A^2 distributed over 40 movie frames. Pixel size: 1.3 A on the sample level (counting mode). Nominal tilt range: -55 to +55 degrees.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.3 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 50000
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: 231688
Details: The particle positions were given by the cross-correlation profile generated by the classical unbending algorithm.
Startup modelType of model: OTHER
Details: An initial model was generated using the tilt geometry determined by the classical 2D electron crystallography approach.
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 5.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN (ver. 9.11)
Details: Resolution estimated based on FSC between spherically-masked half-maps with a soft edge, with the FSC normalized to an expected volume corresponding to a molecular weight of 160 kDa.
Number images used: 27849
Initial angle assignmentType: OTHER / Software - Name: FOCUS
Details: An initial model was generated using the tilt geometry determined by the classical 2D electron crystallography approach.
Final angle assignmentType: OTHER / Software - Name: FREALIGN (ver. 9.11)
Final 3D classificationNumber classes: 8 / Avg.num./class: 28961 / Software - Name: FREALIGN (ver. 9.11)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

6i9d


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsThe consensus model was flexibily fit in to the EM map of this class using Normal Mode Analysis with iMODFIT, and then real-space refined using PHENIX.
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-6iax:
MloK1 model from single particle analysis of 2D crystals, class 1 (extended conformation)

+
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