[English] 日本語
Yorodumi
- EMDB-1424: The structure of the prokaryotic cyclic nucleotide-modulated pota... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1424
TitleThe structure of the prokaryotic cyclic nucleotide-modulated potassium channel MloK1 at 16 A resolution.
Map dataThis is the 3D map of MloK1 in 17-A resolution determined by NS-TEM.
Sample
  • Sample: Full-length prokaryotic potassium channel MloK1
  • Protein or peptide: Prokaryotic potassium channel
  • Ligand: Cyclic nucleotide
Biological speciesMesorhizobium loti (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / negative staining / Resolution: 16.3 Å
AuthorsChiu P-L / Pagel M / Evans J / Chou H-T / Gipson B
CitationJournal: Structure / Year: 2007
Title: The structure of the prokaryotic cyclic nucleotide-modulated potassium channel MloK1 at 16 A resolution.
Authors: Po-Lin Chiu / Matthew D Pagel / James Evans / Hui-Ting Chou / Xiangyan Zeng / Bryant Gipson / Henning Stahlberg / Crina M Nimigean /
Abstract: The gating ring of cyclic nucleotide-modulated channels is proposed to be either a two-fold symmetric dimer of dimers or a four-fold symmetric tetramer based on high-resolution structure data of ...The gating ring of cyclic nucleotide-modulated channels is proposed to be either a two-fold symmetric dimer of dimers or a four-fold symmetric tetramer based on high-resolution structure data of soluble cyclic nucleotide-binding domains and functional data on intact channels. We addressed this controversy by obtaining structural data on an intact, full-length, cyclic nucleotide-modulated potassium channel, MloK1, from Mesorhizobium loti, which also features a putative voltage-sensor. We present here the 3D single-particle structure by transmission electron microscopy and the projection map of membrane-reconstituted 2D crystals of MloK1 in the presence of cAMP. Our data show a four-fold symmetric arrangement of the CNBDs, separated by discrete gaps. A homology model for full-length MloK1 suggests a vertical orientation for the CNBDs. The 2D crystal packing in the membrane-embedded state is compatible with the S1-S4 domains in the vertical "up" state.
History
DepositionJun 7, 2007-
Header (metadata) releaseSep 13, 2007-
Map releaseSep 18, 2007-
UpdateNov 7, 2012-
Current statusNov 7, 2012Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.2
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1424.gif

Downloads & links

-
Map

FileDownload / File: emd_1424.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the 3D map of MloK1 in 17-A resolution determined by NS-TEM.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2 Å/pix.
x 80 pix.
= 160. Å		2 Å/pix.
x 80 pix.
= 160. Å		2 Å/pix.
x 80 pix.
= 160. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.01 / Movie #1: 1.2
Minimum - Maximum-2.31585288 - 4.84229708
Average (Standard dev.)0.01301534 (±0.84763032)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 160.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z222
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z160.000160.000160.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-150-150-149
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS808080
D min/max/mean-2.3164.8420.013

-
Supplemental data

-
Sample components

-
Entire : Full-length prokaryotic potassium channel MloK1

EntireName: Full-length prokaryotic potassium channel MloK1
Components
  • Sample: Full-length prokaryotic potassium channel MloK1
  • Protein or peptide: Prokaryotic potassium channel
  • Ligand: Cyclic nucleotide

-
Supramolecule #1000: Full-length prokaryotic potassium channel MloK1

SupramoleculeName: Full-length prokaryotic potassium channel MloK1 / type: sample / ID: 1000 / Oligomeric state: One tetramer with ligand binding / Number unique components: 2
Molecular weightExperimental: 155.2 KDa / Theoretical: 152.5 KDa / Method: Calculation by the protein sequence

-
Macromolecule #1: Prokaryotic potassium channel

MacromoleculeName: Prokaryotic potassium channel / type: protein_or_peptide / ID: 1 / Name.synonym: MloK1 / Details: Each subunit of the MloK1 / Number of copies: 1 / Oligomeric state: Tetramer / Recombinant expression: Yes
Source (natural)Organism: Mesorhizobium loti (bacteria) / Strain: MloK1 / synonym: Soil bacteria / Tissue: Prokaryote / Organelle: Cell membrane / Location in cell: Cell membrane
Molecular weightExperimental: 37.74 KDa / Theoretical: 38.42 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pASK90

-
Macromolecule #2: Cyclic nucleotide

MacromoleculeName: Cyclic nucleotide / type: ligand / ID: 2 / Name.synonym: cAMP
Details: The ligand for cyclic nucleotide-modulated channel, MloK1
Recombinant expression: No
Source (natural)Organism: synthetic construct (others)
Molecular weightExperimental: 369.2 Da / Theoretical: 369.2 Da

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.2 mg/mL
BufferpH: 7.6 / Details: 100 mM KCl, 20 mM Tris-Cl, 5 mM DM, 200 uM cAMP
StainingType: NEGATIVE
Details: Grids with absorbed proteins deeply stained with 2% uranyl formate
GridDetails: 400 mesh copper grid
VitrificationCryogen name: NONE / Instrument: OTHER

-
Electron microscopy

MicroscopeJEOL 2100F
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 60000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 1.2 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Side-entry room temperature holder / Specimen holder model: HOME BUILD
TemperatureAverage: 298.15 K
DateOct 27, 2005
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Digitization - Sampling interval: 10 µm / Number real images: 34 / Bits/pixel: 16
Tilt angle min0
Tilt angle max0

-
Image processing

CTF correctionDetails: CTF correction of each particle
Final two d classificationNumber classes: 190
Final angle assignmentDetails: Refinement with MRA method built in EMAN package
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 16.3 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER, EMAN / Number images used: 14921

+
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