[English] 日本語
Yorodumi
- PDB-3jcf: Cryo-EM structure of the magnesium channel CorA in the closed sym... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3jcf
TitleCryo-EM structure of the magnesium channel CorA in the closed symmetric magnesium-bound state
ComponentsMagnesium transport protein CorA
KeywordsTRANSPORT PROTEIN / membrane protein / ion channel / magnesium channel / pentameric complex / symmetry vs. asymmetry / conformational change / gating mechanism / direct electron detector / K2
Function / homology
Function and homology information


magnesium ion transmembrane transport / cobalt ion transport / cobalt ion transmembrane transporter activity / magnesium ion transmembrane transporter activity / cobalt ion binding / protein homooligomerization / magnesium ion binding / identical protein binding / plasma membrane
Similarity search - Function
Magnesium transport protein CorA, transmembrane region / CorA soluble domain-like / Magnesium/cobalt transport protein CorA / Mg2+ transporter protein, CorA-like/Zinc transport protein ZntB / CorA, cytoplasmic domain / CorA, transmembrane region / CorA-like Mg2+ transporter protein / Beta Polymerase; domain 2 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle ...Magnesium transport protein CorA, transmembrane region / CorA soluble domain-like / Magnesium/cobalt transport protein CorA / Mg2+ transporter protein, CorA-like/Zinc transport protein ZntB / CorA, cytoplasmic domain / CorA, transmembrane region / CorA-like Mg2+ transporter protein / Beta Polymerase; domain 2 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Cobalt/magnesium transport protein CorA
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsMatthies, D. / Perozo, E. / Subramaniam, S.
CitationJournal: Cell / Year: 2016
Title: Cryo-EM Structures of the Magnesium Channel CorA Reveal Symmetry Break upon Gating.
Authors: Doreen Matthies / Olivier Dalmas / Mario J Borgnia / Pawel K Dominik / Alan Merk / Prashant Rao / Bharat G Reddy / Shahidul Islam / Alberto Bartesaghi / Eduardo Perozo / Sriram Subramaniam /
Abstract: CorA, the major Mg(2+) uptake system in prokaryotes, is gated by intracellular Mg(2+) (KD ∼ 1-2 mM). X-ray crystallographic studies of CorA show similar conformations under Mg(2+)-bound and Mg(2+)- ...CorA, the major Mg(2+) uptake system in prokaryotes, is gated by intracellular Mg(2+) (KD ∼ 1-2 mM). X-ray crystallographic studies of CorA show similar conformations under Mg(2+)-bound and Mg(2+)-free conditions, but EPR spectroscopic studies reveal large Mg(2+)-driven quaternary conformational changes. Here, we determined cryo-EM structures of CorA in the Mg(2+)-bound closed conformation and in two open Mg(2+)-free states at resolutions of 3.8, 7.1, and 7.1 Å, respectively. In the absence of bound Mg(2+), four of the five subunits are displaced to variable extents (∼ 10-25 Å) by hinge-like motions as large as ∼ 35° at the stalk helix. The transition between a single 5-fold symmetric closed state and an ensemble of low Mg(2+), open, asymmetric conformational states is, thus, the key structural signature of CorA gating. This mechanism is likely to apply to other structurally similar divalent ion channels.
History
DepositionDec 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_imaging_optics / em_software
Item: _em_imaging_optics.energyfilter_name / _em_software.image_processing_id / _em_software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-6551
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Magnesium transport protein CorA
B: Magnesium transport protein CorA
C: Magnesium transport protein CorA
D: Magnesium transport protein CorA
E: Magnesium transport protein CorA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,80618
Polymers207,4905
Non-polymers31613
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein
Magnesium transport protein CorA


Mass: 41498.082 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: corA, TM_0561 / Plasmid: CorA-pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) PlysS / References: UniProt: Q9WZ31
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Mg

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: CorA from Thermotoga maritima in the presence of magnesium
Type: COMPLEX / Details: One homopentamer of CorA / Synonym: CorA
Molecular weightValue: 0.2 MDa / Experimental value: NO
Buffer solutionName: 50 mM HEPES, pH 7.3, 150 mM NaCl, 40 mM MgCl2, 0.5 mM DDM
pH: 7.3
Details: 50 mM HEPES, pH 7.3, 150 mM NaCl, 40 mM MgCl2, 0.5 mM DDM
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 300 mesh Cu R1.2/1.3 holey carbon grids from Quantifoil, plasma-cleaned
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Temp: 90 K / Humidity: 86 %
Details: Grids were blotted at 4 degrees Celsius for 7 seconds after a 10-second pre-blotting period, then plunge-frozen in liquid ethane.
Method: Grids were blotted at 4 degrees Celsius for 7 seconds after a 10-second pre-blotting period, then plunge-frozen in liquid ethane.

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Aug 21, 2014 / Details: Parallel beam illumination
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM / Electron beam tilt params: 5
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Calibrated magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 860 nm / Cs: 2.7 mm
Astigmatism: Objective lens astigmatism was corrected at 105,000 times magnification.
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Specimen holder type: Liquid nitrogen-cooled / Temperature: 79.7 K / Temperature (max): 79.8 K / Temperature (min): 79.6 K
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Details: post-column Quantum GIF
EM imaging opticsEnergyfilter name: GIF / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV
Image scansNum. digital images: 959

-
Processing

EM software
IDNameCategory
1Cootmodel fitting
2PHENIXmodel fitting
3UCSF Chimeramodel fitting
4RELION3D reconstruction
CTF correctionDetails: CTF parameters obtained from whole micrograph
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionMethod: RELION / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46206 / Nominal pixel size: 1.275 Å / Actual pixel size: 1.275 Å
Details: Final map was calculated from one dataset. (Single particle details: The particles were selected using an automatic selection program. 3D classification, 3D refinement, and postprocessing ...Details: Final map was calculated from one dataset. (Single particle details: The particles were selected using an automatic selection program. 3D classification, 3D refinement, and postprocessing were done using RELION 1.3.) (Single particle--Applied symmetry: C5)
Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 4I0U

4i0u


Accession code: 4I0U / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms14215 0 13 0 14228

+
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