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- EMDB-13326: T. maritima CorA in DDM micelles without Mg2+ bound in D2O -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-13326
TitleT. maritima CorA in DDM micelles without Mg2+ bound in D2O
Map dataT. maritima CorA in DDM micelles without Mg2 bound (in EDTA).
Sample
  • Complex: CorA pentamer without Mg2+ bound
    • Protein or peptide: Thermotoga maritima CorA
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/cobalt transport protein CorA / CorA, cytoplasmic domain / CorA, transmembrane region / Mg2+ transporter protein, CorA-like/Zinc transport protein ZntB / CorA-like Mg2+ transporter protein
Similarity search - Domain/homology
Cobalt/magnesium transport protein CorA
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
Methodsingle particle reconstruction / negative staining / Resolution: 15.0 Å
AuthorsLarsen AH / Johansen NT / Arleth L
Funding support Denmark, 1 items
OrganizationGrant numberCountry
LundbeckfondenR155-2015-2666 Denmark
CitationJournal: Elife / Year: 2022
Title: Mg-dependent conformational equilibria in CorA and an integrated view on transport regulation.
Authors: Nicolai Tidemand Johansen / Marta Bonaccorsi / Tone Bengtsen / Andreas Haahr Larsen / Frederik Grønbæk Tidemand / Martin Cramer Pedersen / Pie Huda / Jens Berndtsson / Tamim Darwish / ...Authors: Nicolai Tidemand Johansen / Marta Bonaccorsi / Tone Bengtsen / Andreas Haahr Larsen / Frederik Grønbæk Tidemand / Martin Cramer Pedersen / Pie Huda / Jens Berndtsson / Tamim Darwish / Nageshewar Rao Yepuri / Anne Martel / Thomas Günther Pomorski / Andrea Bertarello / Mark Sansom / Mikaela Rapp / Ramon Crehuet / Tobias Schubeis / Kresten Lindorff-Larsen / Guido Pintacuda / Lise Arleth /
Abstract: The CorA family of proteins regulates the homeostasis of divalent metal ions in many bacteria, archaea, and eukaryotic mitochondria, making it an important target in the investigation of the ...The CorA family of proteins regulates the homeostasis of divalent metal ions in many bacteria, archaea, and eukaryotic mitochondria, making it an important target in the investigation of the mechanisms of transport and its functional regulation. Although numerous structures of open and closed channels are now available for the CorA family, the mechanism of the transport regulation remains elusive. Here, we investigated the conformational distribution and associated dynamic behaviour of the pentameric Mg channel CorA at room temperature using small-angle neutron scattering (SANS) in combination with molecular dynamics (MD) simulations and solid-state nuclear magnetic resonance spectroscopy (NMR). We find that neither the Mg-bound closed structure nor the Mg-free open forms are sufficient to explain the average conformation of CorA. Our data support the presence of conformational equilibria between multiple states, and we further find a variation in the behaviour of the backbone dynamics with and without Mg. We propose that CorA must be in a dynamic equilibrium between different non-conducting states, both symmetric and asymmetric, regardless of bound Mg but that conducting states become more populated in Mg-free conditions. These properties are regulated by backbone dynamics and are key to understanding the functional regulation of CorA.
History
DepositionAug 4, 2021-
Header (metadata) releaseFeb 23, 2022-
Map releaseFeb 23, 2022-
UpdateFeb 23, 2022-
Current statusFeb 23, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0365
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0365
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13326.png

Downloads & links

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Map

FileDownload / File: emd_13326.map.gz / Format: CCP4 / Size: 1.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationT. maritima CorA in DDM micelles without Mg2 bound (in EDTA).
Voxel sizeX=Y=Z: 3.14 Å
Density
Contour LevelBy AUTHOR: 0.0365 / Movie #1: 0.0365
Minimum - Maximum-0.10087103 - 0.20043154
Average (Standard dev.)0.001686081 (±0.018797787)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions707070
Spacing707070
CellA=B=C: 219.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.143.143.14
M x/y/z707070
origin x/y/z0.0000.0000.000
length x/y/z219.800219.800219.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS707070
D min/max/mean-0.1010.2000.002

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Supplemental data

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Sample components

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Entire : CorA pentamer without Mg2+ bound

EntireName: CorA pentamer without Mg2+ bound
Components
  • Complex: CorA pentamer without Mg2+ bound
    • Protein or peptide: Thermotoga maritima CorA

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Supramolecule #1: CorA pentamer without Mg2+ bound

SupramoleculeName: CorA pentamer without Mg2+ bound / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Thermotoga maritima (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21(DE3) STAR / Recombinant plasmid: pET
Molecular weightTheoretical: 207.5 kDa/nm

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Macromolecule #1: Thermotoga maritima CorA

MacromoleculeName: Thermotoga maritima CorA / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermotoga maritima (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GMEEKRLSAK KGLPPGTLVY TGKYREDFEI EVMNYSIEEF REFKTTDVES VLPFRDSSTP TWINITGIH RTDVVQRVGE FFGIHPLVLE DILNVHQRPK VEFFENYVFI VLKMFTYDKN L HELESEQV SLILTKNCVL MFQEKIGDVF DPVRERIRYN RGIIRKKRAD ...String:
GMEEKRLSAK KGLPPGTLVY TGKYREDFEI EVMNYSIEEF REFKTTDVES VLPFRDSSTP TWINITGIH RTDVVQRVGE FFGIHPLVLE DILNVHQRPK VEFFENYVFI VLKMFTYDKN L HELESEQV SLILTKNCVL MFQEKIGDVF DPVRERIRYN RGIIRKKRAD YLLYSLIDAL VD DYFVLLE KIDDEIDVLE EEVLERPEKE TVQRTHQLKR NLVELRKTIW PLREVLSSLY RDV PPLIEK ETVPYFRDVY DHTIQIADTV ETFRDIVSGL LDVYLSSVSN KTNEVMKVLT IIAT IFMPL TFIAGIYGMN FEYMPELRWK WGYPVVLAVM GVIAVIMVVY FKKKKWL

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.015 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris
150.0 mMNaClsodium chloride
1.0 mMC10H16N2O8EDTA
0.5 mMC24H46O11DDM

Details: Buffer was made with 100% D2O and titrated with DCl
StainingType: NEGATIVE / Material: Uranyl acetate / Details: Sample stained with 2% uranyl acetate for 15 sec
GridMaterial: COPPER / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE
DetailsSEC-purified prior to fixation.

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 10.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 193606
CTF correctionSoftware - Name: Xmipp (ver. 3.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 36176
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 3.0)
Details: See: J. Struct Biol., 2012, 180, 519-530; doi: 10.1016/j.sjb.2012.09.006; RELION: Implementation of a Bayesian approach to cryo-EM structure determination; Sjors H.W.Scheres
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 3.0)
Details: See: J. Struct Biol., 2012, 180, 519-530; doi: 10.1016/j.sjb.2012.09.006; RELION: Implementation of a Bayesian approach to cryo-EM structure determination; Sjors H.W.Scheres
Final 3D classificationNumber classes: 10 / Avg.num./class: 5710 / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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