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- EMDB-41387: Cryo-EM structure of CorA in complex with conformation-specific s... -

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Basic information

Entry
Database: EMDB / ID: EMD-41387
TitleCryo-EM structure of CorA in complex with conformation-specific synthetic antibody C18 and 100 uM MgCl2, State MG0.1-1C
Map dataDensity modified map used for modeling.
Sample
  • Complex: CorA in complex with conformation-specific sAB C18 and 100 uM MgCl2
    • Protein or peptide: sAB C18 Light Chain
    • Protein or peptide: sAB C18 Heavy Chain
    • Protein or peptide: Cobalt/magnesium transport protein CorA
  • Ligand: MAGNESIUM ION
KeywordsIon Channel / Magnesium Channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


cobalt ion transport / magnesium ion transmembrane 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 / Mg2+ transporter protein, CorA-like/Zinc transport protein ZntB / CorA, cytoplasmic domain / CorA, transmembrane region / CorA-like Mg2+ transporter protein
Similarity search - Domain/homology
Cobalt/magnesium transport protein CorA
Similarity search - Component
Biological speciesThermotoga maritima (bacteria) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsErramilli SK / Perozo E / Kossiakoff AA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM117372 United States
CitationJournal: To Be Published
Title: Structural basis for CorA channel gating using conformation-specific synthetic antibodies
Authors: Erramilli SK / Nosol K / Pietrzak-Lichwa K / Li T / Dutka P / Hou J / Zhao M / Perozo E / Kossiakoff AA
History
DepositionJul 29, 2023-
Header (metadata) releaseFeb 12, 2025-
Map releaseFeb 12, 2025-
UpdateFeb 12, 2025-
Current statusFeb 12, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41387.png

Downloads & links

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Map

FileDownload / File: emd_41387.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDensity modified map used for modeling.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.07 Å/pix.
x 360 pix.
= 384.48 Å		1.07 Å/pix.
x 360 pix.
= 384.48 Å		1.07 Å/pix.
x 360 pix.
= 384.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.068 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.8836273 - 3.2423947
Average (Standard dev.)0.000008760486 (±0.03733673)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 384.47998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41387_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Consensus refinement map.

Fileemd_41387_additional_1.map
AnnotationConsensus refinement map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_41387_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_41387_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CorA in complex with conformation-specific sAB C18 and 100 uM MgCl2

EntireName: CorA in complex with conformation-specific sAB C18 and 100 uM MgCl2
Components
  • Complex: CorA in complex with conformation-specific sAB C18 and 100 uM MgCl2
    • Protein or peptide: sAB C18 Light Chain
    • Protein or peptide: sAB C18 Heavy Chain
    • Protein or peptide: Cobalt/magnesium transport protein CorA
  • Ligand: MAGNESIUM ION

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Supramolecule #1: CorA in complex with conformation-specific sAB C18 and 100 uM MgCl2

SupramoleculeName: CorA in complex with conformation-specific sAB C18 and 100 uM MgCl2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Thermotoga maritima (bacteria)

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Macromolecule #1: sAB C18 Light Chain

MacromoleculeName: sAB C18 Light Chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.258783 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQSSSSLITF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQSSSSLITF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #2: sAB C18 Heavy Chain

MacromoleculeName: sAB C18 Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.228006 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: EISEVQLVES GGGLVQPGGS LRLSCAASGF NVSYYSIHWV RQAPGKGLEW VASISSSSGS TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARSYWYYIWS YSYGNAMDYW GQGTLVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK D YFPEPVTV ...String:
EISEVQLVES GGGLVQPGGS LRLSCAASGF NVSYYSIHWV RQAPGKGLEW VASISSSSGS TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARSYWYYIWS YSYGNAMDYW GQGTLVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK D YFPEPVTV SWNSGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYICNVNHKP SNTKVDKKVE PKSCDKTHT

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Macromolecule #3: Cobalt/magnesium transport protein CorA

MacromoleculeName: Cobalt/magnesium transport protein CorA / type: protein_or_peptide / ID: 3 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Thermotoga maritima (bacteria)
Molecular weightTheoretical: 44.067805 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MGSSHHHHHH SSGRENLYFQ GHMEEKRLSA KKGLPPGTLV YTGKYREDFE IEVMNYSIEE FREFKTTDVE SVLPFRDSST PTWINITGI HRTDVVQRVG EFFGIHPLVL EDILNVHQRP KVEFFENYVF IVLKMFTYDK NLHELESEQV SLILTKNCVL M FQEKIGDV ...String:
MGSSHHHHHH SSGRENLYFQ GHMEEKRLSA KKGLPPGTLV YTGKYREDFE IEVMNYSIEE FREFKTTDVE SVLPFRDSST PTWINITGI HRTDVVQRVG EFFGIHPLVL EDILNVHQRP KVEFFENYVF IVLKMFTYDK NLHELESEQV SLILTKNCVL M FQEKIGDV FDPVRERIRY NRGIIRKKRA DYLLYSLIDA LVDDYFVLLE KIDDEIDVLE EEVLERPEKE TVQRTHQLKR NL VELRKTI WPLREVLSSL YRDVPPLIEK ETVPYFRDVY DHTIQIADTV ETFRDIVSGL LDVYLSSVSN KTNEVMKVLT IIA TIFMPL TFIAGIYGMN FEYMPELRWK WGYPVVLAVM GVIAVIMVVY FKKKKWL

UniProtKB: Cobalt/magnesium transport protein CorA

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
SoftwareName: EPU
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 10849 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 38262
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

SoftwareName: Coot
Output model

PDB-8tmf:
Cryo-EM structure of CorA in complex with conformation-specific synthetic antibody C18 and 100 uM MgCl2, State MG0.1-1C

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