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- PDB-8tmp: Cryo-EM structure of magnesium depleted CorA in complex with conf... -

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Basic information

Entry
Database: PDB / ID: 8tmp
TitleCryo-EM structure of magnesium depleted CorA in complex with conformation-specific synthetic antibody C18, State MGD-1B
Components
  • Cobalt/magnesium transport protein CorA
  • sAB C18 Heavy Chain
  • sAB C18 Light Chain
KeywordsMEMBRANE PROTEIN / Ion Channel / Magnesium Channel
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 speciesHomo sapiens (human)
Thermotoga maritima (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsErramilli, S.K. / Perozo, E. / Kossiakoff, A.A.
Funding support United States, 1items
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, S.K. / Nosol, K. / Pietrzak-Lichwa, K. / Li, T. / Dutka, P. / Hou, J. / Zhao, M. / Perozo, E. / Kossiakoff, A.A.
History
DepositionJul 29, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: sAB C18 Light Chain
H: sAB C18 Heavy Chain
A: Cobalt/magnesium transport protein CorA
B: Cobalt/magnesium transport protein CorA
C: Cobalt/magnesium transport protein CorA
D: Cobalt/magnesium transport protein CorA
E: Cobalt/magnesium transport protein CorA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)254,5519
Polymers254,5027
Non-polymers492
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Antibody sAB C18 Light Chain


Mass: 17167.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21 (bacteria)
#2: Antibody sAB C18 Heavy Chain


Mass: 16995.771 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21 (bacteria)
#3: Protein
Cobalt/magnesium transport protein CorA


Mass: 44067.805 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: corA
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9WZ31
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Magnesium-free CorA in complex with conformation-specific sAB C18
Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Thermotoga maritima (bacteria)2336
31Homo sapiens (human)9606
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 12478

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Processing

EM software
IDNameCategory
1RELIONparticle selection
3EPUimage acquisition
5RELIONCTF correction
8Cootmodel fitting
9PHENIXmodel refinement
10cryoSPARCinitial Euler assignment
11RELIONclassification
12cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 59130 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00316506
ELECTRON MICROSCOPYf_angle_d0.57322380
ELECTRON MICROSCOPYf_dihedral_angle_d4.232166
ELECTRON MICROSCOPYf_chiral_restr0.0412543
ELECTRON MICROSCOPYf_plane_restr0.0052800

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