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- PDB-8rml: Structure of heteromeric CALHM2/4 channel in complex with synthet... -

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Basic information

Entry
Database: PDB / ID: 8rml
TitleStructure of heteromeric CALHM2/4 channel in complex with synthetic nanobody SbC4
Components
  • Calcium homeostasis modulator protein 2
  • Calcium homeostasis modulator protein 4
  • Synthetic nanobody SbC4
KeywordsMEMBRANE PROTEIN / ion channel / large pore channels / sybody / CALHM
Function / homologyCalcium homeostasis modulator family / Calcium homeostasis modulator / monoatomic cation channel activity / positive regulation of apoptotic process / membrane / Calcium homeostasis modulator protein 4 / Calcium homeostasis modulator protein 2
Function and homology information
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.84 Å
AuthorsDrozdzyk, K. / Dutzler, R.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: To Be Published
Title: Structural features of heteromeric channels composed of CALHM2 and CALHM4 paralogs
Authors: Peter, M. / Drozdzyk, K. / Dutzler, R.
History
DepositionJan 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calcium homeostasis modulator protein 4
L: Synthetic nanobody SbC4
B: Calcium homeostasis modulator protein 4
C: Calcium homeostasis modulator protein 2
D: Calcium homeostasis modulator protein 2
E: Calcium homeostasis modulator protein 2
F: Calcium homeostasis modulator protein 2
G: Calcium homeostasis modulator protein 2
H: Calcium homeostasis modulator protein 2
I: Calcium homeostasis modulator protein 2
J: Calcium homeostasis modulator protein 2
K: Calcium homeostasis modulator protein 4
M: Synthetic nanobody SbC4


Theoretical massNumber of molelcules
Total (without water)430,49613
Polymers430,49613
Non-polymers00
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: Protein Calcium homeostasis modulator protein 4 / Protein FAM26D


Mass: 35981.656 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALHM4, C6orf78, FAM26D, UNQ6481/PRO21277 / Production host: Homo sapiens (human) / References: UniProt: Q5JW98
#2: Antibody Synthetic nanobody SbC4


Mass: 12877.380 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli MC1061 (bacteria)
#3: Protein
Calcium homeostasis modulator protein 2 / Protein FAM26B


Mass: 37099.535 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALHM2, FAM26B / Production host: Homo sapiens (human) / References: UniProt: Q9HA72

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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: Complex of heteromeric CALHM2/4 channel with synthetic nanobody SbC4
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.43 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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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: 2400 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 131652 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00725198
ELECTRON MICROSCOPYf_angle_d0.74234300
ELECTRON MICROSCOPYf_dihedral_angle_d3.9913418
ELECTRON MICROSCOPYf_chiral_restr0.0373838
ELECTRON MICROSCOPYf_plane_restr0.0044364

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