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- PDB-8sr8: Cryo-EM structure of TRPM2 chanzyme in the presence of EDTA (apo ... -

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Basic information

Entry
Database: PDB / ID: 8sr8
TitleCryo-EM structure of TRPM2 chanzyme in the presence of EDTA (apo state)
ComponentsTRPM2 chanzyme
KeywordsTRANSPORT PROTEIN / TRPM2 Chanzyme / Channel-enzyme
Function / homology
Function and homology information


calcium channel activity / plasma membrane
Similarity search - Function
TRPM, SLOG domain / SLOG in TRPM / Nudix hydrolase domain profile. / NUDIX hydrolase domain / Voltage-dependent channel domain superfamily / NUDIX hydrolase-like domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
CHOLESTEROL / Nudt9 protein
Similarity search - Component
Biological speciesSalpingoeca rosetta (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.77 Å
AuthorsHuang, Y. / Kumar, S. / Lu, W. / Du, J.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL153219 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS112363 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS111031 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM129547 United States
CitationJournal: To Be Published
Title: Coupling enzymatic activity and gating in an ancient TRPM chanzyme and its molecular evolution
Authors: Huang, Y. / Kumar, S. / Lu, W. / Du, J.
History
DepositionMay 5, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 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: TRPM2 chanzyme
B: TRPM2 chanzyme
C: TRPM2 chanzyme
D: TRPM2 chanzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)677,65016
Polymers673,0104
Non-polymers4,64012
Water0
1


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

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Components

#1: Protein
TRPM2 chanzyme / TRPM2 chanzyme


Mass: 168252.484 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salpingoeca rosetta (eukaryote) / Gene: PTSG_05449 / Production host: Homo sapiens (human) / References: UniProt: F2UB89
#2: Chemical
ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C27H46O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: TRPM2 chanzyme in the presence of EDTA (apo state) / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Salpingoeca rosetta (eukaryote)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenConc.: 8.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingAverage exposure time: 0.2 sec. / Electron dose: 54 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: NONE
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 168854 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01640128
ELECTRON MICROSCOPYf_angle_d1.87254800
ELECTRON MICROSCOPYf_dihedral_angle_d5.5995816
ELECTRON MICROSCOPYf_chiral_restr0.0916428
ELECTRON MICROSCOPYf_plane_restr0.0117048

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