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- PDB-7umz: Cryo-EM structure of rabbit RyR1 in the presence of high Mg2+ and... -

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Basic information

Entry
Database: PDB / ID: 7umz
TitleCryo-EM structure of rabbit RyR1 in the presence of high Mg2+ and AMP-PCP in nanodisc
ComponentsRyanodine receptor 1
KeywordsTRANSPORT PROTEIN / Ryanodine Receptor / RyR1 / Intracellular Calcium channel / Mg2+ / Inhibition / Excitation-Contraction coupling
Function / homologyPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
Function and homology information
Biological speciesOryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.09 Å
AuthorsNayak, A.R. / Samso, M.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)R01 AR068431 United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)R01 HL133182 United States
Other privateMDA 352845
National Institutes of Health/National Cancer Institute (NIH/NCI)HSSN261200800001E United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24 GM116789 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24 GM116790 United States
CitationJournal: Nat Commun / Year: 2024
Title: Interplay between Mg2+ and Ca2+ at multiple sites of the ryanodine receptor
Authors: Nayak, A.R. / Rangubpit, W. / Will, A.H. / Hu, Y. / Castro-Hartmann, P. / Lobo, J.J. / Dryden, K. / Lamb, G.D. / Sompornpisut, P. / Samso, M.
History
DepositionApr 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 2.0Mar 6, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / citation / citation_author / entity_name_com / pdbx_contact_author / pdbx_entity_instance_feature / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conf
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _struct_conf.beg_auth_asym_id / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_asym_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_asym_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_asym_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_class / _struct_conf.pdbx_PDB_helix_length
Description: Polymer backbone linkage / Provider: author / Type: Coordinate replacement
Revision 2.1May 22, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation_author.identifier_ORCID
Revision 2.2Oct 30, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ryanodine receptor 1
B: Ryanodine receptor 1
C: Ryanodine receptor 1
D: Ryanodine receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,180,22733
Polymers2,171,5484
Non-polymers8,67929
Water1448
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, Negative staining
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Ryanodine receptor 1


Mass: 542887.000 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)

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Non-polymers , 5 types, 37 molecules

#2: Chemical
ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-LBN / 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / (2R)-2-[(9Z)-9-Octadecenoyloxy]-3-(palmitoyloxy)propyl 2-(trimethylammonio)ethyl phosphate


Mass: 760.076 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C42H82NO8P / Comment: phospholipid*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY
Sequence detailsResidues that could not be identified were recorded as UNK. The actual amino acid sequence is ...Residues that could not be identified were recorded as UNK. The actual amino acid sequence is identical to Uniprot P11716.

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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: Rabbit RyR1 with AMP-PCP and inhibiting Mg2+ / Type: COMPLEX
Details: Purified RyR1 was reconstituted with membrane scaffold protein, MSP1E3D1 and POPC.
Entity ID: #1 / Source: NATURAL
Molecular weightValue: 2.26 MDa / Experimental value: YES
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / Strain: New Zeland White / Cellular location: Sarcoplasmic reticulum membrane / Organ: Skeletal Muscle / Organelle: Sarcoplasmic reticulum
Buffer solutionpH: 7.4
Details: 20 mM MOPS (pH=7.4), 635mM KCl, 2mM DTT, 11.6mM MgCl2, 1mM AMP-PCP
SpecimenConc.: 4.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Purified RyR1 was reconstituted with membrane scaffold protein MSP1E3D1 and POPC at a 1:2:50 molar ratio.
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: 277 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 magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 9140
EM imaging opticsEnergyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC3.2particle selection
2EPUimage acquisition
4cryoSPARC3.2CTF correction
7Coot0.9.5.8model fitting
12cryoSPARC3.23D reconstruction
19PHENIX1.20rc4-4425model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 525190
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 167778 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL

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