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- PDB-3j8h: Structure of the rabbit ryanodine receptor RyR1 in complex with F... -

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Basic information

Entry
Database: PDB / ID: 3j8h
TitleStructure of the rabbit ryanodine receptor RyR1 in complex with FKBP12 at 3.8 Angstrom resolution
Components
  • Peptidyl-prolyl cis-trans isomerase FKBP1A
  • Ryanodine receptor 1
KeywordsTRANSPORT PROTEIN/ISOMERASE / rabbit ryanodine receptor RyR1 / high-conductance intracellular Ca2+ channels / excitation-contraction coupling / TRANSPORT PROTEIN-ISOMERASE complex
Function / homology
Function and homology information


cytoplasmic side of membrane / ATP-gated ion channel activity / terminal cisterna / ryanodine receptor complex / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / skin development / cellular response to caffeine / intracellularly gated calcium channel activity ...cytoplasmic side of membrane / ATP-gated ion channel activity / terminal cisterna / ryanodine receptor complex / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / skin development / cellular response to caffeine / intracellularly gated calcium channel activity / outflow tract morphogenesis / organelle membrane / toxic substance binding / voltage-gated calcium channel activity / skeletal muscle fiber development / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / release of sequestered calcium ion into cytosol / regulation of ryanodine-sensitive calcium-release channel activity / sarcoplasmic reticulum membrane / cellular response to calcium ion / muscle contraction / sarcoplasmic reticulum / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / calcium ion transmembrane transport / calcium channel activity / intracellular calcium ion homeostasis / disordered domain specific binding / protein homotetramerization / transmembrane transporter binding / calmodulin binding / intracellular membrane-bounded organelle / calcium ion binding / ATP binding / membrane / identical protein binding / cytosol
Similarity search - Function
: / Ryanodine receptor junctional solenoid repeat / Ryanodine receptor, SPRY domain 2 / Ryanodine Receptor TM 4-6 / Ryanodine receptor / Ryanodine receptor, SPRY domain 1 / Ryanodine receptor, SPRY domain 3 / Ryanodine Receptor TM 4-6 / Ryanodine receptor Ryr / RyR domain ...: / Ryanodine receptor junctional solenoid repeat / Ryanodine receptor, SPRY domain 2 / Ryanodine Receptor TM 4-6 / Ryanodine receptor / Ryanodine receptor, SPRY domain 1 / Ryanodine receptor, SPRY domain 3 / Ryanodine Receptor TM 4-6 / Ryanodine receptor Ryr / RyR domain / RyR/IP3 receptor binding core, RIH domain superfamily / : / RyR/IP3R Homology associated domain / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / RyR and IP3R Homology associated / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / MIR motif / MIR domain / MIR domain profile. / Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases / Mir domain superfamily / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / Ion transport domain / Ion transport protein / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Ryanodine receptor 1 / Peptidyl-prolyl cis-trans isomerase FKBP1A
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsYan, Z. / Bai, X. / Yan, C. / Wu, J. / Scheres, S.H.W. / Shi, Y. / Yan, N.
CitationJournal: Nature / Year: 2015
Title: Structure of the rabbit ryanodine receptor RyR1 at near-atomic resolution.
Authors: Zhen Yan / Xiaochen Bai / Chuangye Yan / Jianping Wu / Zhangqiang Li / Tian Xie / Wei Peng / Changcheng Yin / Xueming Li / Sjors H W Scheres / Yigong Shi / Nieng Yan /
Abstract: The ryanodine receptors (RyRs) are high-conductance intracellular Ca(2+) channels that play a pivotal role in the excitation-contraction coupling of skeletal and cardiac muscles. RyRs are the largest ...The ryanodine receptors (RyRs) are high-conductance intracellular Ca(2+) channels that play a pivotal role in the excitation-contraction coupling of skeletal and cardiac muscles. RyRs are the largest known ion channels, with a homotetrameric organization and approximately 5,000 residues in each protomer. Here we report the structure of the rabbit RyR1 in complex with its modulator FKBP12 at an overall resolution of 3.8 Å, determined by single-particle electron cryomicroscopy. Three previously uncharacterized domains, named central, handle and helical domains, display the armadillo repeat fold. These domains, together with the amino-terminal domain, constitute a network of superhelical scaffold for binding and propagation of conformational changes. The channel domain exhibits the voltage-gated ion channel superfamily fold with distinct features. A negative-charge-enriched hairpin loop connecting S5 and the pore helix is positioned above the entrance to the selectivity-filter vestibule. The four elongated S6 segments form a right-handed helical bundle that closes the pore at the cytoplasmic border of the membrane. Allosteric regulation of the pore by the cytoplasmic domains is mediated through extensive interactions between the central domains and the channel domain. These structural features explain high ion conductance by RyRs and the long-range allosteric regulation of channel activities.
History
DepositionOct 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Advisory
Revision 1.2Jan 21, 2015Group: Structure summary
Revision 1.3Feb 25, 2015Group: Database references
Revision 1.4Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

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Assembly

Deposited unit
A: Ryanodine receptor 1
B: Peptidyl-prolyl cis-trans isomerase FKBP1A
C: Ryanodine receptor 1
D: Peptidyl-prolyl cis-trans isomerase FKBP1A
E: Ryanodine receptor 1
F: Peptidyl-prolyl cis-trans isomerase FKBP1A
G: Ryanodine receptor 1
H: Peptidyl-prolyl cis-trans isomerase FKBP1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,048,45412
Polymers2,048,1928
Non-polymers2624
Water0
1


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

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Components

#1: Protein
Ryanodine receptor 1 / / RYR-1 / RyR1 / Skeletal muscle calcium release channel / Skeletal muscle ryanodine receptor / ...RYR-1 / RyR1 / Skeletal muscle calcium release channel / Skeletal muscle ryanodine receptor / Skeletal muscle-type ryanodine receptor / Type 1 ryanodine receptor


Mass: 500211.562 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P11716
#2: Protein
Peptidyl-prolyl cis-trans isomerase FKBP1A / PPIase FKBP1A / 12 kDa FK506-binding protein / 12 kDa FKBP / FKBP-12 / Calstabin-1 / FK506-binding ...PPIase FKBP1A / 12 kDa FK506-binding protein / 12 kDa FKBP / FKBP-12 / Calstabin-1 / FK506-binding protein 1A / FKBP-1A / Immunophilin FKBP12 / Rotamase


Mass: 11836.508 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: FKBP1A, FKBP1, FKBP12 / Production host: Escherichia coli (E. coli) / References: UniProt: P62943, peptidylprolyl isomerase
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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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

Component
IDNameTypeParent-ID
1rabbit ryanodine receptor RyR1 bound to modulator FKBP12COMPLEX0
2RyR1Ryanodine receptor 11
3FKBP11
Buffer solutionName: 20 mM MOPS sodium, pH 7.4, 250 mM NaCl, 2 mM DTT, 2 mM EGTA, 0.015% Tween20, protein inhibitors
pH: 7.4
Details: 20 mM MOPS sodium, pH 7.4, 250 mM NaCl, 2 mM DTT, 2 mM EGTA, 0.015% Tween20, protein inhibitors
SpecimenConc.: 0.06 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: holey carbon grids (Quantifoil CuR2/2), on which a home-made continuous carbon film (estimated to be ~30 Angstrom thick) had previously been deposited
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: NITROGEN / Humidity: 100 %
Details: Protein solution was applied to glow-discharged carbon coated grid and blotted for 2 seconds before plunging into liquid nitrogen (FEI VITROBOT MARK III)
Method: protein solution was applied to glow-discharged carbon coated grid and blotted for 2 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300 / Date: Jun 21, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 78000 X / Calibrated magnification: 104748 X / Nominal defocus max: 5600 nm / Nominal defocus min: 1900 nm / Cs: 2 mm
Specimen holderSpecimen holder type: GATAN LIQUID NITROGEN / Temperature: 85 K / Temperature (max): 90 K / Temperature (min): 80 K
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 2013/08/13 / Classification: refinement / Contact author: Garib N. Murshudov / Contact author email: garib[at]mrc-lmb.cam.ac.uk
Description: (un)restrained refinement or idealisation of macromolecular structures
EM software
IDNameVersionCategory
1CTFFIND3CTF correction
2Cootmodel fitting
3PHENIXmodel fitting
4REFMACmodel fitting
5RELION1.33D reconstruction
CTF correctionDetails: Contrast transfer function parameters were estimated using CTFFIND3
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 65872 / Nominal pixel size: 1.34 Å / Actual pixel size: 1.34 Å
Details: All two- and three-dimensional classifications and refinements were performed using RELION 1.3. The model was built manually in COOT, and was refined in real space using Phenix and in ...Details: All two- and three-dimensional classifications and refinements were performed using RELION 1.3. The model was built manually in COOT, and was refined in real space using Phenix and in reciprocal space using Refmac.
Symmetry type: POINT
RefinementDetails: HYDROGENS HAVE BEEN ADDED IN THEIR RIDING POSITIONS
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms111120 0 4 0 111124

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