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- PDB-9r8o: Primed-state RyR1 in 0.05% POPC micelles, in complex with a nanob... -

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Basic information

Entry
Database: PDB / ID: 9r8o
TitlePrimed-state RyR1 in 0.05% POPC micelles, in complex with a nanobody and FKBP
Components
  • Nanobody 9657
  • Peptidyl-prolyl cis-trans isomerase FKBP1B
  • Ryanodine receptor 1
KeywordsTRANSPORT PROTEIN / Ion channel / Ca2+ / tetramer
Function / homology
Function and homology information


ATP-gated ion channel activity / terminal cisterna / ryanodine-sensitive calcium-release channel activity / ryanodine receptor complex / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / cellular response to caffeine / skin development / organelle membrane / intracellularly gated calcium channel activity ...ATP-gated ion channel activity / terminal cisterna / ryanodine-sensitive calcium-release channel activity / ryanodine receptor complex / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / cellular response to caffeine / skin development / organelle membrane / intracellularly gated calcium channel activity / smooth endoplasmic reticulum / outflow tract morphogenesis / regulation of ryanodine-sensitive calcium-release channel activity / toxic substance binding / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / striated muscle contraction / 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 / sarcoplasmic reticulum membrane / muscle contraction / cellular response to calcium ion / sarcoplasmic reticulum / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / sarcolemma / calcium ion transmembrane transport / calcium channel activity / Z disc / intracellular calcium ion homeostasis / disordered domain specific binding / protein homotetramerization / transmembrane transporter binding / calmodulin binding / intracellular membrane-bounded organelle / calcium ion binding / ATP binding / identical protein binding / membrane
Similarity search - Function
Ryanodine receptor, SPRY domain 2 / : / Ryanodine receptor junctional solenoid repeat / 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, SPRY domain 2 / : / Ryanodine receptor junctional solenoid repeat / 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. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / 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
ADENOSINE-5'-TRIPHOSPHATE / CAFFEINE / Chem-POV / Ryanodine receptor 1 / Peptidyl-prolyl cis-trans isomerase FKBP1B
Similarity search - Component
Biological speciesLama glama (llama)
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLi, C. / Efremov, R.G.
Funding support Belgium, European Union, 3items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G0H5916N Belgium
Research Foundation - Flanders (FWO)G054617N Belgium
European Research Council (ERC)726436European Union
CitationJournal: To Be Published
Title: Open-state RyR1 in 0.05% POPC micelles, in complex with a nanobody and FKBP
Authors: Li, C. / Efremov, R.G.
History
DepositionMay 16, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
K: Nanobody 9657
L: Peptidyl-prolyl cis-trans isomerase FKBP1B
J: Ryanodine receptor 1
A: Nanobody 9657
B: Peptidyl-prolyl cis-trans isomerase FKBP1B
C: Ryanodine receptor 1
D: Nanobody 9657
E: Peptidyl-prolyl cis-trans isomerase FKBP1B
F: Ryanodine receptor 1
G: Nanobody 9657
H: Peptidyl-prolyl cis-trans isomerase FKBP1B
I: Ryanodine receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,395,15968
Polymers2,361,52912
Non-polymers33,63056
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "D"
d_3ens_1chain "G"
d_4ens_1chain "K"
d_1ens_2chain "B"
d_2ens_2chain "E"
d_3ens_2chain "H"
d_4ens_2chain "L"
d_1ens_3chain "J"
d_2ens_3chain "F"
d_3ens_3chain "I"
d_4ens_3chain "C"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1GLNGLNSERSERAD1 - 1261 - 126
d_21ens_1GLNGLNSERSERDG1 - 1261 - 126
d_31ens_1GLNGLNSERSERGJ1 - 1261 - 126
d_41ens_1GLNGLNSERSERKA1 - 1261 - 126
d_11ens_2GLYGLYGLUGLUBE1 - 1071 - 107
d_21ens_2GLYGLYGLUGLUEH1 - 1071 - 107
d_31ens_2GLYGLYGLUGLUHK1 - 1071 - 107
d_41ens_2GLYGLYGLUGLULB1 - 1071 - 107
d_11ens_3VALVALSERSERJC11 - 50371 - 5027
d_12ens_3ATPATPATPATPJM5101
d_13ens_3CFFCFFCFFCFFJN5102
d_14ens_3CACACACAJO5103
d_15ens_3POVPOVPOVPOVJP5104
d_16ens_3POVPOVPOVPOVJQ5105
d_17ens_3POVPOVPOVPOVICB5101
d_18ens_3POVPOVPOVPOVIDB5102
d_19ens_3POVPOVPOVPOVCZ5101
d_110ens_3POVPOVPOVPOVCAA5102
d_111ens_3POVPOVPOVPOVIEB5103
d_112ens_3POVPOVPOVPOVJR5106
d_113ens_3POVPOVPOVPOVJS5107
d_114ens_3POVPOVPOVPOVJT5108
d_21ens_3VALVALSERSERFI11 - 50371 - 5027
d_22ens_3ATPATPATPATPFQA5103
d_23ens_3CFFCFFCFFCFFFRA5104
d_24ens_3CACACACAFSA5105
d_25ens_3POVPOVPOVPOVFTA5106
d_26ens_3POVPOVPOVPOVFUA5107
d_27ens_3POVPOVPOVPOVCLA5113
d_28ens_3POVPOVPOVPOVCMA5114
d_29ens_3POVPOVPOVPOVIFB5104
d_210ens_3POVPOVPOVPOVIGB5105
d_211ens_3POVPOVPOVPOVCNA5115
d_212ens_3POVPOVPOVPOVFVA5108
d_213ens_3POVPOVPOVPOVFWA5109
d_214ens_3POVPOVPOVPOVFXA5110
d_31ens_3VALVALSERSERIL11 - 50371 - 5027
d_32ens_3ATPATPATPATPIHB5106
d_33ens_3CFFCFFCFFCFFIIB5107
d_34ens_3CACACACAIJB5108
d_35ens_3POVPOVPOVPOVIKB5109
d_36ens_3POVPOVPOVPOVILB5110
d_37ens_3POVPOVPOVPOVFZA5112
d_38ens_3POVPOVPOVPOVFAB5113
d_39ens_3POVPOVPOVPOVJX5112
d_310ens_3POVPOVPOVPOVJY5113
d_311ens_3POVPOVPOVPOVFBB5114
d_312ens_3POVPOVPOVPOVIMB5111
d_313ens_3POVPOVPOVPOVINB5112
d_314ens_3POVPOVPOVPOVIOB5113
d_41ens_3VALVALSERSERCF11 - 50371 - 5027
d_42ens_3ATPATPATPATPCBA5103
d_43ens_3CFFCFFCFFCFFCCA5104
d_44ens_3CACACACACDA5105
d_45ens_3POVPOVPOVPOVCEA5106
d_46ens_3POVPOVPOVPOVCFA5107
d_47ens_3POVPOVPOVPOVCGA5108
d_48ens_3POVPOVPOVPOVJV5110
d_49ens_3POVPOVPOVPOVFOA5101
d_410ens_3POVPOVPOVPOVFPA5102
d_411ens_3POVPOVPOVPOVJW5111
d_412ens_3POVPOVPOVPOVCHA5109
d_413ens_3POVPOVPOVPOVCIA5110
d_414ens_3POVPOVPOVPOVCJA5111

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.00698726329148, -0.999974898561, 0.00117490405107), (0.999968089524, -0.00699175638375, -0.00386461857646), (0.00387273621187, 0.0011478634518, 0.999991842129)481.788529083, 2.67638615817, -1.81691657635
2given(-0.999917951804, 0.0114872451198, 0.00566858530853), (-0.0114948301496, -0.999933077658, -0.00130731967079), (0.00565318845202, -0.00137237183288, 0.999983078885)474.878459956, 484.102888171, -1.85088002217
3given(-0.00859069029894, 0.999788631712, -0.0186786492917), (-0.99989381609, -0.00836871361459, 0.0119298439869), (0.0117710061295, 0.0187791515147, 0.999754363273)7.03295222061, 479.145859674, -9.86303241282
4given(-0.00285196915554, -0.999989709533, 0.00352804491593), (0.999995034673, -0.00285667817453, -0.0013304205314), (0.00134048532966, 0.00352423307971, 0.999992891415)479.417708819, 0.897122171292, -1.25061514959
5given(-0.999998438948, 0.00176522078548, -7.80789862771E-5), (-0.00176536365813, -0.999996694635, 0.00186928050018), (-7.47790354048E-5, 0.00186941541994, 0.999998249846)478.766291606, 479.375954515, -0.380842529065
6given(0.0101942432097, 0.999945156832, 0.00240015275125), (-0.999926237823, 0.010178142345, 0.006627543459), (0.00660275088717, -0.00246753850066, 0.999975157159)-4.01580149618, 475.549967617, -1.83190080642
7given(-0.999999999482, -8.00072725792E-6, -3.11809141222E-5), (8.00231956452E-6, -0.999999998664, -5.1066916682E-5), (-3.11805055081E-5, -5.10671661752E-5, 0.99999999821)479.142821226, 479.148446212, 0.0150431869143
8given(1.0241115427E-5, 0.999999998522, 5.33940421073E-5), (-0.999999999743, 1.02421964363E-5, -2.024564191E-5), (-2.02461887524E-5, -5.33938347556E-5, 0.99999999837)-0.0161644507925, 479.140354018, 0.0125914337298
9given(-5.67940862428E-6, -0.999999998223, -5.93423846818E-5), (0.999999998944, -5.68211432939E-6, 4.55947468942E-5), (-4.55950840034E-5, -5.93421256679E-5, 0.9999999972)479.151774312, -0.00891271505816, 0.0208463214602

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Components

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Protein , 2 types, 8 molecules LBEHJCFI

#2: Protein
Peptidyl-prolyl cis-trans isomerase FKBP1B / PPIase FKBP1B / 12.6 kDa FK506-binding protein / 12.6 kDa FKBP / FKBP-12.6 / FK506-binding protein ...PPIase FKBP1B / 12.6 kDa FK506-binding protein / 12.6 kDa FKBP / FKBP-12.6 / FK506-binding protein 1B / FKBP-1B / Immunophilin FKBP12.6 / Rotamase


Mass: 11667.305 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: Q8HYX6, peptidylprolyl isomerase
#3: 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: 564931.750 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P11716

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Antibody , 1 types, 4 molecules KADG

#1: Antibody
Nanobody 9657


Mass: 13783.114 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 56 molecules

#4: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#5: Chemical
ChemComp-CFF / CAFFEINE / 3,7-DIHYDRO-1,3,7-TRIMETHYL-1H-PURINE-2,6-DIONE


Mass: 194.191 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10N4O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical...
ChemComp-POV / (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / POPC


Mass: 760.076 Da / Num. of mol.: 40 / Source method: obtained synthetically / Formula: C42H82NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#8: Chemical
ChemComp-ZN / ZINC ION


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

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Details

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

Component
IDNameTypeEntity IDParent-IDSource
1Ryanodine receptor 1 complex with nanobody and FKBP12COMPLEX#1-#30MULTIPLE SOURCES
2Ryanodine receptor 1COMPLEX#11NATURAL
3Nanobody 9657COMPLEX#21RECOMBINANT
4Peptidyl-prolyl cis-trans isomerase FKBP1BCOMPLEX#31NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Oryctolagus cuniculus (rabbit)9986
33Vicugna pacos (alpaca)30538
44Oryctolagus cuniculus (rabbit)9986
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
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: 1500 nm
Specimen holderSpecimen holder model: JEOL CRYOSPECPORTER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.3.0particle selectiontemplate picking was used for particle picking
4RELION4.1CTF correction
10cryoSPARC3initial Euler assignment
12RELION4.1classification
13cryoSPARC4.313D reconstruction
Image processingDetails: The movies were selected after MotionCor correction and CTF refinement with the parameters: total drift less than 30 angstrom and resolution better than 5 angstrom
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 333223
Details: Particles were picked by template picking in Cryosparc
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39983 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 111.23 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0034148744
ELECTRON MICROSCOPYf_angle_d0.7709201440
ELECTRON MICROSCOPYf_chiral_restr0.044522072
ELECTRON MICROSCOPYf_plane_restr0.00626056
ELECTRON MICROSCOPYf_dihedral_angle_d8.04821024
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2DAELECTRON MICROSCOPYNCS constraints3.15879138924E-13
ens_1d_3DAELECTRON MICROSCOPYNCS constraints1.06259136628E-10
ens_1d_4DAELECTRON MICROSCOPYNCS constraints3.46396283675E-11
ens_2d_2EBELECTRON MICROSCOPYNCS constraints5.81267651268E-12
ens_2d_3EBELECTRON MICROSCOPYNCS constraints3.45712891471E-13
ens_2d_4EBELECTRON MICROSCOPYNCS constraints1.29538200752E-10
ens_3d_2CJELECTRON MICROSCOPYNCS constraints7.18502810635E-11
ens_3d_3CJELECTRON MICROSCOPYNCS constraints6.91848129257E-12
ens_3d_4CJELECTRON MICROSCOPYNCS constraints3.22119085891E-12

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