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- PDB-9rcw: Primed-state RyR1 in 0.01% POPC micelles, in complex with a nanob... -

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Basic information

Entry
Database: PDB / ID: 9rcw
TitlePrimed-state RyR1 in 0.01% POPC micelles, in complex with a nanobody and FKBP12
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: Primed-state RyR1 in 0.01% POPC micelles, in complex with a nanobody and FKBP
Authors: Li, C. / Efremov, R.G.
History
DepositionMay 30, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)2,382,99852
Polymers2,361,52912
Non-polymers21,46940
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 "J"
d_2ens_1chain "C"
d_3ens_1chain "G"
d_4ens_1chain "A"
d_1ens_2chain "D"
d_2ens_2chain "B"
d_3ens_2chain "H"
d_4ens_2chain "K"
d_1ens_3chain "E"
d_2ens_3chain "F"
d_3ens_3chain "I"
d_4ens_3chain "L"
d_1ens_4chain "P"
d_2ens_4chain "N"
d_3ens_4chain "O"
d_4ens_4chain "M"

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_1VALVALSERSERJF11 - 50371 - 5027
d_21ens_1VALVALSERSERCI11 - 50371 - 5027
d_31ens_1VALVALSERSERGC11 - 50371 - 5027
d_41ens_1VALVALSERSERAL11 - 50371 - 5027
d_11ens_2GLNGLNSERSERDG1 - 1261 - 126
d_21ens_2GLNGLNSERSERBJ1 - 1261 - 126
d_31ens_2GLNGLNSERSERHA1 - 1261 - 126
d_41ens_2GLNGLNSERSERKD1 - 1261 - 126
d_11ens_3GLYGLYGLUGLUEH1 - 1071 - 107
d_21ens_3GLYGLYGLUGLUFK1 - 1071 - 107
d_31ens_3GLYGLYGLUGLUIB1 - 1071 - 107
d_41ens_3GLYGLYGLUGLULE1 - 1071 - 107
d_11ens_4ZNZNZNZNJX5102
d_12ens_4ATPATPATPATPJY5103
d_13ens_4CFFCFFCFFCFFJZ5104
d_14ens_4CACACACAJAA5105
d_15ens_4POVPOVPOVPOVJBA5106
d_16ens_4POVPOVPOVPOVJCA5107
d_17ens_4POVPOVPOVPOVJDA5108
d_18ens_4POVPOVPOVPOVCPA5110
d_19ens_4POVPOVPOVPOVJEA5109
d_110ens_4POVPOVPOVPOVJFA5110
d_21ens_4ZNZNZNZNAQA5101
d_22ens_4ATPATPATPATPARA5102
d_23ens_4CFFCFFCFFCFFASA5103
d_24ens_4CACACACAATA5104
d_25ens_4POVPOVPOVPOVAUA5105
d_26ens_4POVPOVPOVPOVAVA5106
d_27ens_4POVPOVPOVPOVAWA5107
d_28ens_4POVPOVPOVPOVAXA5108
d_29ens_4POVPOVPOVPOVAYA5109
d_210ens_4POVPOVPOVPOVAZA5110
d_31ens_4ZNZNZNZNGM5101
d_32ens_4ATPATPATPATPGN5102
d_33ens_4CFFCFFCFFCFFGO5103
d_34ens_4CACACACAGP5104
d_35ens_4POVPOVPOVPOVGQ5105
d_36ens_4POVPOVPOVPOVGR5106
d_37ens_4POVPOVPOVPOVGS5107
d_38ens_4POVPOVPOVPOVGT5108
d_39ens_4POVPOVPOVPOVGU5109
d_310ens_4POVPOVPOVPOVGV5110
d_41ens_4ZNZNZNZNCGA5101
d_42ens_4ATPATPATPATPCHA5102
d_43ens_4CFFCFFCFFCFFCIA5103
d_44ens_4CACACACACJA5104
d_45ens_4POVPOVPOVPOVCKA5105
d_46ens_4POVPOVPOVPOVCLA5106
d_47ens_4POVPOVPOVPOVJW5101
d_48ens_4POVPOVPOVPOVCMA5107
d_49ens_4POVPOVPOVPOVCNA5108
d_410ens_4POVPOVPOVPOVCOA5109

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4

NCS oper:
IDCodeMatrixVector
1given(4.82457169206E-5, -0.999999998494, -2.61706269195E-5), (0.99999999878, 4.82459952751E-5, -1.06356164866E-5), (1.06368790985E-5, -2.61701137646E-5, 0.999999999601)488.542256696, -0.00804259468961, 0.00179361106811
2given(-9.60034120615E-5, 0.999999993645, -5.91106759092E-5), (-0.999999993931, -9.60002171644E-5, 5.40498732345E-5), (5.40441982533E-5, 5.91158645228E-5, 0.999999996792)0.0356505982776, 488.543358309, -0.0219544088926
3given(-0.999999999388, -3.24255397078E-5, 1.31659149268E-5), (3.24257890433E-5, -0.999999999295, 1.89381878958E-5), (1.31653008366E-5, 1.89386147994E-5, 0.999999999734)488.545994718, 488.534626569, -0.0042567655656
4given(-0.00486507913078, -0.999968427687, -0.00628288426276), (0.999976382334, -0.00489542650865, 0.00482385453597), (-0.0048544596339, -0.00625926744167, 0.999968627404)491.901619152, -0.0891756031246, 3.38729025752
5given(-0.999898046275, -0.00319737687123, -0.0139166747754), (0.00333608975602, -0.999944876633, -0.00995561155443), (-0.0138840757993, -0.0100010238189, 0.999853595264)492.468292252, 489.372932268, 7.94049030873
6given(-0.00189912851989, 0.999998177435, -0.000196056125583), (-0.999992614561, -0.00189977296251, -0.00334091097077), (-0.00334127734387, 0.000189709858316, 0.999994399922)0.838334945514, 489.739532499, 1.41557799902
7given(-0.00261305017711, -0.999996059487, 0.00102614792056), (0.999993670207, -0.00261551919534, -0.00241217835672), (0.00241485276109, 0.00101983828217, 0.999996564202)489.236621385, 1.01361205167, -1.03582289689
8given(-0.999992859025, -0.00377026463718, 0.00025884946778), (0.0037687740883, -0.999977575855, -0.00553571404332), (0.000279714770201, -0.00553469896776, 0.999984644316)489.136272708, 488.293799008, 0.701286617727
9given(0.0126318687368, 0.999919913191, 0.000776592304775), (-0.99991104362, 0.0126284226973, 0.00429275980343), (0.00428260887411, -0.00083074880029, 0.999990484514)-4.45956180679, 485.328960391, -1.38194820543
10given(-0.999999999866, -8.25455414315E-6, 1.41197074444E-5), (8.25465568409E-6, -0.99999999994, 7.19139068787E-6), (1.41196480819E-5, 7.19150724023E-6, 0.999999999874)488.541347792, 488.543454712, -0.0046367651787
11given(-1.46950632429E-6, 0.999999999927, -1.19783749591E-5), (-0.999999999885, -1.46932549083E-6, 1.50966475262E-5), (1.50966299249E-5, 1.19783971423E-5, 0.999999999814)0.00161358572328, 488.539573833, -0.00497320163015
12given(-0.00283189831887, -0.999983456694, -0.00500666461793), (0.999990115769, -0.002814685008, -0.00344178914422), (0.00342764002181, -0.00501636192779, 0.999981543528)490.698307369, 1.98337892016, 0.181118606658

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Components

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Protein , 2 types, 8 molecules ILEFGJCA

#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 HKDB

#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, 40 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: 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
#6: 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
#7: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 760.076 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C42H82NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM

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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

ComponentName: Ryanodine receptor 1 complex with nanobody and FKBP12 / Type: COMPLEX / Entity ID: #1-#3 / Source: NATURAL
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
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 softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
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: 151.18 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005147832
ELECTRON MICROSCOPYf_angle_d0.8274200280
ELECTRON MICROSCOPYf_chiral_restr0.047522048
ELECTRON MICROSCOPYf_plane_restr0.006125932
ELECTRON MICROSCOPYf_dihedral_angle_d6.925720592
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2FJELECTRON MICROSCOPYNCS constraints5.71604807807E-10
ens_1d_3FJELECTRON MICROSCOPYNCS constraints9.56578796094E-13
ens_1d_4FJELECTRON MICROSCOPYNCS constraints2.23986474827E-11
ens_2d_2GDELECTRON MICROSCOPYNCS constraints1.21014742622E-11
ens_2d_3GDELECTRON MICROSCOPYNCS constraints1.17071381898E-12
ens_2d_4GDELECTRON MICROSCOPYNCS constraints6.66772906052E-11
ens_3d_2HEELECTRON MICROSCOPYNCS constraints3.47339274503E-12
ens_3d_3HEELECTRON MICROSCOPYNCS constraints8.74073815788E-12
ens_3d_4HEELECTRON MICROSCOPYNCS constraints4.2253369372E-13
ens_4d_2XJELECTRON MICROSCOPYNCS constraints3.18530278091E-11
ens_4d_3XJELECTRON MICROSCOPYNCS constraints8.00600591708E-11
ens_4d_4XJELECTRON MICROSCOPYNCS constraints4.59533739738E-13

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