[English] 日本語
Yorodumi
- PDB-9r8o: Primed-state RyR1 in 0.05% POPC micelles, in complex with a nanob... -

+
Open data


ID or keywords:

Loading...

-
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 receptor complex / ryanodine-sensitive calcium-release channel activity / 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 receptor complex / ryanodine-sensitive calcium-release channel activity / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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)

-
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

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
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

-
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)

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more