[English] 日本語
Yorodumi
- EMDB-71924: Cryo-EM Structure of Pig Ryanodine Receptor 1 R615C Mutant: Atorv... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-71924
TitleCryo-EM Structure of Pig Ryanodine Receptor 1 R615C Mutant: Atorvastatin Bound Open Conformation Composite Map
Map data
Sample
  • Complex: Ryanodine Receptor 1 and FKBP12.6 complex
    • Protein or peptide: Ryanodine receptor 1
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase FKBP1B
  • Ligand: CAFFEINE
  • Ligand: CALCIUM ION
  • Ligand: 7-[2-(4-FLUORO-PHENYL)-5-ISOPROPYL-3-PHENYL-4-PHENYLCARBAMOYL-PYRROL-1-YL]- 3,5-DIHYDROXY-HEPTANOIC ACID
  • Ligand: ZINC ION
KeywordsIon Channel / Calcium Channel / TRANSPORT PROTEIN
Function / homology
Function and homology information


positive regulation of sequestering of calcium ion / negative regulation of calcium-mediated signaling / negative regulation of insulin secretion involved in cellular response to glucose stimulus / neuronal action potential propagation / negative regulation of release of sequestered calcium ion into cytosol / insulin secretion involved in cellular response to glucose stimulus / terminal cisterna / ryanodine-sensitive calcium-release channel activity / ryanodine receptor complex / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum ...positive regulation of sequestering of calcium ion / negative regulation of calcium-mediated signaling / negative regulation of insulin secretion involved in cellular response to glucose stimulus / neuronal action potential propagation / negative regulation of release of sequestered calcium ion into cytosol / insulin secretion involved in cellular response to glucose stimulus / terminal cisterna / ryanodine-sensitive calcium-release channel activity / ryanodine receptor complex / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / response to redox state / ossification involved in bone maturation / 'de novo' protein folding / negative regulation of heart rate / cellular response to caffeine / skin development / FK506 binding / organelle membrane / smooth endoplasmic reticulum / outflow tract morphogenesis / smooth muscle contraction / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / T cell proliferation / voltage-gated calcium channel activity / calcium channel inhibitor activity / skeletal muscle fiber development / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / release of sequestered calcium ion into cytosol / calcium channel complex / sarcoplasmic reticulum membrane / cellular response to calcium ion / muscle contraction / protein maturation / sarcoplasmic reticulum / calcium channel regulator activity / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / calcium-mediated signaling / sarcolemma / calcium ion transmembrane transport / Stimuli-sensing channels / calcium channel activity / Z disc / intracellular calcium ion homeostasis / positive regulation of cytosolic calcium ion concentration / protein refolding / protein homotetramerization / transmembrane transporter binding / calmodulin binding / signaling receptor binding / calcium ion binding / ATP binding / membrane / cytoplasm
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
Ryanodine receptor 1 / Peptidyl-prolyl cis-trans isomerase FKBP1B
Similarity search - Component
Biological speciesSus scrofa (pig) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsMolinarolo SM / Van Petegem F
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Nat Commun / Year: 2025
Title: Cryo-electron microscopy reveals sequential binding and activation of Ryanodine Receptors by statin triplets.
Authors: Steven Molinarolo / Carmen R Valdivia / Héctor H Valdivia / Filip Van Petegem /
Abstract: Statins are the most prescribed class of drugs and inhibit a key enzyme in the cholesterol biosynthesis pathway. Many patients have reported mild to severe muscle related symptoms and a subset are at ...Statins are the most prescribed class of drugs and inhibit a key enzyme in the cholesterol biosynthesis pathway. Many patients have reported mild to severe muscle related symptoms and a subset are at risk for rhabdomyolysis. Sequence variants in RyR1, the skeletal muscle Ryanodine Receptor, correlate with intolerance to statins, but whether RyR1 can bind statins directly has remained unclear. Here we report cryo-EM structures of RyR1 in the absence and presence of atorvastatin, firmly establishing RyR1 as an unintended off-target. Our results show an unusual binding mode whereby three atorvastatin molecules bind together in a cleft formed by the pseudo-voltage sensing domain, making extensive interactions with each other and with RyR1. Atorvastatin activates RyR1 in a sequential way, whereby one statin per subunit can bind to the transmembrane region of a closed RyR1, with small structural perturbations that prime the channel for opening. Binding of two additional statins per subunit is associated with a widening of the pseudo-voltage sensing domain that triggers opening of the pore. Comparison with atorvastatin binding to HMG-CoA reductase, its intended target, offers clues on how to modify the statin to reduce RyR1 binding, while leaving binding to HMG-CoA reductase unperturbed.
History
DepositionAug 4, 2025-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_71924.png

Downloads & links

-
Map

FileDownload / File: emd_71924.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 512 pix.
= 491.52 Å		0.96 Å/pix.
x 512 pix.
= 491.52 Å		0.96 Å/pix.
x 512 pix.
= 491.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.045
Minimum - Maximum0.0 - 0.20893131
Average (Standard dev.)0.0010600815 (±0.0071000913)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 491.52 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Ryanodine Receptor 1 and FKBP12.6 complex

EntireName: Ryanodine Receptor 1 and FKBP12.6 complex
Components
  • Complex: Ryanodine Receptor 1 and FKBP12.6 complex
    • Protein or peptide: Ryanodine receptor 1
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase FKBP1B
  • Ligand: CAFFEINE
  • Ligand: CALCIUM ION
  • Ligand: 7-[2-(4-FLUORO-PHENYL)-5-ISOPROPYL-3-PHENYL-4-PHENYLCARBAMOYL-PYRROL-1-YL]- 3,5-DIHYDROXY-HEPTANOIC ACID
  • Ligand: ZINC ION

-
Supramolecule #1: Ryanodine Receptor 1 and FKBP12.6 complex

SupramoleculeName: Ryanodine Receptor 1 and FKBP12.6 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 2.39 MDa

-
Macromolecule #1: Ryanodine receptor 1

MacromoleculeName: Ryanodine receptor 1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 565.935062 KDa
SequenceString: MGDGGEGEDE VQFLRTDDEV VLQCNATVLK EQLKLCLAAE GFGNRLCFLE PTSNAQNVPP DLAICCFVLE QSLSVRALQE MLANTVEAG VESSQGGGHR TLLYGHAILL RHAHSGMYLS CLTTSRSMTD KLAFDVGLQE DATGEACWWT THPASKQRSE G EKVRVGDD ...String:
MGDGGEGEDE VQFLRTDDEV VLQCNATVLK EQLKLCLAAE GFGNRLCFLE PTSNAQNVPP DLAICCFVLE QSLSVRALQE MLANTVEAG VESSQGGGHR TLLYGHAILL RHAHSGMYLS CLTTSRSMTD KLAFDVGLQE DATGEACWWT THPASKQRSE G EKVRVGDD LILVSVSSER YLHLSTASGE LQVDASFMQT LWNMNPICSG CEEGYVTGGH VLRLFHGHMD ECLTISPADS DD QRRLVYY EGGSVCTHAR SLWRLEPLRI SWSGSHLRWG QPLRIRHVTT GRYLALIEDQ GLVVVDASKA HTKATSFCFR ISK EKLDTA PKRDVEGMGP PEIKYGESLC FVQHVASGLW LTYAAPDPKA LRLGVLKKKA ILHQEGHMDD ALSLTRCQQE ESQA ARMIY STAGLYNHFI KGLDSFSGKP RGSGAPAGTA LPLEGVILSL QDLIGYFEPP SEELQHEEKQ SKLRSLRNRQ SLFQE EGML SLVLNCIDRL NVYTTAAHFA EFAGEEAAES WKEIVNLLYE ILASLIRGNR ANCALFSNNL DWLVSKLDRL EASSGI LEV LYCVLIESPE VLNIIQENHI KSIISLLDKH GRNHKVLDVL CSLCVCNGVA VCSNQDLITE NLLPGRELLL QTNLINY VT SIRPNIFVGR AEGTTQYSKW YFEVMVDEVV PFLTAQATHL RVGWALTEGY SPYPGGGEGW GGNGVGDDLY SYGFDGLH L WTGHVPRLVT SPGQHLLAPE DVVSCCLDLS VPSISFRING CPVQGVFEAF NLNGLFFPVV SFSAGVKVRF LLGGRHGEF KFLPPPGYAP CHEAVLPRER LRLEPIKEYR REGPRGPHLV GPSRCLSHTD FVPCPVDTVQ IVLPPHLERI REKLAENIHE LWALTRIEQ GWTYGPVRDD NKRLHPCLVD FHSLPEPERN YNLQMSGETL KTLLALGCHV GMADEKAEDN LRKTKLPKTY M MSNGYKPA PLDLSHVRLT PAQTTLVDRL AENGHNVWAR DRVAQGWSYS AVQDIPARRN PRLVPYRLLD EATKRSNRDS LC QAVRTLL GYGYNIEPPD QEPSQVESQS RWDRVRIFRA EKSYAVQSGR WYFEFEAVTT GEMRVGWARP ELRPDVELGA DEL AYVFNG HRGQRWHLGS ELFGRPWQSG DVVGCMIDLT ENTIIFTLNG EVLMSDSGSE TAFRDIEVGD GFLPVCSLGP GQVG HLNLG QDVSSLRFFA ICGLQEGFEP FAINMQRPVT TWFSKSLPQF EAVPLEHPHY EVSRVDGTVD TPPCLRLTHR TWGSQ NSLV EMLFLRLSLP VQFHQHFRCT AGATPLAPPG LQPPAEDEAR AAEPDPDYEN LRRSAGRWGE AEGGKEGTAK EGAPGG TAQ AGVEAQPPRA ENEKDATTEK NKKRGFLFKA KKAAMMTQPP ATPTLPRLPH EVVPADDRDD PDIILNTTTY YYSVRVF AG QEPSCVWVGW VTPDYHQHDM NFDLTKVRAV TVTMGDEQGN IHSSLKCSNC YMVWGGDFVS PGQQGRISHT DLVIGCLV D LATGLMTFTA NGKESNTFFQ VEPNTKLFPA VFVLPTHQNV IQFELGKQKN IMPLSAAMFL SERKNPAPQC PPRLEMQML MPVSWSRMPN HFLRVETRRA GERLGWAVQC QEPLTMMALH IPEENRCMDI LELSERLDLQ QFHSHTLRLY RAVCALGNNR VAHALCSHV DQAQLLHALE DAHLPGPLRA GYYDLLISIH LESACRSRRS MLSEYIVPLT PETRAITLFP PGKRTENGPR R HGLPGVGV TTSLRPPHHF SAPCFVAALP AVGAAEAPAR LSPSIPLEAL RDKALRMLGE AVRDGGQHAR DPVGGSVEFQ FV PVLKLVS TLLVMGIFGD EDVKQILKMI EPEVFTEEEE EEEEEEEEEE EDEEEKEEDE EEEAREKEDE EKEEEETAEG EKE EYLEEG LLQMKLPESV KLQMCNLLEY FCDQELQHRV ESLAAFAERY VDKLQANQRD RYGILMKAFT MTAAETARRT REFR SPPQE QINMLLHFKD GEDEEDCPLP DEIRQDLLEF HQDLLTHCGI QLEGEEEEPE EEATLGSRLM SLLEKVRLVK KKEEK SEEE PPAEESKAQS LQELVSHTVV RWAQEDFVQS PELVRAMFSL LHRQYDGLGE LLRALPRAYT ISPSSVEDTM SLLECL GQI RSLLIVQMGP QEENLMIQSI GNIMNNKVFY QHPNLMRALG MHETVMEVMV NVLGGGESKE IRFPKMVTSC CRFLCYF CR ISRQNQRSMF DHLSYLLENS GIGLGMQGST PLDVAAASVI DNNELALALQ EQDLEKVVSY LAGCGLQSCP MLLAKGYP D IGWNPCGGER YLDFLRFAVF VNGESVEENA NVVVRLLIRK PECFGPALRG EGGSGLLATI EEAIRISEDP ARDGPGVRR DRRREHFGEE PPEENRVHLG HAIMSFYAAL IDLLGRCAPE MHLIQAGKGE ALRIRAILRS LVPLDDLVGI ISLPLQIPTL GKDGALVQP KMSASFVPDH KASMVLFLDR VYGIENQDFL LHVLDVGFLP DMRAAASLDT ATFSTTEMAL ALNRYLCLAV L PLITKCAP LFAGTEHRAI MVDSMLHTVY RLSRGRSLTK AQRDVIEECL MALCRYIRPS MLQHLLRRLV FDVPILNEFA KM PLKLLTN HYERCWKYYC LPTGWANFGV TSEEELHLTR KLFWGIFDSL AHKKYDPELY RMAMPCLCAI AGALPPDYVD ASY SSKAEK KATVDAEGNF DPRPVETLNV IIPEKLDSFI NKFAEYTHEK WAFDKIQNNW SYGENIDEEL KTHPMLRPYK TFSE KDKEI YRWPIKESLK AMIAWEWTIE KAREGEEEKT EKKKTRKISQ SAQTYDAREG YNPQPPDLSG VTLSRELQAM AEQLA ENYH NTWGRKKKQE LEAKGGGTHP LLVPYDTLTA KEKARDREKA QELLKFLQMN GYAVTRGLKD MELDTSSIEK RFAFGF LQQ LLRWMDISQE FIAHLEAVVS SGRVEKSPHE QEIKFFAKIL LPLINQYFTN HCLYFLSTPA KVLGSGGHAS NKEKEMI TS LFCKLAALVR HRVSLFGTDA PAVVNCLHIL ARSLDARTVM KSGPEIVKAG LRSFFESASE DIEKMVENLR LGKVSQAR T QVKGVGQNLT YTTVALLPVL TTLFQHIAQH QFGDDVILDD VQVSCYRTLC SIYSLGTTRN PYVEKLRPAL GECLARLAA AMPVAFLEPQ LNEYNACSVY TTKSPRERAI LGLPNSVEEM CPDIPVLERL MADIGGLAES GARYTEMPHV IEITLPMLCS YLPRWWERG PEAPPPALPA GAPPPCTAVT SDHLNSLLGN ILRIIVNNLG IDEASWMKRL AVFAQPIVSR ARPELLHSHF I PTIGRLRK RAGKVVAEEE QLRLEAKAEA EEGELLVRDE FSVLCRDLYA LYPLLIRYVD NNRAHWLTEP NPSAEELFRM VG EIFIYWS KSHNFKREEQ NFVVQNEINN MSFLTADNKS KMAKSGGSDQ ERTKKKRLGD RYSVQTSLIV ATLKKMLPIG LNM CAPTDQ ELITLAKTRY ALKDTDEEVR EFLQNNLHLQ GKVEGSPSLR WQMALYRGLP GREEDADDPE KIVRRVQEVS AVLY HLEQM EHPYKSKKAV WHKLLSKQRR RAVVACFRMT PLYNLPTHRA CNMFLESYKA AWILTEDHSF EDRMIDDLSK AGEQE EEEE EVEEKKPDPL HQLVLHFSRT ALTEKSKLDE DYLYMAYADI MAKSCHLEEG GENGEAQEEV EVSFEEKEME KQRLLY QQA RLHNRGAAEM VLQMISACKG ETGAMVSSTL KLGISILNGG NADVQQKMLD YLKDKKEVGF FQSIQALMQT CSVLDLN AF ERQNKAEGLG MVNEDGTVIN RQNGEKVMAD DEFTQDLFRF LQLLCEGHNN DFQNYLRTQT GNTTTINIII CTVDYLLR L QESISDFYWY YSGKDVIEEQ GKRNFSKAMS VAKQVFNSLT EYIQGPCTGN QQSLAHSRLW DAVVGFLHVF AHMMMKLAQ DSSQIELLKE LLDLQKDMVV MLLSLLEGNV VNGMIARQMV DMLVESSSNV EMILKFFDMF LKLKDIVGSE AFQDYVTDPR GLISKKDFQ KAMDSQKQFT GPEIQFLLSC SEADENEMID CEEFANRFQE PARDIGFNVA VLLTNLSEHV PHDPRLRNFL E LAESILEY FRPYLGRIEI MGASRRIERI YFEISETNRA QWEMPQVKES KRQFIFDVVN EGGESEKMEL FVSFCEDTIF EM QIAAQIS EPEGEPEEDE DEGAGLAEAG AEGAEEGAVG PEGAAGTAAA GLTARLAAAT SRALRGLSYR SLRRRVRRLR RLT AREAAT ALAALLWAAL AHAGAAGAGA AAGALRLLWG SLFGGGLVEG AKKVTVTELL AGMPDPTGDE VHGEQPAGPG GEAD GEGAG EGAGEAWEGA GDEEVAVQEA GPGGADGAVA VAEGGPFRPE GAGGLGDMGD TTPAEPPTPE GSPIIKRKLG VDGEE EELP PEPEPEPEPE PEKADAENGE KEEVPKPPPE PPKKTAPPPP PPKKEEGGSG GLEFWGELEV QRVKFLNYLS RNFYTL RFL ALFLAFAINF ILLFYKVSDS PPGEDDMEGS AAGDLSGAGS GGGSGWGSGA GEEVEGDEDE NMVYYFLEES TGYMEPA LR CLSLLHTLVA FLCIIGYNCL KVPLVIFKRE KELARKLEFD GLYITEQPED DDVKGQWDRL VLNTPSFPSN YWDKFVKR K VLDKHGDIYG RERIAELLGM DLATLEITAH NERKPEPPPG LLTWLMSIDV KYQIWKFGVI FTDNSFLYLG WYMVMSLLG HYNNFFFAAH LLDIAMGVKT LRTILSSVTH NGKQLVMTVG LLAVVVYLYT VVAFNFFRKF YNKSEDEDEP DMKCDDMMTC YLFHMYVGV RAGGGIGDEI EDPAGDEYEL YRVVFDITFF FFVIVILLAI IQGLIIDAFG ELRDQQEQVR EDMETKCFIC G IGSDYFDT TPHRFETHTL EEHNLANYMF FLMYLINKDE TEHTGQESYV WKMYQERCWD FFPAGDCFRK QYEDQLS

UniProtKB: Ryanodine receptor 1

-
Macromolecule #2: Peptidyl-prolyl cis-trans isomerase FKBP1B

MacromoleculeName: Peptidyl-prolyl cis-trans isomerase FKBP1B / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO / EC number: peptidylprolyl isomerase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.070759 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SNAMGVEIET ISPGDGRTFP KKGQTCVVHY TGMLQNGKKF DSSRDRNKPF KFRIGKQEVI KGFEEGAAQM SLGQRAKLTC TPDVAYGAT GHPGVIPPNA TLIFDVELLN LE

UniProtKB: Peptidyl-prolyl cis-trans isomerase FKBP1B

-
Macromolecule #3: CAFFEINE

MacromoleculeName: CAFFEINE / type: ligand / ID: 3 / Number of copies: 4 / Formula: CFF
Molecular weightTheoretical: 194.191 Da
Chemical component information

ChemComp-CFF:
CAFFEINE / medication*YM

-
Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: CA
Molecular weightTheoretical: 40.078 Da

-
Macromolecule #5: 7-[2-(4-FLUORO-PHENYL)-5-ISOPROPYL-3-PHENYL-4-PHENYLCARBAMOYL-PYR...

MacromoleculeName: 7-[2-(4-FLUORO-PHENYL)-5-ISOPROPYL-3-PHENYL-4-PHENYLCARBAMOYL-PYRROL-1-YL]- 3,5-DIHYDROXY-HEPTANOIC ACID
type: ligand / ID: 5 / Number of copies: 12 / Formula: 117
Molecular weightTheoretical: 558.64 Da
Chemical component information

ChemComp-117:
7-[2-(4-FLUORO-PHENYL)-5-ISOPROPYL-3-PHENYL-4-PHENYLCARBAMOYL-PYRROL-1-YL]- 3,5-DIHYDROXY-HEPTANOIC ACID

-
Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration9 mg/mL
BufferpH: 7.5
Component:
ConcentrationName
10.0 mMAtorvastatin
2.0 %DMSO
2.0 mMCaffeine
36.0 uMFree Ca2+
2.0 mMEGTA
25.0 mMTris
250.0 mMSodium Chloride
0.5 mMBenzamidine
0.5 mMTCEP
0.375 %CHAPS
0.001 %DOPC
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 5007 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 96731
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)

-
Atomic model buiding 1

Initial modelPDB ID:

9ol4
PDB Unreleased entry


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-9pwo:
Pig Ryanodine Receptor 1 R615C Mutant: Atorvastatin Bound Open Conformation

+
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