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- EMDB-8303: Structure of rabbit RyR2 in complex with FKBP12.6 in a closed sta... -

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Basic information

Entry
Database: EMDB / ID: EMD-8303
TitleStructure of rabbit RyR2 in complex with FKBP12.6 in a closed state (conformation C1)
Map dataRyanodine Receptor
Sample
  • Complex: Ryanodine Receptor - FKBP12.6
    • Protein or peptide: Ryanodine Receptor
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase FKBP1B
KeywordsCalcium Release Channel / Ryanodine Receptor / TRANSPORT PROTEIN-ISOMERASE complex
Function / homology
Function and homology information


positive regulation of sequestering of calcium ion / cyclic nucleotide binding / negative regulation of release of sequestered calcium ion into cytosol / negative regulation of insulin secretion involved in cellular response to glucose stimulus / neuronal action potential propagation / insulin secretion involved in cellular response to glucose stimulus / cell communication by electrical coupling involved in cardiac conduction / response to redox state / protein maturation by protein folding / 'de novo' protein folding ...positive regulation of sequestering of calcium ion / cyclic nucleotide binding / negative regulation of release of sequestered calcium ion into cytosol / negative regulation of insulin secretion involved in cellular response to glucose stimulus / neuronal action potential propagation / insulin secretion involved in cellular response to glucose stimulus / cell communication by electrical coupling involved in cardiac conduction / response to redox state / protein maturation by protein folding / 'de novo' protein folding / negative regulation of heart rate / negative regulation of phosphoprotein phosphatase activity / FK506 binding / positive regulation of axon regeneration / : / smooth muscle contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / response to vitamin E / calcium channel inhibitor activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / protein peptidyl-prolyl isomerization / T cell proliferation / 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 / Ion homeostasis / sarcoplasmic reticulum membrane / calcium channel complex / regulation of cytosolic calcium ion concentration / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / response to hydrogen peroxide / Stimuli-sensing channels / Z disc / positive regulation of cytosolic calcium ion concentration / protein refolding / transmembrane transporter binding / signaling receptor binding / membrane / cytosol / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase FKBP1B
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 11.0 Å
AuthorsLobo JJ / Dhindwal S / Samso M
Funding support United States, 2 items
OrganizationGrant numberCountry
American Heart Association14GRNT19660003 United States
Muscular Dystrophy AssociationMDA352845 United States
CitationJournal: Sci Signal / Year: 2017
Title: A cryo-EM-based model of phosphorylation- and FKBP12.6-mediated allosterism of the cardiac ryanodine receptor.
Authors: Sonali Dhindwal / Joshua Lobo / Vanessa Cabra / Demetrio J Santiago / Ashok R Nayak / Kelly Dryden / Montserrat Samsó /
Abstract: Type 2 ryanodine receptors (RyR2s) are calcium channels that play a vital role in triggering cardiac muscle contraction by releasing calcium from the sarcoplasmic reticulum into the cytoplasm. ...Type 2 ryanodine receptors (RyR2s) are calcium channels that play a vital role in triggering cardiac muscle contraction by releasing calcium from the sarcoplasmic reticulum into the cytoplasm. Several cardiomyopathies are associated with the abnormal functioning of RyR2. We determined the three-dimensional structure of rabbit RyR2 in complex with the regulatory protein FKBP12.6 in the closed state at 11.8 Å resolution using cryo-electron microscopy and built an atomic model of RyR2. The heterogeneity in the data set revealed two RyR2 conformations that we proposed to be related to the extent of phosphorylation of the P2 domain. Because the more flexible conformation may correspond to RyR2 with a phosphorylated P2 domain, we suggest that phosphorylation may set RyR2 in a conformation that needs less energy to transition to the open state. Comparison of RyR2 from cardiac muscle and RyR1 from skeletal muscle showed substantial structural differences between the two, especially in the helical domain 2 (HD2) structure forming the Clamp domain, which participates in quaternary interactions with the dihydropyridine receptor and neighboring RyRs in RyR1 but not in RyR2. Rigidity of the HD2 domain of RyR2 was enhanced by binding of FKBP12.6, a ligand that stabilizes RyR2 in the closed state. These results help to decipher the molecular basis of the different mechanisms of activation and oligomerization of the RyR isoforms and could be extended to RyR complexes in other tissues.
History
DepositionJul 29, 2016-
Header (metadata) releaseOct 5, 2016-
Map releaseMay 24, 2017-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5l1d
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8303_1.png

emd_8303_2.png

Downloads & links

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Map

FileDownload / File: emd_8303.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRyanodine Receptor
Voxel sizeX=Y=Z: 1.34 Å
Density
Contour LevelBy EMDB: 0.035 / Movie #1: 0.04
Minimum - Maximum-0.04593971 - 0.090070024
Average (Standard dev.)-0.0057047303 (±0.009510952)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 536.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z536.000536.000536.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-152-37
NX/NY/NZ998271
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0460.090-0.006

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Supplemental data

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Sample components

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Entire : Ryanodine Receptor - FKBP12.6

EntireName: Ryanodine Receptor - FKBP12.6
Components
  • Complex: Ryanodine Receptor - FKBP12.6
    • Protein or peptide: Ryanodine Receptor
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase FKBP1B

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Supramolecule #1: Ryanodine Receptor - FKBP12.6

SupramoleculeName: Ryanodine Receptor - FKBP12.6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 2.26 MDa

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Macromolecule #1: Ryanodine Receptor

MacromoleculeName: Ryanodine Receptor / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 487.120906 KDa
SequenceString: MADGGEGEDE IQFLRTDDEV VLQCTATIHK EQQKLCLAAE GFGNRLCFLE STSNSKNVPP DLSICTFVLE QSLLVRALQE MLANTVEKS EGQVDVEKWK FMMKTAQGGG HRTLLYGHAI LLRHSYSGMY LCCLSTSRSS TDKLAFDVGL QEDTTGEACW W TIHPASKQ ...String:
MADGGEGEDE IQFLRTDDEV VLQCTATIHK EQQKLCLAAE GFGNRLCFLE STSNSKNVPP DLSICTFVLE QSLLVRALQE MLANTVEKS EGQVDVEKWK FMMKTAQGGG HRTLLYGHAI LLRHSYSGMY LCCLSTSRSS TDKLAFDVGL QEDTTGEACW W TIHPASKQ RSEGEKVRVG DDLILVSVSS ERYLHLSYGN GSLHVDAAFQ QTLWSVAPIS SGSEAAQGYL IGGDVLRLLH GH MDECLTV PSGEHGEEQR RTVHYEGGAV SVHARSLWRL ETLRVAWSGS HIRWGQPFRL RHVTTGKYLS LMEDKNLLLM DKE KADVKS TAFTFRSSKE KLDGGVRKEV DGMGTSEIKY GDSICYIQHV DTGLWLTYQS VDVKSVRMGS IQRKAIMHHE GHMD DGLNL SRSQHEESRT ARVIRSTVFL FNRFIRGLDA LSKKAKASSV DLPIESVSLS LQDLIGYFHP PDEHLEHEDK QNRLR ALKN RQNLFQEEGM INLVLECIDR LHVYSSAAHF ADVAGREAGE SWKSILNSLY ELLAALIRGN RKNCAQFSGS LDWLIS RLE RLEASSGILE VLHCVLVESP EALNIIKEGH IKSIISLLDK HGRNHKVLDV LCSLCVCHGV AVRSNQHLIC DNLLPGR DL LLQTRLVNHV SSMRPNIFLG VSEGSAQYKK WYYELMVDHT EPFVTAEATH LRVGWASTEG YSPYPGGGEE WGGNGVGD D LFSYGFDGLH LWSGCIARTV SSPNQHLLRT DDVISCCLDL SAPSISFRIN GQPVQGMFEN FNIDGLFFPV VSFSAGIKV RFLLGGRHGE FKFLPPPGYA PCYEAVLPKE KLKVEHSREY KQERTYTRDL LGPTVSLTQA AFTPIPVDTS QIVLPPHLER IREKLAENI HELWVMNKIE LGWQYGPVRD DNKRQHPCLV EFSKLPEQER NYNLQMSLET LKTLLALGCH VGISDEHAEE K VKKMKLPK NYQLTSGYKP APMDLSFIKL TPSQEAMVDK LAENAHNVWA RDRIRQGWTY GIQQDVKNRR NPRLVPYTLL DD RTKKSNK DSLREAVRTL LGYGYNLEAP DQDHAARAEV CSGTGERFRI FRAEKTYAVK AGRWYFEFEA VTSGDMRVGW SRP GCQPDQ ELGSDERAFA FDGFKAQRWH QGNEHYGRSW QAGDVVGCMV DMNEHTMMFT LNGEILLDDS GSELAFKDFD VGDG FIPVC SLGVAQVGRM NFGKDVSTLK YFTICGLQEG YEPFAVNTNR DITMWLSKRL PQFLQVPSNH EHIEVTRIDG TIDSS PCLK VTQKSFGSQN SNTDIMFYRL SMPIECAEVF SKTVPGGLPG AGLFGPKNDL EDYDADSDFE VLMKTAHGHL VPDRVD KDK ETTKAEFNNH KDYAQEKPSR LKQRFLLRRT KPDYSTSHSA RLTEDVLADD RDDYDFLMQT STYYYSVRIF PGQEPAN VW VGWITSDFHQ YDTGFDLDRV RTVTVTLGDE KGKVHESIKR SN(UNK)(UNK)(UNK)(UNK)(UNK)NNN GLEIGCVV D AASGLLTFIA NGKELSTYYQ VEPSTKLFPA VFAQATSPNV FQFELGRIKN VMPLSAGLFK SEHKNPVPQC PPRLHVQFL SHVLWSRMPN QFLKVDVSRI SERQGWLVQC LDPLQFMSLH IPEENRSVDI LELTEQEELL KFHYHTLRLY SAVCALGNHR VAHALCSHV DEPQLLYAIE NKYMPGLLRT GYYDLLIDIH LSSYATARLM MNNEFIVPMT EETKSITLFP DENKKHGLPG I GLSTSLRP RMQFSSPSFV SINNECYQYS PEFPLDILKA KTIQMLTEAV KEGSLHGRDP VGGTTEFLFV PLIKLFYTLL IM GIFHNED LRHILQLIEP SVFKDAATPE EEGDTLEEEP SVEDTKLEGA GEEEAKVGKR PKEGLLQMKL PEPVKLQMCL LLQ YLCDCQ VRHRIEAIVA FSDDFVAKLQ DNQRFR(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)LTIRGRLL SLVEKVTYLK KKQTEKPVES DSRKSSTLQQ LISETMVRWA QE SVIEDPE LVRAMFVLLH RQYDGIGGLV RALPKTYTIN GVSVEDTINL LASLGQIRSL LSVRMGKEEE KLMIRGLGDI MNN KVFYQH PNLMRALGMH ETVMEVMVNV LGGGESKEIT FPKMVANCCR FLCYFCRISR QNQKAMFDHL SYLLENSSVG LASP AMRGS TPLDVAAASV MDNNELALAL REPDLEKVVV RYLAGCGLQS CQMLVSKGYP DIGWNPVEGE RYLDFLRFAV FCNGE SVEE NANVVVRLLI RRPECFGPAL RGEGGNGLLA AMEEAIKIAE DPSRDGPSPT SGSSKTLDTE EEEDDTIHMG NAIMTF YAA LIDLLGRCAP EMHLIHAGKG EAIRIRSILR SL(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)FCP DHKAAMVLFL DRVYGIEVQD FLLHLLEVGF LPDLRAAASL DTAALSATDM AL ALNRYLC TAVLPLL(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)FN PQP VDTSNI IIPEKLEYFI NKYAEHSHDK WSMDKLANGW IYGEIYSDSS KIQPLMKPYK LLSEKEKEIY RWPIKESLKT MLAW GWRIE RTREGDSMAL YNRTRRISQT SQVSVDAAHG YSPRAIDMSN VTLSRDLHAM AEMMAENYHN IWAKKKKLEL ESKGG GNHP LLVPYDTLTA KEKAKDREKA QDILKFLQIN GYAVSRG(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)P RHRAVNLFLQ GYEKSWIETE EHYFEDKLIE DLAKPGAEPP EEDEVTKRVD PLHQLILLFS RTALTEKCK LEEDFLYMAY ADIMAKSCHD EEDDDGEEEV KSFEEKEMEK QKLLYQQARL HDRGAAEMVL QTISASKGET GPMVAATLKL GIAILNGGN STVQQKMLDY LKEKKDVGFF QSLAGLMQSC SVLDLNAFER QNKAEGLGMV TEEGSGEKVL QDDEFTCDLF R FLQLLCEG HNSDFQNYLR TQTGNNTTVN IIISTVDYLL RVQESISDFY WYYSGKDVID EQGQRNFSKA IQVAKQVFNT LT EYIQGPC TGNQQSLAHS RLWDAVVGFL HVFAHMQMKL SQDSSQIELL KELMDLQKDM VVMLLSMLEG NVVNGTIGKQ MVD MLVESS NNVEMILKFF DMFLKLKDLT SSDTFKEYDP DGKGIISKRD FHKAMESHKH YTQSETEFLL SCAETDENET LDYE EFVKR FHEPAKDIGF NVAVLLTNLS EHMPNDTRLQ TFLELAESVL NYFQPFLGRI EIMGSAKRIE RVYFEISESS RTQWE KPQV KESKRQFIFD VVNEGGEKEK MELFVNFCED TIFEMQLAAQ ISESDLNERS ANKEESEKER PEEQGPKMGF FSVLTV RSA LFALRYNILT LMRMLSLKSL KKQMKKMKKM TVKDMVTAFF SSYWSIFMTL LHFVASVFRG FFRIVCSLLL GGSLVEG AK KIKVAELLAN MPDPTQDEVR GDGEEGERKP METTLPSEDL TDLKELTEES DLLSDIFGLD LKREGGQYKL IPHNPNAG L SDLMSNPVLI PEEQEKFQEQ KTKEEEKEEK EETKSEPEKA EGEDGEKEEK VKEDKGKQKL RQLHTHRYGE PEVPESAFW KKIIAYQQKL LNYLARNFYN MRMLALFVAF AINFILLFYK VSTSSVVEGK ELPSRSTSEN AKVTTSLDSS SHRIIAVHYV LEESSGYME PTLRILAILH TVISFFCIIG YYCLKVPLVI FKREKEVARK LEFDGLYITE QPSEDDIKGQ WDRLVINTQS F PNNYWDKF VKRKVMDKYG EFYGRDRISE LLGMDKAALD FSDAREKKKP KKDSSLSAVL NSIDVKYQMW KLGVVFTDNS FL YLAWYMT MSILGHYNNF FFAAHLLDIA MGFKTLRTIL SSVTHNGKQL VLTVGLLAVV VYLYTVVAFN FFRKFYNKSE DGD TPDMKC DDMLTCYMFH MYVGVRAGGG IGDEIEDPAG DEYEIYRIIF DITFFFFVIV ILLAIIQGLI IDAFGELRDQ QEQV KEDME TKCFICGIGN DYFDTVPHGF ETHTLQEHNL ANYLFFLMYL INKDETEHTG QESYVWKMYQ ERCWEFFPAG DCFRK QYED QLN

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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: 17.645984 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MNHKVHHHHH HMDEKTTGWR GGHVVEGLAG ELEQLRARLE HHPQGQREPE LGVEIETISP GDGRTFPKKG QTCVVHYTGM LQNGKKFDS SRDRNKPFKF RIGKQEVIKG FEEGAAQMSL GQRAKLTCTP DVAYGATGHP GVIPPNATLI FDVELLNLE

UniProtKB: Peptidyl-prolyl cis-trans isomerase FKBP1B

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMC7H14NNaO4SMOPS sodium
200.0 mMNaClSodium chloridesodium chloride
2.0 mMC4H10O2S2dithiothreitol
0.015 %C58H114O26Tween 20(Polyoxyethylene (20) sorbitan monolaurate)
2.0 mMC14H24N2O10EGTA

Details: 1x Protease Inhibitor cocktail
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 20
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV
Details: Blot for 2 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV)..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 62000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: OTHER / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 1-7 / Number grids imaged: 1 / Number real images: 858 / Average exposure time: 1.2 sec. / Average electron dose: 20.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 13600
Details: Used Relion 1.3 to auto-pick the particles. Inspected each micrograph for false positives.
Startup modelType of model: EMDB MAP
EMDB ID:

1606


Details: RyR1-FKBP12 in the closed conformation
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: FREALIGN (ver. 9.11)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: FREALIGN (ver. 9.11)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C4 (4 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 11.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: FREALIGN (ver. 9.11) / Details: FREALIGN half maps were used to calculate FSC. / Number images used: 13158

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Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT
Output model

PDB-5l1d:
Structure of rabbit RyR2 in complex with FKBP12.6 in a closed state (conformation C1)

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