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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-22019 | |||||||||
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Title | Pig R615C RyR1 in complex with CaM, EGTA (class 3, closed) | |||||||||
![]() | RELION postprocessed map | |||||||||
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![]() | receptor / calcium / channel / complex / TRANSPORT PROTEIN-ISOMERASE-CALCIUM BINDING PROTEIN complex | |||||||||
Function / homology | ![]() positive regulation of sequestering of calcium ion / cyclic nucleotide binding / negative regulation of calcium-mediated signaling / negative regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of release of sequestered calcium ion into cytosol / neuronal action potential propagation / insulin secretion involved in cellular response to glucose stimulus / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers ...positive regulation of sequestering of calcium ion / cyclic nucleotide binding / negative regulation of calcium-mediated signaling / negative regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of release of sequestered calcium ion into cytosol / neuronal action potential propagation / insulin secretion involved in cellular response to glucose stimulus / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / response to redox state / protein maturation by protein folding / Reduction of cytosolic Ca++ levels / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / Loss of phosphorylation of MECP2 at T308 / 'de novo' protein folding / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / positive regulation of cyclic-nucleotide phosphodiesterase activity / organelle localization by membrane tethering / negative regulation of heart rate / negative regulation of calcium ion export across plasma membrane / CLEC7A (Dectin-1) induces NFAT activation / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / regulation of cardiac muscle cell action potential / Activation of RAC1 downstream of NMDARs / FK506 binding / positive regulation of ryanodine-sensitive calcium-release channel activity / positive regulation of axon regeneration / regulation of cell communication by electrical coupling involved in cardiac conduction / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Unblocking of NMDA receptors, glutamate binding and activation / Phase 0 - rapid depolarisation / negative regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / channel regulator activity / RHO GTPases activate PAKs / : / Ion transport by P-type ATPases / Long-term potentiation / Uptake and function of anthrax toxins / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / catalytic complex / DARPP-32 events / detection of calcium ion / smooth muscle contraction / regulation of cardiac muscle contraction / regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / response to vitamin E / cellular response to interferon-beta / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / Protein methylation / eNOS activation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Activation of AMPK downstream of NMDARs / T cell proliferation / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / release of sequestered calcium ion into cytosol / : / Ion homeostasis / titin binding / regulation of calcium-mediated signaling / positive regulation of protein autophosphorylation / voltage-gated potassium channel complex / sperm midpiece / regulation of cytosolic calcium ion concentration / sarcoplasmic reticulum membrane / calcium channel complex / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / sarcomere / FCERI mediated Ca+2 mobilization / protein serine/threonine kinase activator activity / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation / regulation of cytokinesis / positive regulation of peptidyl-threonine phosphorylation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / spindle microtubule / RAF activation / calcium-mediated signaling / positive regulation of receptor signaling pathway via JAK-STAT Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.7 Å | |||||||||
![]() | Woll KW / Haji-Ghassemi O | |||||||||
Funding support | 1 items
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![]() | ![]() Title: Pathological conformations of disease mutant Ryanodine Receptors revealed by cryo-EM. Authors: Kellie A Woll / Omid Haji-Ghassemi / Filip Van Petegem / ![]() Abstract: Ryanodine Receptors (RyRs) are massive channels that release Ca from the endoplasmic and sarcoplasmic reticulum. Hundreds of mutations are linked to malignant hyperthermia (MH), myopathies, and ...Ryanodine Receptors (RyRs) are massive channels that release Ca from the endoplasmic and sarcoplasmic reticulum. Hundreds of mutations are linked to malignant hyperthermia (MH), myopathies, and arrhythmias. Here, we explore the first MH mutation identified in humans by providing cryo-EM snapshots of the pig homolog, R615C, showing that it affects an interface between three solenoid regions. We also show the impact of apo-calmodulin (apoCaM) and how it can induce opening by bending of the bridging solenoid, mediated by its N-terminal lobe. For R615C RyR1, apoCaM binding abolishes a pathological 'intermediate' conformation, distributing the population to a mixture of open and closed channels, both different from the structure without apoCaM. Comparisons show that the mutation primarily affects the closed state, inducing partial movements linked to channel activation. This shows that disease mutations can cause distinct pathological conformations of the RyR and facilitate channel opening by disrupting interactions between different solenoid regions. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 370.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 24.2 KB 24.2 KB | Display Display | ![]() |
Images | ![]() | 199.2 KB | ||
Filedesc metadata | ![]() | 7.9 KB | ||
Others | ![]() ![]() ![]() | 54.1 MB 331.5 MB 331.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 941.9 KB | Display | ![]() |
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Full document | ![]() | 941.4 KB | Display | |
Data in XML | ![]() | 17.8 KB | Display | |
Data in CIF | ![]() | 21.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6x36MC ![]() 6w1nC ![]() 6x32C ![]() 6x33C ![]() 6x34C ![]() 6x35C C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | RELION postprocessed map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.09 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Density modified map generated from RELION half maps...
File | emd_22019_additional_1.map | ||||||||||||
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Annotation | Density modified map generated from RELION half maps using PHENIX Resolve | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_22019_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_22019_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : ryanodine receptor-FKBP1B-calmodulin complex
Entire | Name: ryanodine receptor-FKBP1B-calmodulin complex |
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Components |
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-Supramolecule #1: ryanodine receptor-FKBP1B-calmodulin complex
Supramolecule | Name: ryanodine receptor-FKBP1B-calmodulin complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: ryanodine receptor
Supramolecule | Name: ryanodine receptor / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #3: FKBP1B
Supramolecule | Name: FKBP1B / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-Supramolecule #4: Calmodulin
Supramolecule | Name: Calmodulin / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Peptidyl-prolyl cis-trans isomerase FKBP1B
Macromolecule | Name: Peptidyl-prolyl cis-trans isomerase FKBP1B / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: peptidylprolyl isomerase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 11.939562 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: SNAGVEIETI SPGDGRTFPK KGQTCVVHYT GMLQNGKKFD SSRDRNKPFK FRIGKQEVIK GFEEGAAQMS LGQRAKLTCT PDVAYGATG HPGVIPPNAT LIFDVELLNL E UniProtKB: Peptidyl-prolyl cis-trans isomerase FKBP1B |
-Macromolecule #2: Ryanodine Receptor
Macromolecule | Name: Ryanodine Receptor / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 392.424781 KDa |
Sequence | String: QFLRTDDEVV LQCNATVLKE QLKLCLAAEG FGNRLCFLEP TSNAQNVPPD LAICCFVLEQ SLSVRALQEM LANGHRTLLY GHAILLRHA HSGMYLSCLT TSRSMTDKLA FDVGLQEDAT GEACWWTTHP ASKQRSEGEK VRVGDDLILV SVSSERYLHL S TASGELQV ...String: QFLRTDDEVV LQCNATVLKE QLKLCLAAEG FGNRLCFLEP TSNAQNVPPD LAICCFVLEQ SLSVRALQEM LANGHRTLLY GHAILLRHA HSGMYLSCLT TSRSMTDKLA FDVGLQEDAT GEACWWTTHP ASKQRSEGEK VRVGDDLILV SVSSERYLHL S TASGELQV DASFMQTLWN MNPICSGCEE GYVTGGHVLR LFHGHMDECL TISPADQRRL VYYEGGSVCT HARSLWRLEP LR ISWSGSH LRWGQPLRIR HVTTGRYLAL IEDQGLVVVD ASKAHTKATS FCFRISKEKL KRDVEGMGPP EIKYGESLCF VQH VASGLW LTYAALKKKA ILHQEGHMDD ALSLTRCQQE ESQAARMIYS TAGLYNHFIK GLDSFSGKPR PAGTALPLEG VILS LQDLI GYFEPPSEEL QHEEKQSKLR SLRNRQSLFQ EEGMLSLVLN CIDRLNVYTT AAHFAEFAGE EAAESWKEIV NLLYE ILAS LIRGNRANCA LFSNNLDWLV SKLDRLEASS GILEVLYCVL IESPEVLNII QENHIKSIIS LLDKHGRNHK VLDVLC SLC VCNGVAVCSN QDLITENLLP GRELLLQTNL INYVTSIRPN IFVGRAEGTT QYSKWYFEVM VDEVVPFLTA QATHLRV GW ALTEGYSPYP GGGEGWGGNG VGDDLYSYGF DGLHLWTGHV PRLVTSPGQH LLAPEDVVSC CLDLSVPSIS FRINGCPV Q GVFEAFNLNG LFFPVVSFSA GVKVRFLLGG RHGEFKFLPP PGYAPCHEAV LPRERLRLEP IKEYRREGPR PHLVGPSRC LSHTDFVPCP IREKLAENIH ELWALTRIEQ GWTYGPVRHP CLVDFHSLPE PERNYNLQMS GETLKTLLAL GCHVGMADEK AEDNLRKTK LPKTYMMSNG YKPAPLDLSH VRLTPAQTTL VDRLAENGHN VWARDRVAQG WSYSAVQDIP ARRNPRLVPY R LLDEATKR SNRDSLCQAV RTLLGYGRVR IFRAEKSYAV QSGRWYFEFE AVTTGEMRVG WARPELRPDV ELGADELAYV FN GHRGQRW HLGSELFGRP WQSGDVVGCM IDLTENTIIF TLNGEVLMSD SGSETAFRDI EVGDGFLPVC SLGPGQVGHL NLG QDVSSL RFFAICGLQE GFEPFAINMQ RPVTTWFSKS LPQFEAVPLE HPHYEVSRVD GTVDTPPCLR LTHRQNSLVE MLFL RLSLP VQFHQLNTTT YYYSVRVFAG QEPSCVWVGW VTPDYHQHDM NFDLTKVRAV TVTMGDNIHS SLKCSNCYMV WGGDF VSHT DLVIGCLVDL ATGLMTFTAN GKESNTFFQV EPNTKLFPAV FVLPTHQNVI QFELGKNIMP LSAAMFLSER KNPAPQ CPP RLEMQMLMPV SWSRMPNHFL RVETRRAGER LGWAVQCQEP LTMMALHIPE ENRCMDILEL SERLDLQQFH SHTLRLY RA VCALGNNRVA HALCSHVDQA QLLHALEDAH LPGPLRAGYY DLLISIHLES ACRSRRSMLS EYIVPLTPET RAITLFPP R HGLPGVGVTT SLRPPHHFSA PCFVAALPEA PARLSPSIPL EALRDKALRM LGEAVRDGGQ HARDPVGGSV EFQFVPVLK LVSTLLVMGI FGDEDVKQIL KMIEPEVEEG LLQMKLPESV KLQMCNLLEY FCDQELQHRV ESLAAFAERY VDKLQANQRD RYGILMKAF TMTAAETARR TREFRSPPQE QINMLLHFKD CPLPDEIRQD LLEFHQDLLT HCGIQLQSLQ ELVSHTVVRW A QEDFVQSP ELVRAMFSLL HRQYDGLGEL LRALPRAYTI SPSSVEDTMS LLECLGQIRS LLIVQMGPQE ENLMIQSIGN IM NNKVFYQ HPNLMRALGM HETVMEVMVN VLGRFPKMVT SCCRFLCYFC RISRQNQRSM FDHLSYLLEN SGGMQGSTPL DVA AASVID NNELALALQE QDLEKVVSYL AGCGLQSCPM LLAKGYPDIG WNPCGGERYL DFLRFAVFVN GESVEENANV VVRL LIRKP ECFGPLLATI EEAMSFYAAL IDLLGRCAPI QAGKGEALRI RAILRSLVPL DDLVGIISLP LQIPTPDHKA SMVLF LDRA LALNRYLCLA VLPLITKCAP LMVDSMLHTV YRLSRGRSLT KAQRDVIEEC LMALCRYIPS MLQHLLRRLV F(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)EFSVL C RDLYALYPLL IRYVDNNRAH WLPSAEELFR MVGEIFIYWS KSHNFKREEQ NFVV(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)RRAVVAC FRMTPLYNLP THR ACNMFL ESYKAAWILT EDHSFEDRMI DDLSKAGEKK PDPLHQLVLH FSRTALTEKS KLDEDYLYMA YADIMAKSCH LEES FEEKE MEKQRLLYQQ ARLHNRGAAE MVLQMISACK GETGAMVSST LKLGISILNG GNADVQQKML DYLKDKKEVG FFQSI QALM QTCSVLDLNA FERQNKAEGL GMVNEDGTVI NRQNGEKVMA DDEFTQDLFR FLQLLCEGHN NDFQNYLRTQ TGNTTT INI IICTVDYLLR LQESISDFYW YYSGKDVIEE QGKRNFSKAM SVAKQVFNSL TEYIQGPCTG NQQSLAHSRL WDAVVGF LH VFAHMMMKLA LKELLDLQKD MVVMLLSLLE GNVVNGMIAR QMVDMLVESS SNVEMILKFF DMFLKLKDIV GSEAFQDY V TDPRGLISKK DFQK(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) EFANRFQEPA RDIGFNVAVL LTNLSEHVPH DPRLR NFLE LAESILEYFR PYLGRIEIMG ASRRIERIYF EISETNRAQW EMPQVKESKR QFIFDVVNGE SEKMELFVSF CEDTIF EMQ (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)EV QRVKFLNYLS RNFYTLRFLA LFLAFAINFI LLFYKVSDSP PVYYFLEEST GYMEPALRCL SLLHTLVA F LCIIGYNCLK VPLVIFKREK ELARKLEFDG LYITEQPEDD DVKGQWDRLV LNTPSFPSNY WDKFVKRKVL DKHGDIYGR ERIAELTWLM SIDVKYQIWK FGVIFTDNSF LYLGWYMVMS LLGHYNNFFF AAHLLDIAMG VKTLRTILSS VTHNGKQLVM TVGLLAVVV YLYTVVAFNF FRKFYNKSKC DDMMTCYLFH MYVGVRAGGG IGDEIEDPAG DEYELYRVVF DITFFFFVIV I LLAIIQGL IIDAFGELRD QQEQVREDME TKCFICGIGS DYFDTTPHRF ETHTLEEHNL ANYMFFLMYL INKDETEHTG QE SYVWKMY QERCWDFFPA GDCFRKQYED QL |
-Macromolecule #3: Calmodulin-1
Macromolecule | Name: Calmodulin-1 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 16.723365 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MADQLTEEQI AEFKEAFSLF DKDGDGTITT KELGTVMRSL GQNPTEAELQ DMINEVDADG NGTIDFPEFL TMMARKMKDT DSEEEIREA FRVFDKDGNG YISAAELRHV MTNLGEKLTD EEVDEMIREA DIDGDGQVNY EEFVQMMTA UniProtKB: Calmodulin-1 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: DIFFRACTION |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: PDB ENTRY |
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Final reconstruction | Applied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX (ver. dev-3714) / Number images used: 7038 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |