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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-8372 | |||||||||
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Title | Structure of rabbit RyR1 (Ca2+-only dataset, class 1) | |||||||||
![]() | Rabbit RyR1-Cs2 complex in presence of 30 uM Ca2+, Class 1. Aligned to transmembrane region of EMDB-8342. Used for model fitting. | |||||||||
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![]() | RyR / Ca2+ / EC coupling / gating / TRANSPORT PROTEIN-ISOMERASE complex | |||||||||
Function / homology | ![]() ATP-gated ion channel activity / 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 / terminal cisterna / ryanodine receptor complex / negative regulation of release of sequestered calcium ion into cytosol / ryanodine-sensitive calcium-release channel activity / neuronal action potential propagation ...ATP-gated ion channel activity / 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 / terminal cisterna / ryanodine receptor complex / negative regulation of release of sequestered calcium ion into cytosol / ryanodine-sensitive calcium-release channel activity / neuronal action potential propagation / insulin secretion involved in cellular response to glucose stimulus / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / response to redox state / protein maturation by protein folding / 'de novo' protein folding / skin development / negative regulation of heart rate / organelle membrane / FK506 binding / positive regulation of axon regeneration / cellular response to caffeine / outflow tract morphogenesis / channel regulator activity / intracellularly gated calcium channel activity / smooth muscle contraction / toxic substance binding / smooth endoplasmic reticulum / response to vitamin E / voltage-gated calcium channel activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / skeletal muscle fiber development / striated muscle contraction / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / muscle contraction / T cell proliferation / release of sequestered calcium ion into cytosol / Ion homeostasis / regulation of cytosolic calcium ion concentration / sarcoplasmic reticulum membrane / calcium channel complex / cellular response to calcium ion / sarcoplasmic reticulum / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / calcium ion transmembrane transport / calcium-mediated signaling / response to hydrogen peroxide / calcium channel activity / Stimuli-sensing channels / sarcolemma / Z disc / intracellular calcium ion homeostasis / disordered domain specific binding / positive regulation of cytosolic calcium ion concentration / protein refolding / protein homotetramerization / transmembrane transporter binding / calmodulin binding / signaling receptor binding / calcium ion binding / ATP binding / identical protein binding / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
![]() | Clarke OB / des Georges A | |||||||||
![]() | ![]() Title: Structural Basis for Gating and Activation of RyR1. Authors: Amédée des Georges / Oliver B Clarke / Ran Zalk / Qi Yuan / Kendall J Condon / Robert A Grassucci / Wayne A Hendrickson / Andrew R Marks / Joachim Frank / ![]() Abstract: The type-1 ryanodine receptor (RyR1) is an intracellular calcium (Ca(2+)) release channel required for skeletal muscle contraction. Here, we present cryo-EM reconstructions of RyR1 in multiple ...The type-1 ryanodine receptor (RyR1) is an intracellular calcium (Ca(2+)) release channel required for skeletal muscle contraction. Here, we present cryo-EM reconstructions of RyR1 in multiple functional states revealing the structural basis of channel gating and ligand-dependent activation. Binding sites for the channel activators Ca(2+), ATP, and caffeine were identified at interdomain interfaces of the C-terminal domain. Either ATP or Ca(2+) alone induces conformational changes in the cytoplasmic assembly ("priming"), without pore dilation. In contrast, in the presence of all three activating ligands, high-resolution reconstructions of open and closed states of RyR1 were obtained from the same sample, enabling analyses of conformational changes associated with gating. Gating involves global conformational changes in the cytosolic assembly accompanied by local changes in the transmembrane domain, which include bending of the S6 transmembrane segment and consequent pore dilation, displacement, and deformation of the S4-S5 linker and conformational changes in the pseudo-voltage-sensor domain. | |||||||||
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 | ![]() | 227 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 32 KB 32 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.9 KB | Display | ![]() |
Images | ![]() | 75.4 KB | ||
Filedesc metadata | ![]() | 8.5 KB | ||
Others | ![]() ![]() ![]() | 228.7 MB 188.3 MB 188.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5t9mMC ![]() 8342C ![]() 8373C ![]() 8374C ![]() 8375C ![]() 8376C ![]() 8377C ![]() 8378C ![]() 8379C ![]() 8380C ![]() 8381C ![]() 8382C ![]() 8383C ![]() 8384C ![]() 8385C ![]() 8386C ![]() 8387C ![]() 8388C ![]() 8389C ![]() 8390C ![]() 8391C ![]() 8392C ![]() 8393C ![]() 8394C ![]() 8395C ![]() 5t15C ![]() 5t9nC ![]() 5t9rC ![]() 5t9sC ![]() 5t9vC ![]() 5ta3C ![]() 5talC ![]() 5tamC ![]() 5tanC ![]() 5tapC ![]() 5taqC ![]() 5tasC ![]() 5tatC ![]() 5tauC ![]() 5tavC ![]() 5tawC ![]() 5taxC ![]() 5tayC ![]() 5tazC ![]() 5tb0C ![]() 5tb1C ![]() 5tb2C ![]() 5tb3C ![]() 5tb4C 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 | Rabbit RyR1-Cs2 complex in presence of 30 uM Ca2+, Class 1. Aligned to transmembrane region of EMDB-8342. Used for model fitting. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.255 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Rabbit RyR1-Cs2 complex in presence of 30 uM...
File | emd_8372_additional.map | ||||||||||||
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Annotation | Rabbit RyR1-Cs2 complex in presence of 30 uM Ca2+, Class 1. Untransformed. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_8372_half_map_1.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2
File | emd_8372_half_map_2.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : RyR1-Cs2 complex
Entire | Name: RyR1-Cs2 complex |
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Components |
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-Supramolecule #1: RyR1-Cs2 complex
Supramolecule | Name: RyR1-Cs2 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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-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: 11.798501 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MGVEIETISP GDGRTFPKKG QTCVVHYTGM LQNGKKFDSS RDRNKPFKFR IGKQEVIKGF EEGAAQMSLG QRAKLTCTPD VAYGATGHP GVIPPNATLI FDVELLNLE UniProtKB: Peptidyl-prolyl cis-trans isomerase FKBP1B |
-Macromolecule #2: Ryanodine receptor 1
Macromolecule | Name: Ryanodine receptor 1 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 501.17075 KDa |
Sequence | String: QFLRTDDEVV LQCSATVLKE QLKLCLAAEG FGNRLCFLEP TSNAQNVPPD LAICCFTLEQ SLSVRALQEM LANTVEAGVE SSQGGGHRT LLYGHAILLR HAHSRMYLSC LTTSRSMTDK LAFDVGLQED ATGEACWWTM HPASKQRSEG EKVRVGDDLI L VSVSSERY ...String: QFLRTDDEVV LQCSATVLKE QLKLCLAAEG FGNRLCFLEP TSNAQNVPPD LAICCFTLEQ SLSVRALQEM LANTVEAGVE SSQGGGHRT LLYGHAILLR HAHSRMYLSC LTTSRSMTDK LAFDVGLQED ATGEACWWTM HPASKQRSEG EKVRVGDDLI L VSVSSERY LHLSTASGEL QVDASFMQTL WNMNPICSCC EEGYVTGGHV LRLFHGHMDE CLTISAADSD DQRRLVYYEG GA VCTHARS LWRLEPLRIS WSGSHLRWGQ PLRIRHVTTG RYLALTEDQG LVVVDACKAH TKATSFCFRV SKEKLDTAPK RDV EGMGPP EIKYGESLCF VQHVASGLWL TYAAPDPKAL RLGVLKKKAI LHQEGHMDDA LFLTRCQQEE SQAARMIHST AGLY NQFIK GLDSFSGKPR GSGPPAGPAL PIEAVILSLQ DLIGYFEPPS EELQHEEKQS KLRSLRNRQS LFQEEGMLSL VLNCI DRLN VYTTAAHFAE YAGEEAAESW KEIVNLLYEL LASLIRGNRA NCALFSTNLD WVVSKLDRLE ASSGILEVLY CVLIES PEV LNIIQENHIK SIISLLDKHG RNHKVLDVLC SLCVCNGVAV RSNQDLITEN LLPGRELLLQ TNLINYVTSI RPNIFVG RA EGSTQYGKWY FEVMVDEVVP FLTAQATHLR VGWALTEGYS PYPGGGEGWG GNGVGDDLYS YGFDGLHLWT GHVARPVT S PGQHLLAPED VVSCCLDLSV PSISFRINGC PVQGVFEAFN LDGLFFPVVS FSAGVKVRFL LGGRHGEFKF LPPPGYAPC HEAVLPRERL RLEPIKEYRR EGPRGPHLVG PSRCLSHTDF VPCPVDTVQI VLPPHLERIR EKLAENIHEL WALTRIEQGW TYGPVRDDN KRLHPCLVNF HSLPEPERNY NLQMSGETLK TLLALGCHVG MADEKAEDNL KKTKLPKTYM MSNGYKPAPL D LSHVRLTP AQTTLVDRLA ENGHNVWARD RVAQGWSYSA VQDIPARRNP RLVPYRLLDE ATKRSNRDSL CQAVRTLLGY GY NIEPPDQ EPSQVENQSR WDRVRIFRAE KSYTVQSGRW YFEFEAVTTG EMRVGWARPE LRPDVELGAD ELAYVFNGHR GQR WHLGSE PFGRPWQSGD VVGCMIDLTE NTIIFTLNGE VLMSDSGSET AFREIEIGDG FLPVCSLGPG QVGHLNLGQD VSSL RFFAI CGLQEGFEPF AINMQRPVTT WFSKSLPQFE PVPPEHPHYE VARMDGTVDT PPCLRLAHR(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)MPLS AAMFLSERKN PAPQCPPRLE VQMLMP VSW SRMPNHFLQV ETRRAGERLG WAVQCQDPLT MMALHIPEEN RCMDILELSE RLDLQRFHSH TLRLYRAVCA LGNNRVA HA LCSHVDQAQL LHALEDAHLP GPLRAGYYDL LISIHLESAC RSRRSMLSEY IVPLTPETRA ITLFPPGRKG GNARRHGL P GVGVTTSLRP PHHFSPPCFV AALPAAGVAE APARLSPAIP LEALRDKALR MLGEAVRDGG QHARDPVGGS VEFQFVPVL KLVSTLLVMG IFGDEDVKQI LKMIEPEVFT EEEEEEEEEE EEEEEEEEDE EEKEEDEEEE EKEDAEKEEE EAPEGEKEDL EEGLLQMKL PESVKLQMCN LLEYFCDQEL QHRVESLAAF AERYVDKLQA NQRSRYALLM RAFTMSAAET ARRTREFRSP P QEQINMLL HFKDEADEED CPLPEDIRQD LQDFHQDLLA HCGIQLEGEE EEPEEETSLS SRLRSLLETV RLVKKKEEKP EE ELPAEEK KPQSLQELVS HMVVRWAQED YVQSPELVRA MFSLLHRQYD GLGELLRALP RAYTISPSSV EDTMSLLECL GQI RSLLIV QMGPQEENLM IQSIGNIMNN KVFYQHPNLM RALGMHETVM EVMVNVLGGG ETKEIRFPKM VTSCCRFLCY FCRI SRQNQ RSMFDHLSYL LENSGIGLGM QGSTPLDVAA ASVIDNNELA LALQEQDLEK VVSYLAGCGL QSCPMLLAKG YPDIG WNPC GGERYLDFLR FAVFVNGESV EENANVVVRL LIRKPECFGP ALRGEGGSGL LAAIEEAIRI SEDPARDGPG VRRDRR REH FGEEPPEENR VHLGHAIMSF YAALIDLLGR CAPEMHLIQA GKGEALRIRA ILRSLVPLDD LVGIISLPLQ IPTL (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) 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LLKELLDLQK DMVVMLLSLL EG NVVNGMI ARQMVDMLVE SSSNVEMILK FFDMFLKLKD IVGSEAFQDY VTDPRGLISK KDFQKAMDSQ KQFTGPEIQF LLS CSEADE NEMINFEEFA NRFQEPARDI GFNVAVLLTN LSEHVPHDPR LRNFLELAES ILEYFRPYLG RIEIMGASRR IERI YFEIS ETNRAQWEMP QVKESKRQFI FDVVNEGGEA EKMELFVSFC EDTIFEMQIA AQISEPEGEP EADEDEGMGE AAAEG AEEG AAGAEGAAGT VAAGATARLA AAAARALRGL SYRSLRRRVR RLRRLTAREA ATALAALLWA VVARAGAAGA GAAAGA LRL LWGSLFGGGL VEGAKKVTVT ELLAGMPDPT SDEVHGEQPA GPGGDADGAG EGEGEGDAAE GDGDEEVAGH EAGPGGA EG VVAVADGGPF RPEGAGGLGD MGDTTPAEPP TPEGSPILKR KLGVDGEEEE LVPEPEPEPE PEPEKADEEN GEKEEVPE A PPEPPKKAPP SPPAKKEEAG GAGMEFWGEL EVQRVKFLNY LSRNFYTLRF LALFLAFAIN FILLFYKVSD SPPGEDDME GSAAGDLAGA GSGGGSGWGS GAGEEAEGDE DENMVYYFLE ESTGYMEPAL WCLSLLHTLV AFLCIIGYNC LKVPLVIFKR EKELARKLE FDGLYITEQP GDDDVKGQWD RLVLNTPSFP SNYWDKFVKR KVLDKHGDIF GRERIAELLG MDLASLEITA H NERKPDPP PGLLTWLMSI DVKYQIWKFG VIFTDNSFLY LGWYMVMSLL GHYNNFFFAA HLLDIAMGVK TLRTILSSVT HN GKQLVMT VGLLAVVVYL YTVVAFNFFR KFYNKSEDED EPDMKCDDMM TCYLFHMYVG VRAGGGIGDE IEDPAGDEYE LYR VVFDIT FFFFVIVILL AIIQGLIIDA FGELRDQQEQ VKEDMETKCF ICGIGSDYFD TTPHGFETHT LEEHNLANYM FFLM YLINK DETEHTGQES YVWKMYQERC WDFFPAGDCF RKQYEDQLS UniProtKB: Ryanodine receptor 1, Ryanodine receptor 1, Ryanodine receptor 1, Ryanodine receptor 1 |
-Macromolecule #3: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #4: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 6.0 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: Quantifoil / Material: GOLD / Mesh: 400 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: Blotted for 3-4 seconds on both sides with Whatman ashless filter paper, blot force 3, wait time 30 seconds. |
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Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |