[English] 日本語
Yorodumi
- EMDB-8383: Structure of rabbit RyR1 (Caffeine/ATP/EGTA dataset, class 1) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-8383
TitleStructure of rabbit RyR1 (Caffeine/ATP/EGTA dataset, class 1)
Map dataRabbit RyR1 Calstabin 2 complex, ATP/caffeine/EGTA dataset, Class 1. Map aligned to transmembrane region of EMD-8342 to facilitate class comparisons. Map used for model fitting.
Sample
  • Complex: RyR1-Cs2 complex
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase FKBP1B
    • Protein or peptide: Ryanodine receptor 1
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: CAFFEINE
  • Ligand: ZINC ION
KeywordsRyR / Ca2+ / EC coupling / gating / TRANSPORT PROTEIN-ISOMERASE complex
Function / homology
Function and homology information


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 / negative regulation of release of sequestered calcium ion into cytosol / terminal cisterna / neuronal action potential propagation / ryanodine receptor complex / insulin secretion involved in cellular response to glucose stimulus ...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 / negative regulation of release of sequestered calcium ion into cytosol / terminal cisterna / neuronal action potential propagation / ryanodine receptor complex / insulin secretion involved in cellular response to glucose stimulus / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / response to redox state / protein maturation by protein folding / ossification involved in bone maturation / 'de novo' protein folding / negative regulation of heart rate / skin development / FK506 binding / organelle membrane / positive regulation of axon regeneration / cellular response to caffeine / channel regulator activity / outflow tract morphogenesis / intracellularly gated calcium channel activity / smooth muscle contraction / response to vitamin E / toxic substance binding / voltage-gated calcium channel activity / smooth endoplasmic reticulum / 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 / T cell proliferation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / release of sequestered calcium ion into cytosol / muscle contraction / regulation of cytosolic calcium ion concentration / calcium channel complex / sarcoplasmic reticulum membrane / cellular response to calcium ion / sarcoplasmic reticulum / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / calcium-mediated signaling / calcium ion transmembrane transport / calcium channel activity / response to hydrogen peroxide / sarcolemma / Stimuli-sensing channels / 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
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 domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / 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 speciesHomo sapiens (human) / Oryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.2 Å
AuthorsClarke OB / des Georges A
CitationJournal: Cell / Year: 2016
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
DepositionSep 29, 2016-
Header (metadata) releaseOct 12, 2016-
Map releaseOct 12, 2016-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.026
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.026
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5tas
  • Surface level: 0.026
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8383.png

Downloads & links

-
Map

FileDownload / File: emd_8383.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRabbit RyR1 Calstabin 2 complex, ATP/caffeine/EGTA dataset, Class 1. Map aligned to transmembrane region of EMD-8342 to facilitate class comparisons. Map used for model fitting.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.26 Å/pix.
x 400 pix.
= 502. Å		1.26 Å/pix.
x 400 pix.
= 502. Å		1.26 Å/pix.
x 400 pix.
= 502. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.255 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.028 / Movie #1: 0.026
Minimum - Maximum-0.02394788 - 0.077278376
Average (Standard dev.)-0.00001672742 (±0.0044777826)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 502.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.2551.2551.255
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z502.000502.000502.000
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-0.0240.077-0.000

-
Supplemental data

-
Additional map: Main map (untransformed)

Fileemd_8383_additional.map
AnnotationMain map (untransformed)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 2

Fileemd_8383_half_map_1.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 1

Fileemd_8383_half_map_2.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : RyR1-Cs2 complex

EntireName: RyR1-Cs2 complex
Components
  • Complex: RyR1-Cs2 complex
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase FKBP1B
    • Protein or peptide: Ryanodine receptor 1
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: CAFFEINE
  • Ligand: ZINC ION

-
Supramolecule #1: RyR1-Cs2 complex

SupramoleculeName: RyR1-Cs2 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

-
Macromolecule #1: Peptidyl-prolyl cis-trans isomerase FKBP1B

MacromoleculeName: Peptidyl-prolyl cis-trans isomerase FKBP1B / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: peptidylprolyl isomerase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.798501 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGVEIETISP GDGRTFPKKG QTCVVHYTGM LQNGKKFDSS RDRNKPFKFR IGKQEVIKGF EEGAAQMSLG QRAKLTCTPD VAYGATGHP GVIPPNATLI FDVELLNLE

UniProtKB: Peptidyl-prolyl cis-trans isomerase FKBP1B

-
Macromolecule #2: Ryanodine receptor 1

MacromoleculeName: Ryanodine receptor 1 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / Tissue: Skeletal muscle
Molecular weightTheoretical: 475.107719 KDa
SequenceString: 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) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)NFDPR PVETLNVIIP EKLDSFINKF AEYTHEKWAF DKIQNNWSY GENVDEELKT HPMLRPYKTF SEKDKEIYRW PIKESLKAMI AWEWTIEKAR EGEEERTEKK KTRKISQTAQ T YDPREGYN PQPPDLSGVT LSRELQAMAE QLAENYHNTW GRKKKQELEA KGGGTHPLLV PYDTLTAKEK ARDREKAQEL LK FLQMNGY AVTR(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)TPLYNLP THRACNMFLE SYKAAWILTE DHSFEDRMID DLSKAGEQEE EEEEVEEKKP DPLHQLVLHF SRTALTEK S KLDEDYLYMA YADIMAKSCH LEEGGENGEA EEEEVEVSFE EKEMEKQRLL YQQSRLHTRG AAEMVLQMIS ACKGETGAM VSSTLKLGIS ILNGGNAEVQ QKMLDYLKDK KEVGFFQSIQ ALMQTCSVLD LNAFERQNKA EGLGMVNEDG TVINRQNGEK VMADDEFTQ DLFRFLQLLC EGHNNDFQNY LRTQTGNTTT INIIICTVDY LLRLQESISD FYWYYSGKDV IEEQGKRNFS K AMSVAKQV FNSLTEYIQG PCTGNQQSLA HSRLWDAVVG FLHVFAHMMM KLAQDSSQIE 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 AQISE(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)FWGELEV QRVKFLNYLS RNFYTLRFLA LFLAFAINFI LLFYKVSDSP PGE DDMEGS AAGDLAGAGS GGGSGWGSGA GEEAEGDEDE NMVYYFLEES TGYMEPALWC LSLLHTLVAF LCIIGYNCLK VPLV IFKRE KELARKLEFD GLYITEQPGD DDVKGQWDRL VLNTPSFPSN YWDKFVKRKV LDKHGDIFGR ERIAELLGMD LASLE ITAH NERKPDPPPG LLTWLMSIDV KYQIWKFGVI FTDNSFLYLG WYMVMSLLGH YNNFFFAAHL LDIAMGVKTL RTILSS VTH NGKQLVMTVG LLAVVVYLYT VVAFNFFRKF YNKSEDEDEP DMKCDDMMTC YLFHMYVGVR AGGGIGDEIE DPAGDEY EL YRVVFDITFF FFVIVILLAI IQGLIIDAFG ELRDQQEQVK EDMETKCFIC GIGSDYFDTT PHGFETHTLE EHNLANYM F FLMYLINKDE TEHTGQESYV WKMYQERCWD FFPAGDCFRK QYEDQLS

UniProtKB: Ryanodine receptor 1, Ryanodine receptor 1, Ryanodine receptor 1, Ryanodine receptor 1, Ryanodine receptor 1

-
Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

-
Macromolecule #4: CAFFEINE

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

ChemComp-CFF:
CAFFEINE / medication*YM

-
Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration6.0 mg/mL
BufferpH: 7.4
GridModel: Quantifoil / Material: GOLD / Mesh: 400
VitrificationCryogen 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.

-
Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / 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
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

2807

Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 6.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4)
Details: The reported resolution is for the core. The resolution of the whole assembly is 6.7 Angstrom.
Number images used: 55564
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 1.4)
FSC plot (resolution estimation)

+
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