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- EMDB-22394: Functional Pathways of Biomolecules Retrieved from Single-particl... -

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Basic information

Entry
Database: EMDB / ID: EMD-22394
TitleFunctional Pathways of Biomolecules Retrieved from Single-particle Snapshots - Frame 35 - State 4 (S4)
Map dataRyR-Cs2 frame 35 - state 4 (S4)
Sample
  • Complex: Ryanodine receptor 1 bound to FKBP1B
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase FKBP1B
    • Protein or peptide: ryanodine receptor type 1
  • Ligand: ZINC ION
  • Ligand: CALCIUM ION
Keywordsion channel / Ca2+ channel / excitation/contraction coupling / MEMBRANE PROTEIN
Function / homology
Function and homology information


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 / 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 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 / response to redox state / protein maturation by protein folding / 'de novo' protein folding / negative regulation of heart rate / FK506 binding / positive regulation of axon regeneration / channel regulator activity / smooth muscle contraction / response to vitamin E / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / T cell proliferation / Ion homeostasis / release of sequestered calcium ion into cytosol / regulation of cytosolic calcium ion concentration / calcium channel complex / sarcoplasmic reticulum membrane / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / calcium-mediated signaling / 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: 4.5 Å
AuthorsDashti A / des Georges A
Funding support United States, 8 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0002164 United States
National Science Foundation (NSF, United States)STC 1231306 United States
National Science Foundation (NSF, United States)1551489 United States
Howard Hughes Medical Institute (HHMI)Joachim Frank United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM55440 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM29169 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM133598 United States
Department of Energy (DOE, United States)DE-AC05-00OR22725 United States
Citation
Journal: Nat Commun / Year: 2020
Title: Retrieving functional pathways of biomolecules from single-particle snapshots.
Authors: Ali Dashti / Ghoncheh Mashayekhi / Mrinal Shekhar / Danya Ben Hail / Salah Salah / Peter Schwander / Amedee des Georges / Abhishek Singharoy / Joachim Frank / Abbas Ourmazd /
Abstract: A primary reason for the intense interest in structural biology is the fact that knowledge of structure can elucidate macromolecular functions in living organisms. Sustained effort has resulted in an ...A primary reason for the intense interest in structural biology is the fact that knowledge of structure can elucidate macromolecular functions in living organisms. Sustained effort has resulted in an impressive arsenal of tools for determining the static structures. But under physiological conditions, macromolecules undergo continuous conformational changes, a subset of which are functionally important. Techniques for capturing the continuous conformational changes underlying function are essential for further progress. Here, we present chemically-detailed conformational movies of biological function, extracted data-analytically from experimental single-particle cryo-electron microscopy (cryo-EM) snapshots of ryanodine receptor type 1 (RyR1), a calcium-activated calcium channel engaged in the binding of ligands. The functional motions differ substantially from those inferred from static structures in the nature of conformationally active structural domains, the sequence and extent of conformational motions, and the way allosteric signals are transduced within and between domains. Our approach highlights the importance of combining experiment, advanced data analysis, and molecular simulations.
#1: Journal: Nat Commun / Year: 2020
Title: Functional Pathways of Biomolecules Retrieved from Single-particle Snapshots
Authors: Dashti A / des Georges A / Singharoy A / Frank J / Ourmazd A
History
DepositionJul 31, 2020-
Header (metadata) releaseAug 12, 2020-
Map releaseAug 12, 2020-
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: 0.16
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.16
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7jmh
  • Surface level: 0.16
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22394.png

Downloads & links

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Map

FileDownload / File: emd_22394.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRyR-Cs2 frame 35 - state 4 (S4)
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 AUTHOR: 0.16 / Movie #1: 0.16
Minimum - Maximum-0.25733182 - 0.48566166
Average (Standard dev.)0.00077986467 (±0.026520612)
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/NZ000
NX/NY/NZ440440440
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.2570.4860.001

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Supplemental data

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Sample components

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Entire : Ryanodine receptor 1 bound to FKBP1B

EntireName: Ryanodine receptor 1 bound to FKBP1B
Components
  • Complex: Ryanodine receptor 1 bound to FKBP1B
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase FKBP1B
    • Protein or peptide: ryanodine receptor type 1
  • Ligand: ZINC ION
  • Ligand: CALCIUM ION

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Supramolecule #1: Ryanodine receptor 1 bound to FKBP1B

SupramoleculeName: Ryanodine receptor 1 bound to FKBP1B / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 2.3 MDa

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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: 11.667305 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GVEIETISPG DGRTFPKKGQ TCVVHYTGML QNGKKFDSSR DRNKPFKFRI GKQEVIKGFE EGAAQMSLGQ RAKLTCTPDV AYGATGHPG VIPPNATLIF DVELLNLE

UniProtKB: Peptidyl-prolyl cis-trans isomerase FKBP1B

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Macromolecule #2: ryanodine receptor type 1

MacromoleculeName: ryanodine receptor type 1 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / Tissue: thigh
Molecular weightTheoretical: 502.246719 KDa
SequenceString: MGDGGEGEDE VQFLRTDDEV VLQCSATVLK EQLKLCLAAE GFGNRLCFLE PTSNAQNVPP DLAICCFTLE QSLSVRALQE MLANTVEAG VESSQGGGHR TLLYGHAILL RHAHSRMYLS CLTTSRSMTD KLAFDVGLQE DATGEACWWT MHPASKQRSE G EKVRVGDD ...String:
MGDGGEGEDE VQFLRTDDEV VLQCSATVLK EQLKLCLAAE GFGNRLCFLE PTSNAQNVPP DLAICCFTLE QSLSVRALQE MLANTVEAG VESSQGGGHR TLLYGHAILL RHAHSRMYLS CLTTSRSMTD KLAFDVGLQE DATGEACWWT MHPASKQRSE G EKVRVGDD LILVSVSSER YLHLSTASGE LQVDASFMQT LWNMNPICSC CEEGYVTGGH VLRLFHGHMD ECLTISAADS DD QRRLVYY EGGAVCTHAR SLWRLEPLRI SWSGSHLRWG QPLRIRHVTT GRYLALTEDQ GLVVVDACKA HTKATSFCFR VSK EKLDTA PKRDVEGMGP PEIKYGESLC FVQHVASGLW LTYAAPDPKA LRLGVLKKKA ILHQEGHMDD ALFLTRCQQE ESQA ARMIH STAGLYNQFI KGLDSFSGKP RGSGPPAGPA LPIEAVILSL QDLIGYFEPP SEELQHEEKQ SKLRSLRNRQ SLFQE EGML SLVLNCIDRL NVYTTAAHFA EYAGEEAAES WKEIVNLLYE LLASLIRGNR ANCALFSTNL DWVVSKLDRL EASSGI LEV LYCVLIESPE VLNIIQENHI KSIISLLDKH GRNHKVLDVL CSLCVCNGVA VRSNQDLITE NLLPGRELLL QTNLINY VT SIRPNIFVGR AEGSTQYGKW YFEVMVDEVV PFLTAQATHL RVGWALTEGY SPYPGGGEGW GGNGVGDDLY SYGFDGLH L WTGHVARPVT SPGQHLLAPE DVVSCCLDLS VPSISFRING CPVQGVFEAF NLDGLFFPVV SFSAGVKVRF LLGGRHGEF KFLPPPGYAP CHEAVLPRER LRLEPIKEYR REGPRGPHLV GPSRCLSHTD FVPCPVDTVQ IVLPPHLERI REKLAENIHE LWALTRIEQ GWTYGPVRDD NKRLHPCLVN FHSLPEPERN YNLQMSGETL KTLLALGCHV GMADEKAEDN LKKTKLPKTY M MSNGYKPA PLDLSHVRLT PAQTTLVDRL AENGHNVWAR DRVAQGWSYS AVQDIPARRN PRLVPYRLLD EATKRSNRDS LC QAVRTLL GYGYNIEPPD QEPSQVENQS RWDRVRIFRA EKSYTVQSGR WYFEFEAVTT GEMRVGWARP ELRPDVELGA DEL AYVFNG HRGQRWHLGS EPFGRPWQSG DVVGCMIDLT ENTIIFTLNG EVLMSDSGSE TAFREIEIGD GFLPVCSLGP GQVG HLNLG QDVSSLRFFA ICGLQEGFEP FAINMQRPVT TWFSKSLPQF EPVPPEHPHY EVARMDGTVD TPPCLRLAHR (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)MPL SAAMFLSERK NPAPQCP PR LEVQMLMPVS WSRMPNHFLQ VETRRAGERL GWAVQCQDPL TMMALHIPEE NRCMDILELS ERLDLQRFHS HTLRLYRA V CALGNNRVAH ALCSHVDQAQ LLHALEDAHL PGPLRAGYYD LLISIHLESA CRSRRSMLSE YIVPLTPETR AITLFPPGR KGGNARRHGL PGVGVTTSLR PPHHFSPPCF VAALPAAGVA EAPARLSPAI PLEALRDKAL RMLGEAVRDG GQHARDPVGG SVEFQFVPV LKLVSTLLVM GIFGDEDVKQ ILKMIEPEVF TEEEEEEEEE EEEEEEEEED EEEKEEDEEE EEKEDAEKEE E EAPEGEKE DLEEGLLQMK LPESVKLQMC NLLEYFCDQE LQHRVESLAA FAERYVDKLQ ANQRSRYALL MRAFTMSAAE TA RRTREFR SPPQEQINML LHFKDEADEE DCPLPEDIRQ DLQDFHQDLL AHCGIQLEGE EEEPEEETSL SSRLRSLLET VRL VKKKEE KPEEELPAEE KKPQSLQELV SHMVVRWAQE DYVQSPELVR AMFSLLHRQY DGLGELLRAL PRAYTISPSS VEDT MSLLE CLGQIRSLLI VQMGPQEENL MIQSIGNIMN NKVFYQHPNL MRALGMHETV MEVMVNVLGG GETKEIRFPK MVTSC CRFL CYFCRISRQN QRSMFDHLSY LLENSGIGLG MQGSTPLDVA AASVIDNNEL ALALQEQDLE KVVSYLAGCG LQSCPM LLA KGYPDIGWNP CGGERYLDFL RFAVFVNGES VEENANVVVR LLIRKPECFG PALRGEGGSG LLAAIEEAIR ISEDPAR DG PGVRRDRRRE HFGEEPPEEN RVHLGHAIMS FYAALIDLLG RCAPEMHLIQ AGKGEALRIR AILRSLVPLD DLVGIISL P LQIPTL(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)NFDP RPVETLNVII PEKLDSFINK F AEYTHEKW AFDKIQNNWS YGENVDEELK THPMLRPYKT FSEKDKEIYR WPIKESLKAM IAWEWTIEKA REGEEERTEK KK TRKISQT AQTYDPREGY NPQPPDLSGV TLSRELQAMA EQLAENYHNT WGRKKKQELE AKGGGTHPLL VPYDTLTAKE KAR DREKAQ ELLKFLQMNG YAVTR(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(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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(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)TPLYNL PTHRACNMFL ESYKAAWILT EDHSFEDRMI DDLSKAGEQE EEEEEVEEKK PDPLHQLVL HFSRTALTEK SKLDEDYLYM AYADIMAKSC HLEEGGENGE AEEEEVEVSF EEKEMEKQRL LYQQSRLHTR GAAEMVLQMI SACKGETGA MVSSTLKLGI SILNGGNAEV QQKMLDYLKD KKEVGFFQSI QALMQTCSVL DLNAFERQNK AEGLGMVNED G TVINRQNG EKVMADDEFT QDLFRFLQLL CEGHNNDFQN YLRTQTGNTT TINIIICTVD YLLRLQESIS DFYWYYSGKD VI EEQGKRN FSKAMSVAKQ VFNSLTEYIQ GPCTGNQQSL AHSRLWDAVV GFLHVFAHMM MKLAQDSSQI ELLKELLDLQ KDM VVMLLS LLEGNVVNGM IARQMVDMLV ESSSNVEMIL KFFDMFLKLK DIVGSEAFQD YVTDPRGLIS KKDFQKAMDS QKQF TGPEI QFLLSCSEAD ENEMINFEEF ANRFQEPARD IGFNVAVLLT NLSEHVPHDP RLRNFLELAE SILEYFRPYL GRIEI MGAS RRIERIYFEI SETNRAQWEM PQVKESKRQF IFDVVNEGGE AEKMELFVSF CEDTIFEMQI AAQISEPEGE PEADED EGM GEAAAEGAEE GAAGAEGAAG TVAAGATARL AAAAARALRG LSYRSLRRRV RRLRRLTARE AATALAALLW AVVARAG AA GAGAAAGALR LLWGSLFGGG LVEGAKKVTV TELLAGMPDP TSDEVHGEQP AGPGGDADGA GEGEGEGDAA EGDGDEEV A GHEAGPGGAE GVVAVADGGP FRPEGAGGLG DMGDTTPAEP PTPEGSPILK RKLGVDGEEE ELVPEPEPEP EPEPEKADE ENGEKEEVPE APPEPPKKAP PSPPAKKEEA GGAGMEFWGE LEVQRVKFLN YLSRNFYTLR FLALFLAFAI NFILLFYKVS DSPPGEDDM EGSAAGDLAG AGSGGGSGWG SGAGEEAEGD EDENMVYYFL EESTGYMEPA LWCLSLLHTL VAFLCIIGYN C LKVPLVIF KREKELARKL EFDGLYITEQ PGDDDVKGQW DRLVLNTPSF PSNYWDKFVK RKVLDKHGDI FGRERIAELL GM DLASLEI TAHNERKPDP PPGLLTWLMS IDVKYQIWKF GVIFTDNSFL YLGWYMVMSL LGHYNNFFFA AHLLDIAMGV KTL RTILSS VTHNGKQLVM TVGLLAVVVY LYTVVAFNFF RKFYNKSEDE DEPDMKCDDM MTCYLFHMYV GVRAGGGIGD EIED PAGDE YELYRVVFDI TFFFFVIVIL LAIIQGLIID AFGELRDQQE QVKEDMETKC FICGIGSDYF DTTPHGFETH TLEEH NLAN YMFFLMYLIN KDETEHTGQE SYVWKMYQER CWDFFPAGDC FRKQYEDQLS

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #4: CALCIUM ION

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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

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Sample preparation

Concentration8 mg/mL
BufferpH: 7.4
GridModel: UltrAuFoil / Material: GOLD / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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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
Sample stageSpecimen holder model: GATAN ULTST ULTRA LOW TEMPERATURE SINGLE TILT HELIUM COOLING HOLDER
Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

8391


Details: RyR1-Cs2 (EGTA-only)
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: OTHER
Details: RESMAP and visual inspection. FSC not possible as no half-sets are available with the manifold embedding method
Number images used: 791956
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelPDB ID:

5tb4


Chain - Source name: PDB / Chain - Initial model type: experimental model
Detailsfitted to a model domain by domain with the rigid-body fit function in COOT 71, using multiple starting models to avoid model bias (PDB ID: 5TB4, 5T9R, 5TAP, 5T9V, 5TAL, 5TAQ) 22. The models were then refined in real-space using phenix.real_space_refine
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-7jmh:
Functional Pathways of Biomolecules Retrieved from Single-particle Snapshots - Frame 35 - State 4 (S4)

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