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Basic information

Entry
Database: PDB / ID: 6pv6
TitleFunctional Pathways of Biomolecules Retrieved from Single-particle Snapshots
Components
  • Peptidyl-prolyl cis-trans isomerase FKBP1B
  • Ryanodine receptor 1
KeywordsMEMBRANE PROTEIN / ion channel / Ca2+ channel / excitation/contraction coupling
Function / homology
Function and homology information


positive regulation of sequestering of calcium ion / negative regulation of calcium-mediated signaling / negative regulation of insulin secretion involved in cellular response to glucose stimulus / neuronal action potential propagation / negative regulation of release of sequestered calcium ion into cytosol / insulin secretion involved in cellular response to glucose stimulus / response to redox state / 'de novo' protein folding / negative regulation of heart rate / FK506 binding ...positive regulation of sequestering of calcium ion / negative regulation of calcium-mediated signaling / negative regulation of insulin secretion involved in cellular response to glucose stimulus / neuronal action potential propagation / negative regulation of release of sequestered calcium ion into cytosol / insulin secretion involved in cellular response to glucose stimulus / response to redox state / 'de novo' protein folding / negative regulation of heart rate / FK506 binding / smooth muscle contraction / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / T cell proliferation / calcium channel inhibitor activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / release of sequestered calcium ion into cytosol / calcium channel complex / sarcoplasmic reticulum membrane / protein maturation / calcium channel regulator activity / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / calcium-mediated signaling / Stimuli-sensing channels / Z disc / positive regulation of cytosolic calcium ion concentration / protein refolding / transmembrane transporter binding / signaling receptor binding / membrane / cytoplasm
Similarity search - Function
: / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase FKBP1B
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsDashti, A. / des Georges, A. / Frank, J. / Ourmazd, A.
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. / Frank, J. / Ourmazd, A.
History
DepositionJul 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Category: citation / citation_author
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

Movie
  • Deposited structure unit
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Structure viewerMolecule:
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Assembly

Deposited unit
B: Ryanodine receptor 1
E: Ryanodine receptor 1
I: Ryanodine receptor 1
G: Ryanodine receptor 1
F: Peptidyl-prolyl cis-trans isomerase FKBP1B
A: Peptidyl-prolyl cis-trans isomerase FKBP1B
H: Peptidyl-prolyl cis-trans isomerase FKBP1B
J: Peptidyl-prolyl cis-trans isomerase FKBP1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,056,60316
Polymers2,056,1818
Non-polymers4228
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Ryanodine receptor 1


Mass: 502246.719 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: thigh
#2: Protein
Peptidyl-prolyl cis-trans isomerase FKBP1B / PPIase FKBP1B / 12.6 kDa FK506-binding protein / FKBP-12.6 / FK506-binding protein 1B / FKBP-1B / ...PPIase FKBP1B / 12.6 kDa FK506-binding protein / FKBP-12.6 / FK506-binding protein 1B / FKBP-1B / Immunophilin FKBP12.6 / Rotamase / h-FKBP-12


Mass: 11798.501 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP1B, FKBP12.6, FKBP1L, FKBP9, OTK4 / Production host: Escherichia coli (E. coli) / References: UniProt: P68106, peptidylprolyl isomerase
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Sequence detailsThe full sequence for the bigger protein of chains B,E,I,G is the following: ...The full sequence for the bigger protein of chains B,E,I,G is the following: MGDGGEGEDEVQFLRTDDEVVLQCSATVLKEQLKLCLAAEGFGNRLCFLEPTSNAQNVPPDLAICCFTLEQSLSVRALQE MLANTVEAGVESSQGGGHRTLLYGHAILLRHAHSRMYLSCLTTSRSMTDKLAFDVGLQEDATGEACWWTMHPASKQRSEG EKVRVGDDLILVSVSSERYLHLSTASGELQVDASFMQTLWNMNPICSCCEEGYVTGGHVLRLFHGHMDECLTISAADSDD QRRLVYYEGGAVCTHARSLWRLEPLRISWSGSHLRWGQPLRIRHVTTGRYLALTEDQGLVVVDACKAHTKATSFCFRVSK EKLDTAPKRDVEGMGPPEIKYGESLCFVQHVASGLWLTYAAPDPKALRLGVLKKKAILHQEGHMDDALFLTRCQQEESQA ARMIHSTAGLYNQFIKGLDSFSGKPRGSGPPAGPALPIEAVILSLQDLIGYFEPPSEELQHEEKQSKLRSLRNRQSLFQE EGMLSLVLNCIDRLNVYTTAAHFAEYAGEEAAESWKEIVNLLYELLASLIRGNRANCALFSTNLDWVVSKLDRLEASSGI LEVLYCVLIESPEVLNIIQENHIKSIISLLDKHGRNHKVLDVLCSLCVCNGVAVRSNQDLITENLLPGRELLLQTNLINY VTSIRPNIFVGRAEGSTQYGKWYFEVMVDEVVPFLTAQATHLRVGWALTEGYSPYPGGGEGWGGNGVGDDLYSYGFDGLH LWTGHVARPVTSPGQHLLAPEDVVSCCLDLSVPSISFRINGCPVQGVFEAFNLDGLFFPVVSFSAGVKVRFLLGGRHGEF KFLPPPGYAPCHEAVLPRERLRLEPIKEYRREGPRGPHLVGPSRCLSHTDFVPCPVDTVQIVLPPHLERIREKLAENIHE LWALTRIEQGWTYGPVRDDNKRLHPCLVNFHSLPEPERNYNLQMSGETLKTLLALGCHVGMADEKAEDNLKKTKLPKTYM MSNGYKPAPLDLSHVRLTPAQTTLVDRLAENGHNVWARDRVAQGWSYSAVQDIPARRNPRLVPYRLLDEATKRSNRDSLC QAVRTLLGYGYNIEPPDQEPSQVENQSRWDRVRIFRAEKSYTVQSGRWYFEFEAVTTGEMRVGWARPELRPDVELGADEL AYVFNGHRGQRWHLGSEPFGRPWQSGDVVGCMIDLTENTIIFTLNGEVLMSDSGSETAFREIEIGDGFLPVCSLGPGQVG HLNLGQDVSSLRFFAICGLQEGFEPFAINMQRPVTTWFSKSLPQFEPVPPEHPHYEVARMDGTVDTPPCLRLAHRTWGSQ NSLVEMLFLRLSLPVQFHQHFRCTAGATPLAPPGLQPPAEDEARAAEPDPDYENLRRSAGGWGEAEGGKEGTAKEGTPGG TPQPGVEAQPVRAENEKDATTEKNKKRGFLFKAKKAAMMTQPPATPALPRLPHDVVPADNRDDPEIILNTTTYYYSVRVF AGQEPSCVWVGWVTPDYHQHDMNFDLSKVRAVTVTMGDEQGNVHSSLKCSNCYMVWGGDFVSPGQQGRISHTDLVIGCLV DLATGLMTFTANGKESNTFFQVEPNTKLFPAVFVLPTHQNVIQFELGKQKNIMPLSAAMFLSERKNPAPQCPPRLEVQML MPVSWSRMPNHFLQVETRRAGERLGWAVQCQDPLTMMALHIPEENRCMDILELSERLDLQRFHSHTLRLYRAVCALGNNR VAHALCSHVDQAQLLHALEDAHLPGPLRAGYYDLLISIHLESACRSRRSMLSEYIVPLTPETRAITLFPPGRKGGNARRH GLPGVGVTTSLRPPHHFSPPCFVAALPAAGVAEAPARLSPAIPLEALRDKALRMLGEAVRDGGQHARDPVGGSVEFQFVP VLKLVSTLLVMGIFGDEDVKQILKMIEPEVFTEEEEEEEEEEEEEEEEEEDEEEKEEDEEEEEKEDAEKEEEEAPEGEKE DLEEGLLQMKLPESVKLQMCNLLEYFCDQELQHRVESLAAFAERYVDKLQANQRSRYALLMRAFTMSAAETARRTREFRS PPQEQINMLLHFKDEADEEDCPLPEDIRQDLQDFHQDLLAHCGIQLEGEEEEPEEETSLSSRLRSLLETVRLVKKKEEKP EEELPAEEKKPQSLQELVSHMVVRWAQEDYVQSPELVRAMFSLLHRQYDGLGELLRALPRAYTISPSSVEDTMSLLECLG QIRSLLIVQMGPQEENLMIQSIGNIMNNKVFYQHPNLMRALGMHETVMEVMVNVLGGGETKEIRFPKMVTSCCRFLCYFC RISRQNQRSMFDHLSYLLENSGIGLGMQGSTPLDVAAASVIDNNELALALQEQDLEKVVSYLAGCGLQSCPMLLAKGYPD IGWNPCGGERYLDFLRFAVFVNGESVEENANVVVRLLIRKPECFGPALRGEGGSGLLAAIEEAIRISEDPARDGPGVRRD RRREHFGEEPPEENRVHLGHAIMSFYAALIDLLGRCAPEMHLIQAGKGEALRIRAILRSLVPLDDLVGIISLPLQIPTLG KDGALVQPKMSASFVPDHKASMVLFLDRVYGIENQDFLLHVLDVGFLPDMRAAASLDTATFSTTEMALALNRYLCLAVLP LITKCAPLFAGTEHRAIMVDSMLHTVYRLSRGRSLTKAQRDVIEDCLMALCRYIRPSMLQHLLRRLVFDVPILNEFAKMP LKLLTNHYERCWKYYCLPTGWANFGVTSEEELHLTRKLFWGIFDSLAHKKYDQELYRMAMPCLCAIAGALPPDYVDASYS SKAEKKATVDAEGNFDPRPVETLNVIIPEKLDSFINKFAEYTHEKWAFDKIQNNWSYGENVDEELKTHPMLRPYKTFSEK DKEIYRWPIKESLKAMIAWEWTIEKAREGEEERTEKKKTRKISQTAQTYDPREGYNPQPPDLSGVTLSRELQAMAEQLAE NYHNTWGRKKKQELEAKGGGTHPLLVPYDTLTAKEKARDREKAQELLKFLQMNGYAVTRGLKDMELDTSSIEKRFAFGFL QQLLRWMDISQEFIAHLEAVVSSGRVEKSPHEQEIKFFAKILLPLINQYFTNHCLYFLSTPAKVLGSGGHASNKEKEMIT SLFCKLAALVRHRVSLFGTDAPAVVNCLHILARSLDARTVMKSGPEIVKAGLRSFFESASEDIEKMVENLRLGKVSQART QVKGVGQNLTYTTVALLPVLTTLFQHIAQHQFGDDVILDDVQVSCYRTLCSIYSLGTTKNTYVEKLRPALGECLARLAAA MPVAFLEPQLNEYNACSVYTTKSPRERAILGLPNSVEEMCPDIPVLDRLMADIGGLAESGARYTEMPHVIEITLPMLCSY LPRWWERGPEAPPPALPAGAPPPCTAVTSDHLNSLLGNILRIIVNNLGIDEATWMKRLAVFAQPIVSRARPELLHSHFIP TIGRLRKRAGKVVAEEEQLRLEAKAEAEEGELLVRDEFSVLCRDLYALYPLLIRYVDNNRAHWLTEPNANAEELFRMVGE IFIYWSKSHNFKREEQNFVVQNEINNMSFLTADSKSKMAKAGDAQSGGSDQERTKKKRRGDRYSVQTSLIVATLKKMLPI GLNMCAPTDQDLIMLAKTRYALKDTDEEVREFLQNNLHLQGKVEGSPSLRWQMALYRGLPGREEDADDPEKIVRRVQEVS AVLYHLEQTEHPYKSKKAVWHKLLSKQRRRAVVACFRMTPLYNLPTHRACNMFLESYKAAWILTEDHSFEDRMIDDLSKA GEQEEEEEEVEEKKPDPLHQLVLHFSRTALTEKSKLDEDYLYMAYADIMAKSCHLEEGGENGEAEEEEVEVSFEEKEMEK QRLLYQQSRLHTRGAAEMVLQMISACKGETGAMVSSTLKLGISILNGGNAEVQQKMLDYLKDKKEVGFFQSIQALMQTCS VLDLNAFERQNKAEGLGMVNEDGTVINRQNGEKVMADDEFTQDLFRFLQLLCEGHNNDFQNYLRTQTGNTTTINIIICTV DYLLRLQESISDFYWYYSGKDVIEEQGKRNFSKAMSVAKQVFNSLTEYIQGPCTGNQQSLAHSRLWDAVVGFLHVFAHMM MKLAQDSSQIELLKELLDLQKDMVVMLLSLLEGNVVNGMIARQMVDMLVESSSNVEMILKFFDMFLKLKDIVGSEAFQDY VTDPRGLISKKDFQKAMDSQKQFTGPEIQFLLSCSEADENEMINFEEFANRFQEPARDIGFNVAVLLTNLSEHVPHDPRL RNFLELAESILEYFRPYLGRIEIMGASRRIERIYFEISETNRAQWEMPQVKESKRQFIFDVVNEGGEAEKMELFVSFCED TIFEMQIAAQISEPEGEPEADEDEGMGEAAAEGAEEGAAGAEGAAGTVAAGATARLAAAAARALRGLSYRSLRRRVRRLR RLTAREAATALAALLWAVVARAGAAGAGAAAGALRLLWGSLFGGGLVEGAKKVTVTELLAGMPDPTSDEVHGEQPAGPGG DADGAGEGEGEGDAAEGDGDEEVAGHEAGPGGAEGVVAVADGGPFRPEGAGGLGDMGDTTPAEPPTPEGSPILKRKLGVD GEEEELVPEPEPEPEPEPEKADEENGEKEEVPEAPPEPPKKAPPSPPAKKEEAGGAGMEFWGELEVQRVKFLNYLSRNFY TLRFLALFLAFAINFILLFYKVSDSPPGEDDMEGSAAGDLAGAGSGGGSGWGSGAGEEAEGDEDENMVYYFLEESTGYME PALWCLSLLHTLVAFLCIIGYNCLKVPLVIFKREKELARKLEFDGLYITEQPGDDDVKGQWDRLVLNTPSFPSNYWDKFV KRKVLDKHGDIFGRERIAELLGMDLASLEITAHNERKPDPPPGLLTWLMSIDVKYQIWKFGVIFTDNSFLYLGWYMVMSL LGHYNNFFFAAHLLDIAMGVKTLRTILSSVTHNGKQLVMTVGLLAVVVYLYTVVAFNFFRKFYNKSEDEDEPDMKCDDMM TCYLFHMYVGVRAGGGIGDEIEDPAGDEYELYRVVFDITFFFFVIVILLAIIQGLIIDAFGELRDQQEQVKEDMETKCFI CGIGSDYFDTTPHGFETHTLEEHNLANYMFFLMYLINKDETEHTGQESYVWKMYQERCWDFFPAGDCFRKQYEDQLS

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ryanodine receptor 1 bound to FKBP1B / Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES
Molecular weightValue: 2.3 MDa / Experimental value: NO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenConc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: UltrAuFoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Specimen holderCryogen: NITROGEN
Specimen holder model: GATAN ULTST ULTRA LOW TEMPERATURE SINGLE TILT HELIUM COOLING HOLDER
Image recordingElectron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
2Leginonimage acquisition
7PHENIXmodel fitting
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 4.5 Å / Resolution method: OTHER / Num. of particles: 791956
Details: RESMAP and visual inspection. FSC not possible as no half-sets are available with the manifold embedding method
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Details: fitted 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 ...Details: fitted 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
Atomic model buildingPDB-ID: 5TB4

5tb4


Accession code: 5TB4 / Source name: PDB / Type: experimental model

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