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- EMDB-11071: Structure of Ryanodine Receptor 2 in lipid nano discs in complex ... -

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Basic information

Entry
Database: EMDB / ID: EMD-11071
TitleStructure of Ryanodine Receptor 2 in lipid nano discs in complex with nanobody and FKBP12.6 in presence of calcium
Map data
Sample
  • Complex: Complex of Ryanodine receptor 2 with auxiliary protein FKBP12.6 and high affinity nanobody
    • Protein or peptide: Ryanodine receptor 2
Function / homology
Function and homology information


Stimuli-sensing channels / establishment of protein localization to endoplasmic reticulum / type B pancreatic cell apoptotic process / Purkinje myocyte to ventricular cardiac muscle cell signaling / suramin binding / regulation of SA node cell action potential / regulation of atrial cardiac muscle cell action potential / Ion homeostasis / left ventricular cardiac muscle tissue morphogenesis / : ...Stimuli-sensing channels / establishment of protein localization to endoplasmic reticulum / type B pancreatic cell apoptotic process / Purkinje myocyte to ventricular cardiac muscle cell signaling / suramin binding / regulation of SA node cell action potential / regulation of atrial cardiac muscle cell action potential / Ion homeostasis / left ventricular cardiac muscle tissue morphogenesis / : / regulation of AV node cell action potential / regulation of ventricular cardiac muscle cell action potential / ventricular cardiac muscle cell action potential / positive regulation of sequestering of calcium ion / cyclic nucleotide binding / embryonic heart tube morphogenesis / cardiac muscle hypertrophy / 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 / ryanodine-sensitive calcium-release channel activity / insulin secretion / calcium ion transport into cytosol / response to muscle activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / response to redox state / negative regulation of heart rate / positive regulation of heart rate / FK506 binding / positive regulation of axon regeneration / protein kinase A regulatory subunit binding / cellular response to caffeine / negative regulation of ryanodine-sensitive calcium-release channel activity / protein kinase A catalytic subunit binding / positive regulation of the force of heart contraction / protein peptidyl-prolyl isomerization / detection of calcium ion / smooth muscle contraction / response to vitamin E / regulation of ryanodine-sensitive calcium-release channel activity / smooth endoplasmic reticulum / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / response to glucose / striated muscle contraction / T cell proliferation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / release of sequestered calcium ion into cytosol / regulation of cytosolic calcium ion concentration / calcium channel complex / cellular response to epinephrine stimulus / response to muscle stretch / sarcoplasmic reticulum membrane / regulation of heart rate / sarcoplasmic reticulum / establishment of localization in cell / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / response to hydrogen peroxide / sarcolemma / Z disc / intracellular calcium ion homeostasis / positive regulation of cytosolic calcium ion concentration / transmembrane transporter binding / calmodulin binding / response to hypoxia / intracellular membrane-bounded organelle / signaling receptor binding / calcium ion binding / identical protein binding / membrane / 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 / EF-hand domain pair / EF-hand calcium-binding domain profile. / EF-hand domain / Ion transport domain / Ion transport protein / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Ryanodine receptor 2 / Peptidyl-prolyl cis-trans isomerase FKBP1B
Similarity search - Component
Biological speciesBos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.5 Å
AuthorsWillegems K / Efremov R
Funding support Belgium, 2 items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)131261 Belgium
Research Foundation - Flanders (FWO)G.0266.15N Belgium
CitationJournal: To Be Published
Title: Rapid purification and reconstitution into lipid nanodiscs of cardiac Ryanodine Receptor using nanobodies.
Authors: Willegems K / Efremov RG
History
DepositionMay 23, 2020-
Header (metadata) releaseJun 9, 2021-
Map releaseJun 9, 2021-
UpdateJun 9, 2021-
Current statusJun 9, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.8
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.8
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11071.png

Downloads & links

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Map

FileDownload / File: emd_11071.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 360 pix.
= 504. Å		1.4 Å/pix.
x 360 pix.
= 504. Å		1.4 Å/pix.
x 360 pix.
= 504. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8 / Movie #1: 0.8
Minimum - Maximum-1.0241436 - 3.1146193
Average (Standard dev.)0.016309194 (±0.1693005)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 504.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z504.000504.000504.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-1.0243.1150.016

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Supplemental data

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Half map: #2

Fileemd_11071_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_11071_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of Ryanodine receptor 2 with auxiliary protein FKBP12.6 a...

EntireName: Complex of Ryanodine receptor 2 with auxiliary protein FKBP12.6 and high affinity nanobody
Components
  • Complex: Complex of Ryanodine receptor 2 with auxiliary protein FKBP12.6 and high affinity nanobody
    • Protein or peptide: Ryanodine receptor 2

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Supramolecule #1: Complex of Ryanodine receptor 2 with auxiliary protein FKBP12.6 a...

SupramoleculeName: Complex of Ryanodine receptor 2 with auxiliary protein FKBP12.6 and high affinity nanobody
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 2.2 MDa

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Macromolecule #1: Ryanodine receptor 2

MacromoleculeName: Ryanodine receptor 2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle) / Tissue: Heart
SequenceString: SNLSGSGEKT DDEVVLQCTA TIHKEQQKLC LAAEGFGNRL CFLESTSNSK NVPPDLSICT FVLEQSLSV RALQEMLANT VEKSEGAKEN PCTAQGGGHR TLLYGHAILL RHSYSGMYLC C LSTSRSST DKLAFDVGLQ EDTTGEACWW IIHPASKQRS EGEKVRVGDD ...String:
SNLSGSGEKT DDEVVLQCTA TIHKEQQKLC LAAEGFGNRL CFLESTSNSK NVPPDLSICT FVLEQSLSV RALQEMLANT VEKSEGAKEN PCTAQGGGHR TLLYGHAILL RHSYSGMYLC C LSTSRSST DKLAFDVGLQ EDTTGEACWW IIHPASKQRS EGEKVRVGDD LILVSVSSER YL HLSYGNG SLHVDAAFQQ TLWSVAPISS GSEAAQGYLI GGDVLRLLHG HMDECLTVPS GEH GEEQRR TVHYEGGAVS VHARSLWRLE TLRVAWSGSH IRWGQPFRLR HVTTGKYLSL MEDK SLLLM DKEKADVKST AFTFRSSKEK LDVGVRKEVD GMGTSEIKYG DSVCYIQHIN TGLWL TYQS VDVKSVRMGS IQRKAIMHHE GHMDDGLNLS RSQHEESRTA RVIRSTVFLF NRFIRG LDA LSKKVKASTV DLPIESVSLS LQDLIGYFHP PDEHLEHEDK QNRLRALKNR QNLFQEE GM INLVLECIDR LHVYSSAAHF ADVAGREAGE SWKSILNSLY ELLAALIRGN RKNCAQFS G SLDWLISRLE RLEASSGILE VLHCVLVESP EALNIIKEGH IKSIISLLDK HGRNHKVLD VLCSLCVCHG VAVRSNQHLI CDNLLPGRDL LLQTRLVNHV SSMRPNIFLG VSEGSAQYKK WYYELMVDH TEPFVTAEAT HLRVGWASTE GYSPYPGGGE EWGGNGVGDD LFSYGFDGLH L WSGCIART VSSPNQHLLR TDDVISCCLD LSAPSISFRI NGQPVQGMFE NFNIDGLFFP VV SFSAGIK VRFLLGGRHG EFKFLPPPGY APCYEAVLPK EKLKVEHSRE YKQERTYTRD LLG PTVSLT QAAFTPIPVD TSQIVLPPHL ERIREKLAEN IHELWVMNKI ELGWQYGPVR DDNK RQHPC LVEFSKLPEQ ERNYNLQMSL ETLKTLLALG CHVGISDEHA EEKVKKMKLP KNYQL TSGY KPAPMDLSFI KLTPSQEAMV DKLAENAHNV WARDRIRQGW TYGIQQDVKN RRNPRL VPY ALLDDRTKKS NKDSLREAVR TLLGYGYNLE APDQDHAARA EVCSGTGERF RIFRAEK TY AVKAGRWYFE FEAVTAGDMR VGWCRPGCQP DQELGSDERA FAFDGFKAQR WHQGNEHY G RSWQAGDVVG CMVDMTEHTM MFTLNGEILL DDSGSELAFK DFDVGDGFIP VCSLGVAQV GRLNFGKDVS TLKYFTICGL QEGYEPFAVN TNRDITMWLS KRLPQFLQVP SNHEHIEVTR IDGTIDSSP CLKVTQKSFG SQNSSTDIMF YRLSMPIECA EVFSKTAAGG IPGTGLFGPK N DLEDYDVD SDFEVLMKTA HGHLVPDRGD RDKEATKPEF NNHKDYAQEK PSRLKQRFLL RR TKPDYST SHSARLTEDV LADERDDYDY LMQTSTYYYS VRIFPGQEPA NVWVGWITSD FHQ YDTGFD LDRVRTVTVT LGDEKGKVHE SIKRSNCYMV CAGESLSPGQ GRNNNGLEIG CVVD AASGL LTFTANGKEL STYYQVEPST KLFPAVFAQA TSPNVFQFEL GRIKNVMPLS AGLFK SEHK NPVPQCPPRL HVQFLSHVLW SRMPNQFLKV DVSRISERQG WLVQCMEPLQ FMSLHI PEE NRSVDILELT EQEELLKFHY HTLRLYSAVC ALGNHRVAHA LCSHVDEPQL LYAIENK YM PGLLRTGYYD LLIDIHLSSY ATARLMMNNE FIVPMTEETK SITLFPDEKK KHGLPGIG L STSLRPRMQF SSPSFVSINT EGYQYSPEFP LDILKAKTIQ MLTEAVKEGS LHARDPVGG TTEFLFVPLI KLFYTLLIMG VFHNEDLKHV LQLIEPSVFK EAASPEEESE VAEKEPFVED SKLEGAAEE ENKGAKRPKE GLLQMKLPEP VKLQMCLLLQ YLCDCQVRHR IEAIVAFSDD F VAKLQDNQ RFRYNEVMQA LNMSAALTAR KTKEFRSPPQ EQINMLLNFK DDKSECPCPE EI RDQLLDF HEDLMTHCGI ELDEDRSLDG NNDLTIRGRL LSLVEKVTYL KKKQAEKPVE SDS KKSSTL QQLISETMVR WAQESVIEDP ELVRAMFVLL HRQYDGIGGL VRALPKTYTI NGVS VEDTI NLLASLGQIR SLLSVRMGKE EEKLMIRGLG DIMNNKVFYQ HPNLMRALGM HETVM EVMV NVLGGGESKE ITFPKMVANC CRFLCYFCRI SRQNQKAMFD HLSYLLENSS VGLASP AMR GSTPLDVAAA SVMDNNELAL ALREPDLEKV VRYLAGCGLQ SCQMLVSKGY PDIGWNP VE GERYLDFLRF AVFCNGESVE ENANVVVRLL IRRPECFGPA LRGEGGNGLL AAMEEAIK I AEDPSRDGPS PTTGSSKTPD TEEEEDDTIH MGNAIMTFYS ALIDLLGRCA PEMHLIHAA KGEAIRIRSI LRSLIPLGDL VGVISIAFQM PTIAKDGNVV EPDMSAGFCP DHKAAMVLFL DRVYGIEVQ DFLLHLLEVG FLPDLRAAAS LDTAALSATD MALALNRYLC TAVLPLLTRC A PLFAGTEH HASLIDSLLH TVYRLSKGCS LTKAQRDSIE VCLLSICGQL RPSMMQHLLR RL VFDVPLL NEHAKMPLKL LTNHYERCWK YYCLPGGWGN FGAASEEELH LSRKLFWGIF DAL SQKKYE QELFKLALPC LSAVAGALPP DYMESNYVSM MEKQSSMDSE GNFNPQPVDT SNIT IPEKL EYFINKYAEH AHDKWSMDKL ANGWIYGEIY SDSSKVQPLM KPYKLLSEKE KEIYR WPIK ESLKTMLAWG WRIERTREGD SMALYNRTRR ISQTSQVSVD AAHGYSPRAI DMSNVT LSR DLHAMAEMMA ENYHNIWAKK KKLELEAKGG GNHPLLVPYD TLTAKEKAKD REKAQDI LK FLQINGYAVS RGFKDLELDT PSIEKRFAYS FLQQLIRYVD EAHQYILEFD GGSRSKGE H FPYEQEIKFF AKVVLPLIDQ YFKNHRLYFL SAASRPLCSG GHASNKEKEM NFSEQFIQL FVSSLGNDAT SIVNCLHILG QTLDARTVMK TGLESVKSAL RAFLDNAAED LEKTMENLKQ GQFTHTRNQ PKGVTQIINY TTVALLPMLS SLFEHIGQHQ FGEDLILEDV QVSCYRILTS L YALGTSKS IYVERQRSAL GECLAAFAGA FPVAFLETHL DKHNIYSIYN TKSSRERAAL NL PANVEDV CPNIPSLEKL MEEIVDLAES GIRYTQMPHV MEVVLPMLCS YMSRWWEHGP ENN PGRAEM CCTALNSEHM NTLLGNILKI IYNNLGIDEG AWMKRLAVFS QPIINKVKPQ LLKT HFLPL MEKLKKKAAM VVSEEDHLKS EARGDMSEAE LLILDEFTTL ARDLYAFYPL LIRFV DYNR AKWLKEPNQE AEDLFRMVAE VFIYWSKSHN FKREEQNFVV QNEINNMSFL IMDTKS KMS KAAVSDQERK KMKRKGDRYS MQTSLIVAAL KRLLPIGLNI CAPGDQELIA LAKNRFS LK DTEDEVRDII RSNIHLQGKL EDPAIRWQMA LYKDLPNRTE DTSDPEKTVE RVLDIANV L FHLEQVSFCV EHPQRSKKAV WHKLLSKQRK RAVVACFRMA PLYNLPRHRA VNLFLQGYE KSWIETEEHY FEDKLIEDLA KPGAEPPEED EGTKRVDPLH QLILLFSRTA LTEKWYGWGS CHDEEDDDG EEEVKSFEEK EMEKQKLLYQ QARLHDRGAA EMVLQTISAS KGETGPMVAA T LKLGIAIL NGGNSTVQQK MLDYLKEKKD VGFFQSLAGL MQSCSVLDLN AFERQNKAEG LG MVTEEGS GEKVLQDDEF TCDLFRFLQL LCEGHNSVQN WTDVIDEQGQ RNFSKAIQVA KQV FNTLTE YIQGPCTGNQ QSLAHSRLWD AVVGFLHVFA HMQMKLSQDS SQIELLKELM DLQK DMVVM LLSMLEGNVV NGTIGKQMVD MLVESSNNVE MILKFFDMFL KLKDLTSSDT FKEYD PDGK GVISKRDFHK AMESHKHYTQ SETEFLLSCA ETDENETLDY EEFVKRFHEP AKDIGF NVA VLLTNLSEHM PNDTRLQTFL ELAESVLNYF QPFLGRIEIM GSAKRIERVY FEISESS RT QWEKPQVKES KRQFIFDVVN EGGEKEKMEL FVNFCEDTIF EMQLAAQISE SDLNERSA N KEESEKEKPE EQGPRMGFFS IMTVKSALFA LRYNILTLMR MLSLKSLKKQ MKKVKKMTV KDMITAFFTS YWSILMSLLH FVASVFRGFS RIIGSLLLGG SLVEGAKKIK VAELLANMPD PTQDEVRGD GEEGERKTLE GALPSEDLTD LKELSEESDL LSDIFGLDLK REGGQYKLIP H NPNAGLSD LMSNPVPIPE VQEKFQEQKA KEEEKEEKEE SKSEPEKAEG EDGEKEEKAK ED KGKQKLR QLHTHRYGEP EVPESAFWKK IIAYQQKLLN YFARNFYNMR MLALFVAFAI NFI LLFYKV STSSVVEGKE LPTRSSSENA RVSSLDSSSP RIIAVHYVLE ESSGYMEPTL RILA ILHTV ISFFCIIGYY CLKVPLVIFK REKEVARKLE FDGLYITEQP SEDDIKGQWD RLVIN TQSF PNNYWDKFVK RKVMDKYGEF YGRDRISELL GMDKAALDFS DAREKKKPKK DSSLSA VLN SIDVKYQMWK LGVVFTDNSF LYLAWYMTMS ILGHYNNFFF AAHLLDIAMG FKTLRTI LS SVTHNGKQLV LTVGLLAVVV YLYTVVAFNF FRKFYNKSED GDTPDMKCDD MLTCYMFH M YVGVRAGGGI GDEIEDPAGD EYEIYRIIFD ITFFFFVIVI LLAIIQGLII DAFGELRDQ QEQVKEDMET KCFICGIGND YFDTVPHGFE THTLQEHNLA NYLFFLMYLI NKDETEHTGQ ESYVWKMYQ ERCWEFFPAG DCFRKQYEDQ LN

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
25.0 mMTris2-Amino-2-(hydroxymethyl)-1,3-propanediol
50.0 mMHEPES4-(2-Hydroxyethyl)piperazine-1-ethanesulfonic acid
200.0 mMNaClsodium chloride
5.0 mMTCEPTris(2-carboxyethyl)phosphine hydrochloride
0.06 %fOMfluorinated octyl maltoside
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 400 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: GRAPHENE OXIDE / Support film - #1 - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 400.0 kPa
Details: Grid was glow discharged before the application of fresh graphene oxide, 30min prior to plunging
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293.15 K / Instrument: GATAN CRYOPLUNGE 3
Details: .Grid was blotted manually from the back in CP3 cryoplunge (Gatan) for 2s.
DetailsThe RyR2 tetrameric channels formed channel-dimers with the nanobody at the dimer-interface bound to the repeat12 domain of the individual channels

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsSpherical aberration corrector: Microscope was modified with a Cs corrector
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 4088 / Average electron dose: 47.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.0 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 418936
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Startup modelType of model: OTHER / Details: ab initio model generated in cryoSPARC
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C4 (4 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.12.4) / Number images used: 41112
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 2.12.4)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 2.12.4)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 2.12.4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6jh6

RefinementProtocol: RIGID BODY FIT

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