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- EMDB-22017: Pig R615C RyR1 EGTA (all classes, open) -

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Basic information

Entry
Database: EMDB / ID: EMD-22017
TitlePig R615C RyR1 EGTA (all classes, open)
Map dataRyR1, FKBP12.6
Sample
  • Complex: ryanodine receptor-FKBP1B complex
    • Complex: ryanodine receptor
      • Protein or peptide: Ryanodine Receptor
    • Complex: FKBP1B
      • Protein or peptide: Peptidyl-prolyl cis-trans isomerase FKBP1B
  • Ligand: ZINC ION
Keywordsreceptor / calcium / channel / complex / TRANSPORT PROTEIN-ISOMERASE complex
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 / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / 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 speciesSus scrofa (pig) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsWoll KW / Haji-Ghassemi O
Funding support1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)
CitationJournal: Nat Commun / Year: 2021
Title: Pathological conformations of disease mutant Ryanodine Receptors revealed by cryo-EM.
Authors: Kellie A Woll / Omid Haji-Ghassemi / Filip Van Petegem /
Abstract: Ryanodine Receptors (RyRs) are massive channels that release Ca from the endoplasmic and sarcoplasmic reticulum. Hundreds of mutations are linked to malignant hyperthermia (MH), myopathies, and ...Ryanodine Receptors (RyRs) are massive channels that release Ca from the endoplasmic and sarcoplasmic reticulum. Hundreds of mutations are linked to malignant hyperthermia (MH), myopathies, and arrhythmias. Here, we explore the first MH mutation identified in humans by providing cryo-EM snapshots of the pig homolog, R615C, showing that it affects an interface between three solenoid regions. We also show the impact of apo-calmodulin (apoCaM) and how it can induce opening by bending of the bridging solenoid, mediated by its N-terminal lobe. For R615C RyR1, apoCaM binding abolishes a pathological 'intermediate' conformation, distributing the population to a mixture of open and closed channels, both different from the structure without apoCaM. Comparisons show that the mutation primarily affects the closed state, inducing partial movements linked to channel activation. This shows that disease mutations can cause distinct pathological conformations of the RyR and facilitate channel opening by disrupting interactions between different solenoid regions.
History
DepositionMay 21, 2020-
Header (metadata) releaseJan 13, 2021-
Map releaseJan 13, 2021-
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: 0.702
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.702
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6x34
  • Surface level: 0.702
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22017.png

Downloads & links

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Map

FileDownload / File: emd_22017.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRyR1, FKBP12.6
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 480 pix.
= 672. Å		1.4 Å/pix.
x 480 pix.
= 672. Å		1.4 Å/pix.
x 480 pix.
= 672. 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: 0.702 / Movie #1: 0.702
Minimum - Maximum-1.0917286 - 2.839103
Average (Standard dev.)-0.00010917625 (±0.09230443)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 672.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z672.000672.000672.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ410410410
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-1.0922.839-0.000

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Supplemental data

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Additional map: Density modified map generated from PHENIX Resolve

Fileemd_22017_additional_1.map
AnnotationDensity modified map generated from PHENIX Resolve
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_22017_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_22017_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 : ryanodine receptor-FKBP1B complex

EntireName: ryanodine receptor-FKBP1B complex
Components
  • Complex: ryanodine receptor-FKBP1B complex
    • Complex: ryanodine receptor
      • Protein or peptide: Ryanodine Receptor
    • Complex: FKBP1B
      • Protein or peptide: Peptidyl-prolyl cis-trans isomerase FKBP1B
  • Ligand: ZINC ION

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Supramolecule #1: ryanodine receptor-FKBP1B complex

SupramoleculeName: ryanodine receptor-FKBP1B complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Supramolecule #2: ryanodine receptor

SupramoleculeName: ryanodine receptor / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Sus scrofa (pig)

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Supramolecule #3: FKBP1B

SupramoleculeName: FKBP1B / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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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: 11.538191 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GVEIETISPG DGRTFPKKGQ TCVVHYTGML QNGKKFDSSR DRNKPFKFRI GKQEVIKGFE EGAAQMSLGQ RAKLTCTPDV AYGATGHPG VIPPNATLIF DVELLNL

UniProtKB: Peptidyl-prolyl cis-trans isomerase FKBP1B

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Macromolecule #2: Ryanodine Receptor

MacromoleculeName: Ryanodine Receptor / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 414.496875 KDa
SequenceString: FLRTDDEVVL QCNATVLKEQ LKLCLAAEGF GNRLCFLEPT SNAQNVPPDL AICCFVLEQS LSVRALQEML ANGHRTLLYG HAILLRHAH SGMYLSCLTT SRSMTDKLAF DVGLQEDATG EACWWTTHPA SKQRSEGEKV RVGDDLILVS VSSERYLHLS T ASGELQVD ...String:
FLRTDDEVVL QCNATVLKEQ LKLCLAAEGF GNRLCFLEPT SNAQNVPPDL AICCFVLEQS LSVRALQEML ANGHRTLLYG HAILLRHAH SGMYLSCLTT SRSMTDKLAF DVGLQEDATG EACWWTTHPA SKQRSEGEKV RVGDDLILVS VSSERYLHLS T ASGELQVD ASFMQTLWNM NPICSGCEEG YVTGGHVLRL FHGHMDECLT ISPADSDDQR RLVYYEGGSV CTHARSLWRL EP LRISWSG SHLRWGQPLR IRHVTTGRYL ALIEDQGLVV DASKAHTKAT SFCFRISKEK LKRDVEGMGP PEIKYGESLC FVQ HVASGL WLTYAALKKK AILHQEGHMD DALSLTRCQQ EESQAARMIY STAGLYNHFI KGLDSFSGKP RGSGAPAGTA LPLE GVILS LQDLIGYFEP PSEELQHEEK QSKLRSLRNR QSLFQEEGML SLVLNCIDRL NVYTTAAHFA EFAGEEAAES WKEIV NLLY EILASLIRGN RANCALFSNN LDWLVSKLDR LEASSGILEV LYCVLIESPE VLNIIQENHI KSIISLLDKH GRNHKV LDV LCSLCVCNGV AVCSNQDLIT ENLLPGRELL LQTNLINYVT SIRPNIFVGR AEGTTQYSKW YFEVMVDEVV PFLTAQA TH LRVGWALTEG YSPYPGGGEG WGGNGVGDDL YSYGFDGLHL WTGHVPRLVT SPGQHLLAPE DVVSCCLDLS VPSISFRI N GCPVQGVFEA FNLNGLFFPV VSFSAGVKVR FLLGGRHGEF KFLPPPGYAP CHEAVLPRER LRLEPIKEYR REGPRGPHL VGPSRCLSHT DFVPCPLPPH LERIREKLAE NIHELWALTR IEQGWTYGPV RDDNKRLHPC LVDFHSLPEP ERNYNLQMSG ETLKTLLAL GCHVGMADEK AEDNLRKTKL PKTYMMSNGY KPAPLDAQTT LVDRLAENGH NVWARDRVAQ GWSYSAVQDI P ARRNPRLV PYRLLDEATK RSNRDSLCQA VRTLLGYGYN IERVRIFRAE KSYAVQSGRW YFEFEAVTTG EMRVGWARPE LR PDVELGA DELAYVFNGH RGQRWHLGSE LFGRPWQSGD VVGCMIDLTE NTIIFTLNGE VLMSDSGSET AFRDIEVGDG FLP VCSLGP GQVGHLNLGQ DVSSLRFFAI CGLQEGFEPF AINMQRPVTT WFSKSLPQFE AVPLEHPHYE VSRVDGTVDT PPCL RLTHR SLVEMLFLRL SLPVQFHQLN TTTYYYSVRV FAGQEPSCVW VGWVTPDYHQ HDMNFDLTKV RAVTVTMGDN IHSSL KCSN CYMVWGGDFV SHTDLVIGCL VDLATGLMTF TANGKESNTF FQVEPNTKLF PAVFVLPTHQ NVIQFELGKQ KNIMPL SAA MFLSERKNPA PQCPPRLEMQ MLMPVSWSRM PNHFLRVETR RAGERLGWAV PLTMMALHIP EENRCMDILE LSERLDL QQ FHSHTLRLYR AVCALGNNRV AHALCSHVDQ AQLLHALEDA HLPGPLRAGY YDLLISIHLE SACRSRRSML SEYIVPLT P ETRAITLFPP RHGLPGVGVT TSLRPPHHFS APCFVAALPE APARLSPSIP LEALRDKALR MLGEAVRDGG QHARDPVGG SVEFQFVPVL KLVSTLLVMG IFGDEDVKQI LKMIEPEVEE GLLQMKLPES VKLQMCNLLE YFCDQELQHR VESLAAFAER YVDKLQANQ RDRYGILMKA FTMTAAETAR RTREFRSPPQ EQINMLLHFK PLPDEIRQDL LEFHQDLLTH CGIQLQSLQE L VSHTVVRW AQEDFVQSPE LVRAMFSLLH RQYDGLGELL RALPRAYTIS PSSVEDTMSL LECLGQIRSL LIVQMGPQEE NL MIQSIGN IMNNKVFYQH PNLMRALGMH ETVMEVMVNV LRFPKMVTSC CRFLCYFCRI SRQNQRSMFD HLSYLLENSG STP LDVAAA SVIDNNELAL ALQEQDLEKV VSYLAGCGLQ SCPMLLAKGY PDIGWNPCGG ERYLDFLRFA VFVNGESVEE NANV VVRLL IRKPECFGPA LRLLATIEEA IAIMSFYAAL IDLLGRCAPE MHLIQAGKGE ALRIRAILRS LVPLDDLVGI ISLPL QIPT MSASFVPDHK ASMVLFLDRV YGFLLHVLDV GFALALNRYL CLAVLPLITK CAPLFAMVDS MLHTVYRLSR GRSLTK AQR DVIEECLMAL CRYIRPSMLQ HLLRRLVF(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)DPR PVETLNVIIP EKLDSFINKF AEYTHEKWAF DKIQNNWSYG ENIDEELKTH PM LRPYKTF SEKDKEIYRW PIKESLKAMI AWEWTIEKAR EGEYNPQPPD LSGVTLSREL QAMAEQLAEN YHNTWGRKKK QEL EAKGGG THPLLVPYDT LTAKEKARDR EKAQELLKFL QMNGYAVTR(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)EFSVLCRDL YALYPLLIRY VDNNRAHWLT E PNPSAEEL FRMVGEIFIY WSKSKHNFKR EEQNFVV(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)P LYNLPTHRAC NMFLESYKAA WILT EDHSF EDRMIDDLSK AKKPDPLHQL VLHFSRTALT EKSKLDEDYL YMAYADIMAK SCHLSFEEKE MEKQRLLYQQ ARLHN RGAA EMVLQMISAC KGETGAMVSS TLKLGISILN GGNADVQQKM LDYLKDKKEV GFFQSIQALM QTCSVLDLNA FERQNK AEG LGEKVMADDE FTQDLFRFLQ LLCEGHNNDF QNYLRTQTGN TTTINIIICT VDYLLRLQES ISDFYWYYSG KDVIEEQ GK RNFSKAMSVA KQVFNSLTEY IQGPCTGNQQ SLAHSRLWDA VVGFLHVFAH MMMKLAQDSS QIELLKELLD LQKDMVVM L LSLLEGNVVN GMIARQMVDM LVESSSNVEM ILKFFDMFLK LKDIVGSEAF QDYVTDPRGL ISKKDFQK(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)EFANR FQEPARDIGF NVAVLLTNLS EHVPHDPRLR NFLELAESIL EYFRPYLGRI EIMGA SRRI ERIYFEISET NRAQWEMPQV KESKRQFIFD VVNEGGESEK MELFVSFCED TIFEEVQRVK FLNYLSRNFY TLRFLA LFL AFAINFILLF YKVSDSPVYY FLEESTGYME PALRCLSLLH TLVAFLCIIG YNCLKVPLVI FKREKELARK LEFDGLY IT EQPVKGQWDR LVLNTPSFPS NYWDKFVKRK VLDKHGDIYG RERIAEGLLT WLMSIDVKYQ IWKFGVIFTD NSFLYLGW Y MVMSLLGHYN NFFFAAHLLD IAMGVKTLRT ILSSVTHNGK QLVMTVGLLA VVVYLYTVVA FNFFRKFYNK SEDEDEPDM KCDDMMTCYL FHMYVGVRAG GGIGDEIEDP AGDEYELYRV VFDITFFFFV IVILLAIIQG LIIDAFGELR DQQEQVREDM ETKCFICGI GSDYFDTTPH RFETHTLEEH NLANYMFFLM YLINKDETEH TGQESYVWKM YQERCWDFFP AGDCFRKQ

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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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: DIFFRACTION
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX (ver. dev-3714) / Number images used: 58822
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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