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- EMDB-29903: Structure of LARP7 protein p65-telomerase RNA complex in telomerase -

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Basic information

Entry
Database: EMDB / ID: EMD-29903
TitleStructure of LARP7 protein p65-telomerase RNA complex in telomerase
Map data
Sample
  • Complex: tetrahymena telomerase holoenzyme
    • Protein or peptide: Telomerase reverse transcriptase
    • Protein or peptide: Telomerase holoenzyme Teb1 subunit
    • Protein or peptide: Telomerase holoenzyme Teb2 subunit
    • Protein or peptide: Telomerase holoenzyme Teb3 subunit
    • Protein or peptide: Telomerase associated protein p50
    • DNA: telomere DNA
    • RNA: Telomerase RNA
    • Protein or peptide: Telomerase La-related protein p65
  • Ligand: ZINC ION
KeywordsLa protein / La-related protein / telomerase / ribonucleoprotein / RNA BINDING PROTEIN
Function / homology
Function and homology information


telomerase catalytic core complex assembly / telomerase RNA stabilization / telomerase catalytic core complex / : / DNA replication factor A complex / single-stranded telomeric DNA binding / telomerase holoenzyme complex / telomerase RNA binding / telomeric DNA binding / telomere maintenance via telomerase ...telomerase catalytic core complex assembly / telomerase RNA stabilization / telomerase catalytic core complex / : / DNA replication factor A complex / single-stranded telomeric DNA binding / telomerase holoenzyme complex / telomerase RNA binding / telomeric DNA binding / telomere maintenance via telomerase / RNA-directed DNA polymerase / DNA recombination / DNA replication / chromosome, telomeric region / DNA repair / DNA binding / zinc ion binding / metal ion binding
Similarity search - Function
: / Telomerase reverse transcriptase TEN domain / Replication factor A protein 3 / Replication factor A protein 3 / xRRM domain profile. / La protein, xRRM domain / La domain containing protein / La domain / Domain in the RNA-binding Lupus La protein; unknown function / La-type HTH domain ...: / Telomerase reverse transcriptase TEN domain / Replication factor A protein 3 / Replication factor A protein 3 / xRRM domain profile. / La protein, xRRM domain / La domain containing protein / La domain / Domain in the RNA-binding Lupus La protein; unknown function / La-type HTH domain / La-type HTH domain profile. / Telomerase ribonucleoprotein complex - RNA binding domain / : / Telomerase reverse transcriptase / Telomerase ribonucleoprotein complex - RNA-binding domain / Telomerase ribonucleoprotein complex - RNA binding domain / Replication factor A, C-terminal / Replication factor-A C terminal domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Winged helix DNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Replication protein A 32 kDa subunit / Replication protein A 14 kDa subunit / Telomeric repeat-binding subunit 1 / Telomerase-associated protein of 50 kDa / Telomerase reverse transcriptase / La-related protein 7 homolog
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsWang Y / He Y / Yang Y / Singh M / Eichhorn CD / Zhou ZH / Feigon J
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM131901 United States
National Science Foundation (NSF, United States)MCB2016540 United States
CitationJournal: J Mol Biol / Year: 2023
Title: Structure of LARP7 Protein p65-telomerase RNA Complex in Telomerase Revealed by Cryo-EM and NMR.
Authors: Yaqiang Wang / Yao He / Yanjiao Wang / Yuan Yang / Mahavir Singh / Catherine D Eichhorn / Xinyi Cheng / Yi Xiao Jiang / Z Hong Zhou / Juli Feigon /
Abstract: La-related protein 7 (LARP7) are a family of RNA chaperones that protect the 3'-end of RNA and are components of specific ribonucleoprotein complexes (RNP). In Tetrahymena thermophila telomerase, ...La-related protein 7 (LARP7) are a family of RNA chaperones that protect the 3'-end of RNA and are components of specific ribonucleoprotein complexes (RNP). In Tetrahymena thermophila telomerase, LARP7 protein p65 together with telomerase reverse transcriptase (TERT) and telomerase RNA (TER) form the core RNP. p65 has four known domains-N-terminal domain (NTD), La motif (LaM), RNA recognition motif 1 (RRM1), and C-terminal xRRM2. To date, only the xRRM2 and LaM and their interactions with TER have been structurally characterized. Conformational dynamics leading to low resolution in cryo-EM density maps have limited our understanding of how full-length p65 specifically recognizes and remodels TER for telomerase assembly. Here, we combined focused classification of Tetrahymena telomerase cryo-EM maps with NMR spectroscopy to determine the structure of p65-TER. Three previously unknown helices are identified, one in the otherwise intrinsically disordered NTD that binds the La module, one that extends RRM1, and another preceding xRRM2, that stabilize p65-TER interactions. The extended La module (αN, LaM and RRM1) interacts with the four 3' terminal U nucleotides, while LaM and αN additionally interact with TER pseudoknot, and LaM with stem 1 and 5' end. Our results reveal the extensive p65-TER interactions that promote TER 3'-end protection, TER folding, and core RNP assembly and stabilization. The structure of full-length p65 with TER also sheds light on the biological roles of genuine La and LARP7 proteins as RNA chaperones and core RNP components.
History
DepositionFeb 23, 2023-
Header (metadata) releaseJun 28, 2023-
Map releaseJun 28, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29903.png

Downloads & links

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Map

FileDownload / File: emd_29903.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.36 Å
Density
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.022916643 - 0.073858164
Average (Standard dev.)0.0003023681 (±0.002483133)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 348.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_29903_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_29903_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 : tetrahymena telomerase holoenzyme

EntireName: tetrahymena telomerase holoenzyme
Components
  • Complex: tetrahymena telomerase holoenzyme
    • Protein or peptide: Telomerase reverse transcriptase
    • Protein or peptide: Telomerase holoenzyme Teb1 subunit
    • Protein or peptide: Telomerase holoenzyme Teb2 subunit
    • Protein or peptide: Telomerase holoenzyme Teb3 subunit
    • Protein or peptide: Telomerase associated protein p50
    • DNA: telomere DNA
    • RNA: Telomerase RNA
    • Protein or peptide: Telomerase La-related protein p65
  • Ligand: ZINC ION

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Supramolecule #1: tetrahymena telomerase holoenzyme

SupramoleculeName: tetrahymena telomerase holoenzyme / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Tetrahymena thermophila (eukaryote)

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Macromolecule #1: Telomerase reverse transcriptase

MacromoleculeName: Telomerase reverse transcriptase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed DNA polymerase
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 133.486938 KDa
SequenceString: MQKINNINNN KQMLTRKEDL LTVLKQISAL KYVSNLYEFL LATEKIVQTS ELDTQFQEFL TTTIIASEQN LVENYKQKYN QPNFSQLTI KQVIDDSIIL LGNKQNYVQQ IGTTTIGFYV EYENINLSRQ TLYSSNFRNL LNIFGEEDFK YFLIDFLVFT K VEQNGYLQ ...String:
MQKINNINNN KQMLTRKEDL LTVLKQISAL KYVSNLYEFL LATEKIVQTS ELDTQFQEFL TTTIIASEQN LVENYKQKYN QPNFSQLTI KQVIDDSIIL LGNKQNYVQQ IGTTTIGFYV EYENINLSRQ TLYSSNFRNL LNIFGEEDFK YFLIDFLVFT K VEQNGYLQ VAGVCLNQYF SVQVKQKKWY KNNFNMNGKA TSNNNQNNAN LSNEKKQENQ YIYPEIQRSQ IFYCNHMGRE PG VFKSSFF NYSEIKKGFQ FKVIQEKLQG RQFINSDKIK PDHPQTIIKK TLLKEYQSKN FSCQEERDLF LEFTEKIVQN FHN INFNYL LKKFCKLPEN YQSLKSQVKQ IVQSENKANQ QSCENLFNSL YDTEISYKQI TNFLRQIIQN CVPNQLLGKK NFKV FLEKL YEFVQMKRFE NQKVLDYICF MDVFDVEWFV DLKNQKFTQK RKYISDKRKI LGDLIVFIIN KIVIPVLRYN FYITE KHKE GSQIFYYRKP IWKLVSKLTI VKLEEENLEK VEEKLIPEDS FQKYPQGKLR IIPKKGSFRP IMTFLRKDKQ KNIKLN LNQ ILMDSQLVFR NLKDMLGQKI GYSVFDNKQI SEKFAQFIEK WKNKGRPQLY YVTLDIKKCY DSIDQMKLLN FFNQSDL IQ DTYFINKYLL FQRNKRPLLQ IQQTNNLNSA MEIEEEKINK KPFKMDNINF PYYFNLKERQ IAYSLYDDDD QILQKGFK E IQSDDRPFIV INQDKPRCIT KDIIHNHLKH ISQYNVISFN KVKFRQKRGI PQGLNISGVL CSFYFGKLEE EYTQFLKNA EQVNGSINLL MRLTDDYLFI SDSQQNALNL IVQLQNCANN NGFMFNDQKI TTNFQFPQED YNLEHFKISV QNECQWIGKS IDMNTLEIK SIQKQTQQEI NQTINVAISI KNLKSQLKNK LRSLFLNQLI DYFNPNINSF EGLCRQLYHH SKATVMKFYP F MTKLFQID LKKSKQYSVQ YGKENTNENF LKDILYYTVE DVCKILCYLQ FEDEINSNIK EIFKNLYSWI MWDIIVSYLK KK KQFKGYL NKLLQKIRKS RFFYLKEGCK SLQLILSQQK YQLNKKELEA IEFIDLNNLI QDIKTLIPKI SAKSNQQNTN

UniProtKB: Telomerase reverse transcriptase

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Macromolecule #2: Telomerase holoenzyme Teb1 subunit

MacromoleculeName: Telomerase holoenzyme Teb1 subunit / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 82.040289 KDa
SequenceString: MKLTKGGSYI LKKVDRKQFY QDEEIVMQIK KILGQKTTDC KQYIKCECID GLGDEALIYF EMLANQNQHL QKNDVIMIQD YLNDKTQND KIVVLVTRFQ FCKASHVQPK TAQKESIQLL NTEKTIIQKS KITKNPAEEV LKFIEVNEKD NSSNSEDMII E QQKQEIKN ...String:
MKLTKGGSYI LKKVDRKQFY QDEEIVMQIK KILGQKTTDC KQYIKCECID GLGDEALIYF EMLANQNQHL QKNDVIMIQD YLNDKTQND KIVVLVTRFQ FCKASHVQPK TAQKESIQLL NTEKTIIQKS KITKNPAEEV LKFIEVNEKD NSSNSEDMII E QQKQEIKN NQKEKQSING FNLEDSYSNI SDITNFGGKS NFNIGSLSDQ LSKQTLLISQ LQVGKNRFSF KFEGRVVYKS ST FQNQQDS KYFFITAQDA NNQEINLSFW QKVDQSYQTL KVGQYYYFIG GEVKQFKNNL ELKFKFGDYQ IIPKETLSAN YVQ PLALQP SKQFGNDSIG DSDYSIHNLI EKEESIAQKG YNGQKNNKYR QNNNNSKHTL LISEVLKTSK QYLSVLAQVV DIQS SDKNI RLKICDNSCN QELKVVIFPD LCYEWRDKFS INKWYYFNEF VRQIYNDEVQ LKNNIHSSIK ESDDQRKVIT YNQEQ GVFK KSISINSNDS FEIKPKISYK NNSNQEQRIY SSIEEIIQQA QASEIGQKKE FYVYGNLVSI QMKNKLYYYR CTCQGK SVL KYHGDSFFCE SCQQFINPQV HLMLRAFVQD STGTIPVMIF DQQSSQLINQ IDPSIHVQEA GQYVKNCIEN GQEEIIR QL FSKLDFARFI FEIQFENKEF NNEQEIAYKV LKIEKENIKE ESKYLLKKLE HLINNNQNN

UniProtKB: Telomeric repeat-binding subunit 1

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Macromolecule #3: Telomerase holoenzyme Teb2 subunit

MacromoleculeName: Telomerase holoenzyme Teb2 subunit / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 30.993035 KDa
SequenceString: MSNRVQGGFD NNSGNNQSAQ KQQAEKIPQI TVPLNCFMIN QIVKAAKENP QAHSGNHYEW YGAFENAIIT AKFEFLQSIN DSPKIMGKL SDSTGCIEVV IQKSKMSDEL PEFVQAYEIE LQNNGNRHKY VRAMLKMRKN AQIQLLYFSI VNDANEISRH G LDLCLRYL ...String:
MSNRVQGGFD NNSGNNQSAQ KQQAEKIPQI TVPLNCFMIN QIVKAAKENP QAHSGNHYEW YGAFENAIIT AKFEFLQSIN DSPKIMGKL SDSTGCIEVV IQKSKMSDEL PEFVQAYEIE LQNNGNRHKY VRAMLKMRKN AQIQLLYFSI VNDANEISRH G LDLCLRYL QRKHGIEDFM HMTNDKAHNN HNASAQKVHY QIDRNQQPKE QVLELMRQIL KHNPNDQIPK SKIIEFFQSQ LN QVQINQI LQQLVSANEI FSVGSDNYLL NV

UniProtKB: Replication protein A 32 kDa subunit

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Macromolecule #4: Telomerase holoenzyme Teb3 subunit

MacromoleculeName: Telomerase holoenzyme Teb3 subunit / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 14.007626 KDa
SequenceString:
MDAEQEQVMY PRILFEQMAQ FRGKKVTVVG NVCNEDQNDS LVIEFGPTGL NQHVVIDNYR RVDLNNTTKF VEIRGVVLNQ NIVSCEELT EFEQKDPFDF DTYSKLIHLS QSDKLSSLFT DQ

UniProtKB: Replication protein A 14 kDa subunit

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Macromolecule #5: Telomerase associated protein p50

MacromoleculeName: Telomerase associated protein p50 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 50.049688 KDa
SequenceString: MKLLLQNQNI FQKLKNTLNG CIKKFYDTYQ DLEQMQKFEM IVEDKLLFRY SCSQSEMFSA QIQAHYLEKR VLQLTDGNVK YIVNFRDKG VLDKANFFDT PNNSLVIIRQ WSYEIYYTKN TFQINLVIDE MRCIDIITTI FYCKLELDFT QGIKGISKSS S FSNQIYEY ...String:
MKLLLQNQNI FQKLKNTLNG CIKKFYDTYQ DLEQMQKFEM IVEDKLLFRY SCSQSEMFSA QIQAHYLEKR VLQLTDGNVK YIVNFRDKG VLDKANFFDT PNNSLVIIRQ WSYEIYYTKN TFQINLVIDE MRCIDIITTI FYCKLELDFT QGIKGISKSS S FSNQIYEY SAQYYKAIQL LKKLLINDSY ISELYNSTKS KQQPRLFIFQ SFKPKMNLAE QNLSRQFEQC QQDDFGDGCL LQ IVNYTHQ SLKQIENKNN SNQIVNGQNE ISKKKRVLKS NEDLYKISLQ KQLKIFQEEE IELHSQSTIR NQTNQQLETF ESD TSKRNS EKILHSINEL NTSKQKVNQM NSSQHQIQKL ENNNLNKNIL NQINENDIKN ELEERQQQHL TQSFNSKAQL KKII TLKKN QDILLFKPQE QEGSKKY

UniProtKB: Telomerase-associated protein of 50 kDa

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Macromolecule #8: Telomerase La-related protein p65

MacromoleculeName: Telomerase La-related protein p65 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 64.207363 KDa
SequenceString: MDEYLENTNL EELEQECFME DYQHEDVVEQ ENHQVDANDI YENQQMNDES QLNQDVKISQ QKEQAVEMIE EQQQNNQDKF KQFQDCMAH ITELNFKRNY QNLTEQSSSN NVVAEELDIK ESLKLQMEYY FCDTNLTHDS YLRGIISKSP KNCVDIKVFL K FNKIQQIL ...String:
MDEYLENTNL EELEQECFME DYQHEDVVEQ ENHQVDANDI YENQQMNDES QLNQDVKISQ QKEQAVEMIE EQQQNNQDKF KQFQDCMAH ITELNFKRNY QNLTEQSSSN NVVAEELDIK ESLKLQMEYY FCDTNLTHDS YLRGIISKSP KNCVDIKVFL K FNKIQQIL KQIQDKQIVS TYGIENQSQK KNHKNYKNQN ATFSKKDLIH LIRDSLKESK ILKVKMDSLK VKRRFPFNLE QA LKNSKQR TLYIDFLPPK CSKQTLVSIF GNFRIININL PLQKNSQLCQ GFAFIEFFSE EEANQALITK NSSIPKELIL LTE KKIGQG SIRIITYKKW QEEKQSFKEL SKNQNEQKNK NMNQSRKASD EFVSIDVEIK QNCLIKIINI PQGTLKAEVV LAVR HLGYE FYCDYIDENS NQINSNKISL STQQQNTAQC SNIQIENNLI QQDQHPQLND LLKEGQAMIR FQNSDEQRLA IQKLL NHNN NKLQIEIRGQ ICDVISTIPE DEEKNYWNYI KFKKNEFRKF FFMKKQQKKQ NITQNYNK

UniProtKB: La-related protein 7 homolog

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Macromolecule #6: telomere DNA

MacromoleculeName: telomere DNA / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 9.581087 KDa
SequenceString:
(DG)(DT)(DT)(DG)(DG)(DG)(DG)(DT)(DT)(DG) (DG)(DG)(DG)(DT)(DT)(DG)(DG)(DG)(DG)(DT) (DT)(DG)(DG)(DG)(DG)(DT)(DT)(DG)(DG) (DG)

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Macromolecule #7: Telomerase RNA

MacromoleculeName: Telomerase RNA / type: rna / ID: 7 / Number of copies: 1
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 50.746984 KDa
SequenceString:
AUACCCGCUU AAUUCAUUCA GAUCUGUAAU AGAACUGUCA UUCAACCCCA AAAAUCUAGU GCUGAUAUAA CCUUCACCAA UUAGGUUCA AAUAAGUGGU AAUGCGGGAC AAAAGACUAU CGACAUUUGA UACACUAUUU AUCAAUGGAU GUCUUAUUUU

GENBANK: GENBANK: AF399707.1

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Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / Number of copies: 1 / 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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

23437

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 162358
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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