+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23021 | |||||||||
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Title | Cryo-EM structure of PRC2:EZH1-AEBP2-JARID2 | |||||||||
Map data | Cryo-EM structure of PRC2:EZH1-AEBP2-JARID2 | |||||||||
Sample |
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Keywords | Chromatin / methyltransferase / nucleosome-modifying complex / GENE REGULATION / GENE REGULATION-Transferase complex | |||||||||
Function / homology | Function and homology information protein localization to pericentric heterochromatin / [histone H3]-lysine27 N-trimethyltransferase / sex chromatin / CAF-1 complex / histone H3K27 trimethyltransferase activity / random inactivation of X chromosome / ubiquitin-modified histone reader activity / histone H3K27 methyltransferase activity / negative regulation of cardiac muscle hypertrophy / negative regulation of cardiac muscle cell proliferation ...protein localization to pericentric heterochromatin / [histone H3]-lysine27 N-trimethyltransferase / sex chromatin / CAF-1 complex / histone H3K27 trimethyltransferase activity / random inactivation of X chromosome / ubiquitin-modified histone reader activity / histone H3K27 methyltransferase activity / negative regulation of cardiac muscle hypertrophy / negative regulation of cardiac muscle cell proliferation / facultative heterochromatin formation / NURF complex / NuRD complex / regulation of cell fate specification / DNA replication-dependent chromatin assembly / negative regulation of stem cell population maintenance / Transcription of E2F targets under negative control by DREAM complex / chromatin silencing complex / ESC/E(Z) complex / RSC-type complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / regulation of stem cell differentiation / Polo-like kinase mediated events / lncRNA binding / cardiac muscle cell proliferation / histone methyltransferase complex / ATPase complex / G1/S-Specific Transcription / spinal cord development / Sin3-type complex / positive regulation of stem cell population maintenance / histone methyltransferase activity / oligodendrocyte differentiation / Transcriptional Regulation by E2F6 / subtelomeric heterochromatin formation / RNA Polymerase I Transcription Initiation / negative regulation of cell differentiation / histone deacetylase complex / G0 and Early G1 / enzyme activator activity / anatomical structure morphogenesis / heterochromatin / heterochromatin formation / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / Deposition of new CENPA-containing nucleosomes at the centromere / spleen development / methylated histone binding / Regulation of TP53 Activity through Acetylation / cellular response to leukemia inhibitory factor / SUMOylation of chromatin organization proteins / negative regulation of cell migration / transcription corepressor binding / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / thymus development / liver development / PRC2 methylates histones and DNA / ubiquitin binding / Regulation of PTEN gene transcription / central nervous system development / Defective pyroptosis / promoter-specific chromatin binding / HDACs deacetylate histones / stem cell differentiation / hippocampus development / transcription coregulator activity / negative regulation of transforming growth factor beta receptor signaling pathway / brain development / chromatin DNA binding / PKMTs methylate histone lysines / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / histone deacetylase binding / transcription corepressor activity / chromosome / chromatin organization / methylation / histone binding / regulation of gene expression / Oxidative Stress Induced Senescence / cell population proliferation / Potential therapeutics for SARS / DNA replication / chromosome, telomeric region / nuclear body / chromatin remodeling / cell cycle / ribonucleoprotein complex / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of cell population proliferation / chromatin / nucleolus / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Grau DJ / Armache KJ | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2021 Title: Structures of monomeric and dimeric PRC2:EZH1 reveal flexible modules involved in chromatin compaction. Authors: Daniel Grau / Yixiao Zhang / Chul-Hwan Lee / Marco Valencia-Sánchez / Jenny Zhang / Miao Wang / Marlene Holder / Vladimir Svetlov / Dongyan Tan / Evgeny Nudler / Danny Reinberg / Thomas ...Authors: Daniel Grau / Yixiao Zhang / Chul-Hwan Lee / Marco Valencia-Sánchez / Jenny Zhang / Miao Wang / Marlene Holder / Vladimir Svetlov / Dongyan Tan / Evgeny Nudler / Danny Reinberg / Thomas Walz / Karim-Jean Armache / Abstract: Polycomb repressive complex 2 (PRC2) is a histone methyltransferase critical for maintaining gene silencing during eukaryotic development. In mammals, PRC2 activity is regulated in part by the ...Polycomb repressive complex 2 (PRC2) is a histone methyltransferase critical for maintaining gene silencing during eukaryotic development. In mammals, PRC2 activity is regulated in part by the selective incorporation of one of two paralogs of the catalytic subunit, EZH1 or EZH2. Each of these enzymes has specialized biological functions that may be partially explained by differences in the multivalent interactions they mediate with chromatin. Here, we present two cryo-EM structures of PRC2:EZH1, one as a monomer and a second one as a dimer bound to a nucleosome. When bound to nucleosome substrate, the PRC2:EZH1 dimer undergoes a dramatic conformational change. We demonstrate that mutation of a divergent EZH1/2 loop abrogates the nucleosome-binding and methyltransferase activities of PRC2:EZH1. Finally, we show that PRC2:EZH1 dimers are more effective than monomers at promoting chromatin compaction, and the divergent EZH1/2 loop is essential for this function, thereby tying together the methyltransferase, nucleosome-binding, and chromatin-compaction activities of PRC2:EZH1. We speculate that the conformational flexibility and the ability to dimerize enable PRC2 to act on the varied chromatin substrates it encounters in the cell. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_23021.map.gz | 20.8 MB | EMDB map data format | |
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Header (meta data) | emd-23021-v30.xml emd-23021.xml | 20.1 KB 20.1 KB | Display Display | EMDB header |
Images | emd_23021.png | 96.4 KB | ||
Filedesc metadata | emd-23021.cif.gz | 8.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23021 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23021 | HTTPS FTP |
-Related structure data
Related structure data | 7ksoMC 7ksrC 7ktpC 7ktqC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_23021.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of PRC2:EZH1-AEBP2-JARID2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : PRC2:EZH1-AEBP2-JARID2
Entire | Name: PRC2:EZH1-AEBP2-JARID2 |
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Components |
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-Supramolecule #1: PRC2:EZH1-AEBP2-JARID2
Supramolecule | Name: PRC2:EZH1-AEBP2-JARID2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 330 KDa |
-Macromolecule #1: Histone-lysine N-methyltransferase EZH1
Macromolecule | Name: Histone-lysine N-methyltransferase EZH1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: [histone H3]-lysine27 N-trimethyltransferase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 85.394141 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MEIPNPPTSK CITYWKRKVK SEYMRLRQLK RLQANMGAKA LYVANFAKVQ EKTQILNEEW KKLRVQPVQS MKPVSGHPFL KKCTIESIF PGFASQHMLM RSLNTVALVP IMYSWSPLQQ NFMVEDETVL CNIPYMGDEV KEEDETFIEE LINNYDGKVH G EEEMIPGS ...String: MEIPNPPTSK CITYWKRKVK SEYMRLRQLK RLQANMGAKA LYVANFAKVQ EKTQILNEEW KKLRVQPVQS MKPVSGHPFL KKCTIESIF PGFASQHMLM RSLNTVALVP IMYSWSPLQQ NFMVEDETVL CNIPYMGDEV KEEDETFIEE LINNYDGKVH G EEEMIPGS VLISDAVFLE LVDALNQYSD EEEEGHNDTS DGKQDDSKED LPVTRKRKRH AIEGNKKSSK KQFPNDMIFS AI ASMFPEN GVPDDMKERY RELTEMSDPN ALPPQCTPNI DGPNAKSVQR EQSLHSFHTL FCRRCFKYDC FLHPFHATPN VYK RKNKEI KIEPEPCGTD CFLLLEGAKE YAMLHNPRSK CSGRRRRRHH IVSASCSNAS ASAVAETKEG DSDRDTGNDW ASSS SEANS RCQTPTKQKA SPAPPQLCVV EAPSEPVEWT GAEESLFRVF HGTYFNNFCS IARLLGTKTC KQVFQFAVKE SLILK LPTD ELMNPSQKKK RKHRLWAAHC RKIQLKKDNS STQVYNYQPC DHPDRPCDST CPCIMTQNFC EKFCQCNPDC QNRFPG CRC KTQCNTKQCP CYLAVRECDP DLCLTCGASE HWDCKVVSCK NCSIQRGLKK HLLLAPSDVA GWGTFIKESV QKNEFIS EY CGELISQDEA DRRGKVYDKY MSSFLFNLNN DFVVDATRKG NKIRFANHSV NPNCYAKVVM VNGDHRIGIF AKRAIQAG E ELFFDYRYSQ ADALKYVGIE RETDVL UniProtKB: Histone-lysine N-methyltransferase EZH1 |
-Macromolecule #2: Polycomb protein EED
Macromolecule | Name: Polycomb protein EED / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 50.267691 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MSEREVSTAP AGTDMPAAKK QKLSSDENSN PDLSGDENDD AVSIESGTNT ERPDTPTNTP NAPGRKSWGK GKWKSKKCKY SFKCVNSLK EDHNQPLFGV QFNWHSKEGD PLVFATVGSN RVTLYECHSQ GEIRLLQSYV DADADENFYT CAWTYDSNTS H PLLAVAGS ...String: MSEREVSTAP AGTDMPAAKK QKLSSDENSN PDLSGDENDD AVSIESGTNT ERPDTPTNTP NAPGRKSWGK GKWKSKKCKY SFKCVNSLK EDHNQPLFGV QFNWHSKEGD PLVFATVGSN RVTLYECHSQ GEIRLLQSYV DADADENFYT CAWTYDSNTS H PLLAVAGS RGIIRIINPI TMQCIKHYVG HGNAINELKF HPRDPNLLLS VSKDHALRLW NIQTDTLVAI FGGVEGHRDE VL SADYDLL GEKIMSCGMD HSLKLWRINS KRMMNAIKES YDYNPNKTNR PFISQKIHFP DFSTRDIHRN YVDCVRWLGD LIL SKSCEN AIVCWKPGKM EDDIDKIKPS ESNVTILGRF DYSQCDIWYM RFSMDFWQKM LALGNQVGKL YVWDLEVEDP HKAK CTTLT HHKCGAAIRQ TSFSRDSSIL IAVCDDASIW RWDRLR UniProtKB: Polycomb protein EED |
-Macromolecule #3: Polycomb protein SUZ12
Macromolecule | Name: Polycomb protein SUZ12 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 83.181922 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MAPQKHGGGG GGGSGPSAGS GGGGFGGSAA VAAATASGGK SGGGSCGGGG SYSASSSSSA AAAAGAAVLP VKKPKMEHVQ ADHELFLQA FEKPTQIYRF LRTRNLIAPI FLHRTLTYMS HRNSRTNIKR KTFKVDDMLS KVEKMKGEQE SHSLSAHLQL T FTGFFHKN ...String: MAPQKHGGGG GGGSGPSAGS GGGGFGGSAA VAAATASGGK SGGGSCGGGG SYSASSSSSA AAAAGAAVLP VKKPKMEHVQ ADHELFLQA FEKPTQIYRF LRTRNLIAPI FLHRTLTYMS HRNSRTNIKR KTFKVDDMLS KVEKMKGEQE SHSLSAHLQL T FTGFFHKN DKPSPNSENE QNSVTLEVLL VKVCHKKRKD VSCPIRQVPT GKKQVPLNPD LNQTKPGNFP SLAVSSNEFE PS NSHMVKS YSLLFRVTRP GRREFNGMIN GETNENIDVN EELPARRKRN REDGEKTFVA QMTVFDKNRR LQLLDGEYEV AMQ EMEECP ISKKRATWET ILDGKRLPPF ETFSQGPTLQ FTLRWTGETN DKSTAPIAKP LATRNSESLH QENKPGSVKP TQTI AVKES LTTDLQTRKE KDTPNENRQK LRIFYQFLYN NNTRQQTEAR DDLHCPWCTL NCRKLYSLLK HLKLCHSRFI FNYVY HPKG ARIDVSINEC YDGSYAGNPQ DIHRQPGFAF SRNGPVKRTP ITHILVCRPK RTKASMSEFL ESEDGEVEQQ RTYSSG HNR LYFHSDTCLP LRPQEMEVDS EDEKDPEWLR EKTITQIEEF SDVNEGEKEV MKLWNLHVMK HGFIADNQMN HACMLFV EN YGQKIIKKNL CRNFMLHLVS MHDFNLISIM SIDKAVTKLR EMQQKLEKGE SASPANEEIT EEQNGTANGF SEINSKEK A LETDSVSGVS KQSKKQKL UniProtKB: Polycomb protein SUZ12 |
-Macromolecule #4: Histone-binding protein RBBP4
Macromolecule | Name: Histone-binding protein RBBP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 47.709527 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MADKEAAFDD AVEERVINEE YKIWKKNTPF LYDLVMTHAL EWPSLTAQWL PDVTRPEGKD FSIHRLVLGT HTSDEQNHLV IASVQLPND DAQFDASHYD SEKGEFGGFG SVSGKIEIEI KINHEGEVNR ARYMPQNPCI IATKTPSSDV LVFDYTKHPS K PDPSGECN ...String: MADKEAAFDD AVEERVINEE YKIWKKNTPF LYDLVMTHAL EWPSLTAQWL PDVTRPEGKD FSIHRLVLGT HTSDEQNHLV IASVQLPND DAQFDASHYD SEKGEFGGFG SVSGKIEIEI KINHEGEVNR ARYMPQNPCI IATKTPSSDV LVFDYTKHPS K PDPSGECN PDLRLRGHQK EGYGLSWNPN LSGHLLSASD DHTICLWDIS AVPKEGKVVD AKTIFTGHTA VVEDVSWHLL HE SLFGSVA DDQKLMIWDT RSNNTSKPSH SVDAHTAEVN CLSFNPYSEF ILATGSADKT VALWDLRNLK LKLHSFESHK DEI FQVQWS PHNETILASS GTDRRLNVWD LSKIGEEQSP EDAEDGPPEL LFIHGGHTAK ISDFSWNPNE PWVICSVSED NIMQ VWQMA ENIYNDEDPE GSVDPEGQGS UniProtKB: Histone-binding protein RBBP4 |
-Macromolecule #5: Zinc finger protein AEBP2
Macromolecule | Name: Zinc finger protein AEBP2 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 33.012668 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSSDGEPLSR MDSEDSISST IMDVDSTISS GRSTPAMMNG QGSTTSSSKN IAYNCCWDQC QACFNSSPDL ADHIRSIHVD GQRGGVFVC LWKGCKVYNT PSTSQSWLQR HMLTHSGDKP FKCVVGGCNA SFASQGGLAR HVPTHFSQQN SSKVSSQPKA K EESPSKAG ...String: MSSDGEPLSR MDSEDSISST IMDVDSTISS GRSTPAMMNG QGSTTSSSKN IAYNCCWDQC QACFNSSPDL ADHIRSIHVD GQRGGVFVC LWKGCKVYNT PSTSQSWLQR HMLTHSGDKP FKCVVGGCNA SFASQGGLAR HVPTHFSQQN SSKVSSQPKA K EESPSKAG MNKRRKLKNK RRRSLPRPHD FFDAQTLDAI RHRAICFNLS AHIESLGKGH SVVFHSTVIA KRKEDSGKIK LL LHWMPED ILPDVWVNES ERHQLKTKVV HLSKLPKDTA LLLDPNIYRT MPQKRLKR UniProtKB: Zinc finger protein AEBP2 |
-Macromolecule #6: Protein Jumonji
Macromolecule | Name: Protein Jumonji / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 138.979719 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSKERPKRNI IQKKYDDSDG IPWSEERVVR KVLYLSLKEF KNSQKRQHAE GIAGSLKTVN GLLGNDQSKG LGPASEQSEN EKDDASQVS STSNDVSSSD FEEGPSRKRP RLQAQRKFAQ SQPNSPSTTP VKIVEPLLPP PATQISDLSK RKPKTEDFLT F LCLRGSPA ...String: MSKERPKRNI IQKKYDDSDG IPWSEERVVR KVLYLSLKEF KNSQKRQHAE GIAGSLKTVN GLLGNDQSKG LGPASEQSEN EKDDASQVS STSNDVSSSD FEEGPSRKRP RLQAQRKFAQ SQPNSPSTTP VKIVEPLLPP PATQISDLSK RKPKTEDFLT F LCLRGSPA LPNSMVYFGS SQDEEEVEEE DDETEDVKTA TNNASSSCQS TPRKGKTHKH VHNGHVFNGS SRSTREKEPV QK HKSKEAT PAKEKHSDHR ADSRREQASA NHPAAAPSTG SSAKGLAATH HHPPLHRSAQ DLRKQVSKVN GVTRMSSLGA GVT SAKKMR EVRPSPSKTV KYTATVTKGA VTYTKAKREL VKDTKPNHHK PSSAVNHTIS GKTESSNAKT RKQVLSLGGA SKST GPAVN GLKVSGRLNP KSCTKEVGGR QLREGLQLRE GLRNSKRRLE EAHQAEKPQS PPKKMKGAAG PAEGPGKKAP AERGL LNGH VKKEVPERSL ERNRPKRATA GKSTPGRQAH GKADSASCEN RSTSQPESVH KPQDSGKAEK GGGKAGWAAM DEIPVL RPS AKEFHDPLIY IESVRAQVEK FGMCRVIPPP DWRPECKLND EMRFVTQIQH IHKLGRRWGP NVQRLACIKK HLKSQGI TM DELPLIGGCE LDLACFFRLI NEMGGMQQVT DLKKWNKLAD MLRIPRTAQD RLAKLQEAYC QYLLSYDSLS PEEHRRLE K EVLMEKEILE KRKGPLEGHT ENDHHKFHPL PRFEPKNGLI HGVAPRNGFR SKLKEVGQAQ LKTGRRRLFA QEKEVVKEE EEDKGVLNDF HKCIYKGRSV SLTTFYRTAR NIMSMCFSKE PAPAEIEQEY WRLVEEKDCH VAVHCGKVDT NTHGSGFPVG KSEPFSRHG WNLTVLPNNT GSILRHLGAV PGVTIPWLNI GMVFSTSCWS RDQNHLPYID YLHTGADCIW YCIPAEEENK L EDVVHTLL QANGTPGLQM LESNVMISPE VLCKEGIKVH RTVQQSGQFV VCFPGSFVSK VCCGYSVSET VHFATTQWTS MG FETAKEM KRRHIAKPFS MEKLLYQIAQ AEAKKENGPT LSTISALLDE LRDTELRQRR QLFEAGLHSS ARYGSHDGSS TVA DGKKKP RKWLQLETSE RRCQICQHLC YLSMVVQENE NVVFCLECAL RHVEKQKSCR GLKLMYRYDE EQIISLVNQI CGKV SGKNG SIENCLSKPT PKRGPRKRAT VDVPPSRLSA SSSSKSASSS S UniProtKB: Protein Jumonji |
-Macromolecule #7: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 7 / Number of copies: 8 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.05 mg/mL | |||||||||||||||
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Buffer | pH: 7.9 Component:
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 47.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 1608434 |
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Startup model | Type of model: INSILICO MODEL |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final 3D classification | Number classes: 6 / Software - Name: RELION (ver. 3.0) |
Final angle assignment | Type: ANGULAR RECONSTITUTION |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 211110 |