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- EMDB-31040: Human SETD2 bound to a nucleosome containing oncohistone mutations -

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Basic information

Entry
Database: EMDB / ID: EMD-31040
TitleHuman SETD2 bound to a nucleosome containing oncohistone mutations
Map datamain map
Sample
  • Complex: Human SETD2-NCP(H3.3K36M)-SAM complex structure
    • Complex: Histone-lysine N-methyltransferase SETD2
      • Protein or peptide: Histone-lysine N-methyltransferase SETD2
    • Complex: Histone
      • Protein or peptide: Histone H3.3H3F3A
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1-D
      • Protein or peptide: Histone H2B type 2-E
    • Complex: DNA
      • DNA: 601-DNA
      • DNA: 601-DNA
  • Ligand: ZINC ION
  • Ligand: S-ADENOSYLMETHIONINES-Adenosyl methionine
KeywordsSETD2 / methyltransferase / nucleosome / H3.3K36M / GENE REGULATION
Function / homology
Function and homology information


mesoderm morphogenesis / coronary vasculature morphogenesis / morphogenesis of a branching structure / peptidyl-lysine trimethylation / cell migration involved in vasculogenesis / microtubule cytoskeleton organization involved in mitosis / [histone H3]-lysine36 N-trimethyltransferase / histone H3K36 trimethyltransferase activity / embryonic placenta morphogenesis / regulation of mRNA export from nucleus ...mesoderm morphogenesis / coronary vasculature morphogenesis / morphogenesis of a branching structure / peptidyl-lysine trimethylation / cell migration involved in vasculogenesis / microtubule cytoskeleton organization involved in mitosis / [histone H3]-lysine36 N-trimethyltransferase / histone H3K36 trimethyltransferase activity / embryonic placenta morphogenesis / regulation of mRNA export from nucleus / pericardium development / nucleosome organization / stem cell development / histone H3K36 methyltransferase activity / protein-lysine N-methyltransferase activity / response to alkaloid / response to type I interferon / positive regulation of ossification / embryonic cranial skeleton morphogenesis / regulation of protein localization to chromatin / response to metal ion / histone H3 methyltransferase activity / regulation of double-strand break repair via homologous recombination / endodermal cell differentiation / positive regulation of interferon-alpha production / alpha-tubulin binding / mismatch repair / Replacement of protamines by nucleosomes in the male pronucleus / positive regulation of autophagy / Packaging Of Telomere Ends / forebrain development / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / Transferases; Transferring one-carbon groups; Methyltransferases / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / innate immune response in mucosa / PRC2 methylates histones and DNA / regulation of cytokinesis / Defective pyroptosis / neural tube closure / HDACs deacetylate histones / transcription elongation by RNA polymerase II / stem cell differentiation / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / response to organic cyclic compound / Metalloprotease DUBs / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / UCH proteinases / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Processing of DNA double-strand break ends / HATs acetylate histones / antibacterial humoral response / Senescence-Associated Secretory Phenotype (SASP) / regulation of gene expression / defense response to virus / angiogenesis / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / Ub-specific processing proteases / defense response to Gram-positive bacterium / Amyloid fiber formation / protein heterodimerization activity / regulation of DNA-templated transcription / DNA binding / extracellular space / extracellular exosome / nucleoplasm
Similarity search - Function
Histone-lysine N-methyltransferase SETD2, animal / Set2 Rpb1 interacting domain / Set2 Rpb1 interacting domain superfamily / SRI (Set2 Rpb1 interacting) domain / SETD2/Set2, SET domain / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / TFIIS/LEDGF domain superfamily ...Histone-lysine N-methyltransferase SETD2, animal / Set2 Rpb1 interacting domain / Set2 Rpb1 interacting domain superfamily / SRI (Set2 Rpb1 interacting) domain / SETD2/Set2, SET domain / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / TFIIS/LEDGF domain superfamily / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
Histone H2A type 1-D / Histone H2B type 2-E / Histone-lysine N-methyltransferase SETD2
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsJing H / Liu Y
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32022036 China
National Natural Science Foundation of China (NSFC)31570766 China
National Natural Science Foundation of China (NSFC)U1632130 China
CitationJournal: Cell Discov / Year: 2021
Title: Cryo-EM structure of SETD2/Set2 methyltransferase bound to a nucleosome containing oncohistone mutations.
Authors: Yingying Liu / Yanjun Zhang / Han Xue / Mi Cao / Guohui Bai / Zongkai Mu / Yanli Yao / Shuyang Sun / Dong Fang / Jing Huang /
Abstract: Substitution of lysine 36 with methionine in histone H3.3 (H3.3K36M) is an oncogenic mutation that inhibits SETD2-mediated histone H3K36 tri-methylation in tumors. To investigate how the oncohistone ...Substitution of lysine 36 with methionine in histone H3.3 (H3.3K36M) is an oncogenic mutation that inhibits SETD2-mediated histone H3K36 tri-methylation in tumors. To investigate how the oncohistone mutation affects the function of SETD2 at the nucleosome level, we determined the cryo-EM structure of human SETD2 associated with an H3.3K36M nucleosome and cofactor S-adenosylmethionine (SAM), and revealed that SETD2 is attached to the N-terminal region of histone H3 and the nucleosome DNA at superhelix location 1, accompanied with the partial unwrapping of nucleosome DNA to expose the SETD2-binding site. These structural features were also observed in the previous cryo-EM structure of the fungal Set2-nucleosome complex. By contrast with the stable association of SETD2 with the H3.3K36M nucleosome, the EM densities of SETD2 could not be observed on the wild-type nucleosome surface, suggesting that the association of SETD2 with wild-type nucleosome might be transient. The linker histone H1, which stabilizes the wrapping of nucleosome DNA at the entry/exit sites, exhibits an inhibitory effect on the activities of SETD2 and displays inversely correlated genome distributions with that of the H3K36me3 marks. Cryo-EM analysis of yeast H3K36 methyltransferase Set2 complexed with nucleosomes further revealed evolutionarily conserved structural features for nucleosome recognition in eukaryotes, and provides insights into the mechanism of activity regulation. These findings have advanced our understanding of the structural basis for the tumorigenesis mechanism of the H3.3K36M mutation and highlight the effect of nucleosome conformation on the regulation of histone modification.
History
DepositionMar 6, 2021-
Header (metadata) releaseJul 14, 2021-
Map releaseJul 14, 2021-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.02
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  • Surface view with fitted model
  • Atomic models: PDB-7ea8
  • Surface level: 0.02
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31040.png

Downloads & links

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Map

FileDownload / File: emd_31040.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.013 / Movie #1: 0.02
Minimum - Maximum-0.11519042 - 0.20442076
Average (Standard dev.)-0.000000044490562 (±0.005688012)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 264.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z264.000264.000264.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.1150.204-0.000

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Supplemental data

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Sample components

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Entire : Human SETD2-NCP(H3.3K36M)-SAM complex structure

EntireName: Human SETD2-NCP(H3.3K36M)-SAM complex structure
Components
  • Complex: Human SETD2-NCP(H3.3K36M)-SAM complex structure
    • Complex: Histone-lysine N-methyltransferase SETD2
      • Protein or peptide: Histone-lysine N-methyltransferase SETD2
    • Complex: Histone
      • Protein or peptide: Histone H3.3H3F3A
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1-D
      • Protein or peptide: Histone H2B type 2-E
    • Complex: DNA
      • DNA: 601-DNA
      • DNA: 601-DNA
  • Ligand: ZINC ION
  • Ligand: S-ADENOSYLMETHIONINES-Adenosyl methionine

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Supramolecule #1: Human SETD2-NCP(H3.3K36M)-SAM complex structure

SupramoleculeName: Human SETD2-NCP(H3.3K36M)-SAM complex structure / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Histone-lysine N-methyltransferase SETD2

SupramoleculeName: Histone-lysine N-methyltransferase SETD2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Histone

SupramoleculeName: Histone / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#5

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Supramolecule #4: DNA

SupramoleculeName: DNA / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #6-#7

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Macromolecule #1: Histone-lysine N-methyltransferase SETD2

MacromoleculeName: Histone-lysine N-methyltransferase SETD2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: [histone H3]-lysine36 N-trimethyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.580467 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: DDFRDPQRWK ECAKQGKMPC YFDLIEENVY LTERKKNKSH RDIKRMQCEC TPLSKDERAQ GEIACGEDCL NRLLMIECSS RCPNGDYCS NRRFQRKQHA DVEVILTEKK GWGLRAAKDL PSNTFVLEYC GEVLDHKEFK ARVKEYARNK NIHYYFMALK N DEIIDATQ ...String:
DDFRDPQRWK ECAKQGKMPC YFDLIEENVY LTERKKNKSH RDIKRMQCEC TPLSKDERAQ GEIACGEDCL NRLLMIECSS RCPNGDYCS NRRFQRKQHA DVEVILTEKK GWGLRAAKDL PSNTFVLEYC GEVLDHKEFK ARVKEYARNK NIHYYFMALK N DEIIDATQ KGNCSRFMNH SCEPNCETQK WTVNGQLRVG FFTTKLVPSG SELTFDYQFQ RYGKEAQKCF CGSANCRGYL GG ENRVS

UniProtKB: Histone-lysine N-methyltransferase SETD2

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Macromolecule #2: Histone H3.3

MacromoleculeName: Histone H3.3 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.657632 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GGVMKPHRYR PGTVALREIR RYQKSTELLI RKLPFQRLVR EIAQDFKTDL RFQSAAIGAL QEASEAYLVG LFEDTNLCAI HAKRVTIMP KDIQLARRIR GE

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Macromolecule #3: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.853342 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
DNIQGITKPA IRRLARRGGV KRISGLIYEE TRGVLKVFLE NVIRDAVTYT EHAKRKTVTA MDVVYALKRQ GRTLYGFG

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Macromolecule #4: Histone H2A type 1-D

MacromoleculeName: Histone H2A type 1-D / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.351226 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
AKTRSSRAGL QFPVGRVHRL LRKGNYSERV GAGAPVYLAA VLEYLTAEIL ELAGNAARDN KKTRIIPRHL QLAIRNDEEL NKLLGKVTI AQGGVLPNIQ AVLLP

UniProtKB: Histone H2A type 1-D

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Macromolecule #5: Histone H2B type 2-E

MacromoleculeName: Histone H2B type 2-E / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.820045 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
PEPAKSAPAP KKGSKKAVTK AQKKDGKKRK RSRKESYSIY VYKVLKQVHP DTGISSKAMG IMNSFVNDIF ERIAGEASRL AHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSSK

UniProtKB: Histone H2B type 2-E

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Macromolecule #6: 601-DNA

MacromoleculeName: 601-DNA / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 37.436836 KDa
SequenceString: (DC)(DG)(DA)(DG)(DA)(DA)(DT)(DC)(DC)(DC) (DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG)(DG) (DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA)(DT) (DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG)(DA) (DC) (DA)(DG)(DC)(DT)(DC)(DT) ...String:
(DC)(DG)(DA)(DG)(DA)(DA)(DT)(DC)(DC)(DC) (DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG)(DG) (DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA)(DT) (DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG)(DA) (DC) (DA)(DG)(DC)(DT)(DC)(DT)(DA)(DG) (DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT)(DA)(DA) (DA)(DC) (DG)(DC)(DA)(DC)(DG)(DT)(DA) (DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT)(DC)(DC) (DC)(DC)(DC) (DG)(DC)(DG)(DT)(DT)(DT) (DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC)(DA)(DA) (DG)(DG)(DG)(DG) (DA)(DT)(DT)(DA)(DC) (DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT)(DC)(DT) (DC)(DC)(DA)(DG)(DG) (DC)(DA)

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Macromolecule #7: 601-DNA

MacromoleculeName: 601-DNA / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 37.86809 KDa
SequenceString: (DT)(DG)(DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA) (DC)(DT)(DA)(DG)(DG)(DG)(DA)(DG)(DT)(DA) (DA)(DT)(DC)(DC)(DC)(DC)(DT)(DT)(DG) (DG)(DC)(DG)(DG)(DT)(DT)(DA)(DA)(DA)(DA) (DC) (DG)(DC)(DG)(DG)(DG)(DG) ...String:
(DT)(DG)(DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA) (DC)(DT)(DA)(DG)(DG)(DG)(DA)(DG)(DT)(DA) (DA)(DT)(DC)(DC)(DC)(DC)(DT)(DT)(DG) (DG)(DC)(DG)(DG)(DT)(DT)(DA)(DA)(DA)(DA) (DC) (DG)(DC)(DG)(DG)(DG)(DG)(DG)(DA) (DC)(DA)(DG)(DC)(DG)(DC)(DG)(DT)(DA)(DC) (DG)(DT) (DG)(DC)(DG)(DT)(DT)(DT)(DA) (DA)(DG)(DC)(DG)(DG)(DT)(DG)(DC)(DT)(DA) (DG)(DA)(DG) (DC)(DT)(DG)(DT)(DC)(DT) (DA)(DC)(DG)(DA)(DC)(DC)(DA)(DA)(DT)(DT) (DG)(DA)(DG)(DC) (DG)(DG)(DC)(DC)(DT) (DC)(DG)(DG)(DC)(DA)(DC)(DC)(DG)(DG)(DG) (DA)(DT)(DT)(DC)(DT) (DC)(DG)

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Macromolecule #8: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 8 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #9: S-ADENOSYLMETHIONINE

MacromoleculeName: S-ADENOSYLMETHIONINE / type: ligand / ID: 9 / Number of copies: 1 / Formula: SAM
Molecular weightTheoretical: 398.437 Da
Chemical component information

ChemComp-SAM:
S-ADENOSYLMETHIONINE / S-Adenosyl methionine

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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

Concentration0.3 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.5625 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 154984

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