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- EMDB-22695: Active state Dot1 bound to the unacetylated H4 nucleosome, Ubiqui... -

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Basic information

Entry
Database: EMDB / ID: EMD-22695
TitleActive state Dot1 bound to the unacetylated H4 nucleosome, Ubiquitin focused map
Map dataActive state Dot1L bound to the H4K16 unacetylated nucleosome
Sample
  • Complex: Active state Dot1 bound to the unacetylated H4 nucleosome
    • Complex: HistonesHistone
      • Protein or peptide: Histone H3.2
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1
      • Protein or peptide: Histone H2B 1.1
    • Complex: Histone-lysine N-methyltransferase, H3 lysine-79 specificHistone methyltransferase
      • Protein or peptide: Histone-lysine N-methyltransferase, H3 lysine-79 specificHistone methyltransferase
    • Complex: Polyubiquitin-B
      • Protein or peptide: Polyubiquitin-B
    • Complex: DNA (146-MER)
      • DNA: DNA (146-MER)
      • DNA: DNA (146-MER)
Function / homology
Function and homology information


negative regulation of heterochromatin formation / meiotic recombination checkpoint signaling / : / histone H3K79 trimethyltransferase activity / [histone H3]-lysine79 N-trimethyltransferase / histone H3K79 methyltransferase activity / global genome nucleotide-excision repair / recombinational repair / postreplication repair / mitotic intra-S DNA damage checkpoint signaling ...negative regulation of heterochromatin formation / meiotic recombination checkpoint signaling / : / histone H3K79 trimethyltransferase activity / [histone H3]-lysine79 N-trimethyltransferase / histone H3K79 methyltransferase activity / global genome nucleotide-excision repair / recombinational repair / postreplication repair / mitotic intra-S DNA damage checkpoint signaling / subtelomeric heterochromatin formation / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of FZD by ubiquitination / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / mitotic G1 DNA damage checkpoint signaling / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / DNA damage checkpoint signaling / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Recognition of DNA damage by PCNA-containing replication complex / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / nucleotide-excision repair / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Termination of translesion DNA synthesis / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Regulation of TNFR1 signaling / Defective CFTR causes cystic fibrosis
Similarity search - Function
Histone H3-K79 methyltransferase, fungi / Histone-lysine N-methyltransferase DOT1 domain / Histone H3-K79 methyltransferase / Histone methylation protein DOT1 / Histone-lysine N-methyltransferase DOT1 (EC 2.1.1.43) domain profile. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. ...Histone H3-K79 methyltransferase, fungi / Histone-lysine N-methyltransferase DOT1 domain / Histone H3-K79 methyltransferase / Histone methylation protein DOT1 / Histone-lysine N-methyltransferase DOT1 (EC 2.1.1.43) domain profile. / 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 H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H3 signature 1. / Ubiquitin conserved site / Ubiquitin domain / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Ubiquitin domain signature. / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Histone H2B 1.1 / Histone H2A type 1 / Polyubiquitin-C / Histone H4 / Histone H3.2 / Histone-lysine N-methyltransferase, H3 lysine-79 specific
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Xenopus laevis (African clawed frog) / Homo sap (brewer's yeast) / Synthetic (others) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsValencia-Sanchez MI / De Ioannes PE / Miao W / Truong DM / Lee R / Armache J-P / Boeke JD / Armache K-J
Funding support United States, 2 items
OrganizationGrant numberCountry
David and Lucile Packard Foundation United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM115882-03 United States
CitationJournal: Science / Year: 2021
Title: Regulation of the Dot1 histone H3K79 methyltransferase by histone H4K16 acetylation.
Authors: Marco Igor Valencia-Sánchez / Pablo De Ioannes / Miao Wang / David M Truong / Rachel Lee / Jean-Paul Armache / Jef D Boeke / Karim-Jean Armache /
Abstract: Dot1 (disruptor of telomeric silencing-1), the histone H3 lysine 79 (H3K79) methyltransferase, is conserved throughout evolution, and its deregulation is found in human leukemias. Here, we provide ...Dot1 (disruptor of telomeric silencing-1), the histone H3 lysine 79 (H3K79) methyltransferase, is conserved throughout evolution, and its deregulation is found in human leukemias. Here, we provide evidence that acetylation of histone H4 allosterically stimulates yeast Dot1 in a manner distinct from but coordinating with histone H2B ubiquitination (H2BUb). We further demonstrate that this stimulatory effect is specific to acetylation of lysine 16 (H4K16ac), a modification central to chromatin structure. We provide a mechanism of this histone cross-talk and show that H4K16ac and H2BUb play crucial roles in H3K79 di- and trimethylation in vitro and in vivo. These data reveal mechanisms that control H3K79 methylation and demonstrate how H4K16ac, H3K79me, and H2BUb function together to regulate gene transcription and gene silencing to ensure optimal maintenance and propagation of an epigenetic state.
History
DepositionSep 21, 2020-
Header (metadata) releaseFeb 10, 2021-
Map releaseFeb 10, 2021-
UpdateFeb 10, 2021-
Current statusFeb 10, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22695.png

Downloads & links

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Map

FileDownload / File: emd_22695.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationActive state Dot1L bound to the H4K16 unacetylated nucleosome
Voxel sizeX=Y=Z: 1.035 Å
Density
Contour LevelBy AUTHOR: 5.0 / Movie #1: 5
Minimum - Maximum-15.261581 - 22.436789
Average (Standard dev.)-0.029017715 (±0.9852864)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 310.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0351.0351.035
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z310.500310.500310.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-15.26222.437-0.029

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Supplemental data

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Additional map: Unsharpened Active state Dot1L bound to the H4K16...

Fileemd_22695_additional_1.map
AnnotationUnsharpened Active state Dot1L bound to the H4K16 unacetylated nucleosome
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map Active state Dot1L bound to the...

Fileemd_22695_half_map_1.map
AnnotationHalf map Active state Dot1L bound to the H4K16 unacetylated nucleosome
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map Active state Dot1L bound to the...

Fileemd_22695_half_map_2.map
AnnotationHalf map Active state Dot1L bound to the H4K16 unacetylated nucleosome
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Active state Dot1 bound to the unacetylated H4 nucleosome

EntireName: Active state Dot1 bound to the unacetylated H4 nucleosome
Components
  • Complex: Active state Dot1 bound to the unacetylated H4 nucleosome
    • Complex: HistonesHistone
      • Protein or peptide: Histone H3.2
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1
      • Protein or peptide: Histone H2B 1.1
    • Complex: Histone-lysine N-methyltransferase, H3 lysine-79 specificHistone methyltransferase
      • Protein or peptide: Histone-lysine N-methyltransferase, H3 lysine-79 specificHistone methyltransferase
    • Complex: Polyubiquitin-B
      • Protein or peptide: Polyubiquitin-B
    • Complex: DNA (146-MER)
      • DNA: DNA (146-MER)
      • DNA: DNA (146-MER)

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Supramolecule #1: Active state Dot1 bound to the unacetylated H4 nucleosome

SupramoleculeName: Active state Dot1 bound to the unacetylated H4 nucleosome
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: H2BK120 Ubiquitinated H3K79M
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #2: Histones

SupramoleculeName: Histones / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #3: Histone-lysine N-methyltransferase, H3 lysine-79 specific

SupramoleculeName: Histone-lysine N-methyltransferase, H3 lysine-79 specific
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #4: Polyubiquitin-B

SupramoleculeName: Polyubiquitin-B / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #6
Source (natural)Organism: Homo sap (brewer's yeast)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #5: DNA (146-MER)

SupramoleculeName: DNA (146-MER) / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #7-#8
Source (natural)Organism: Synthetic (others)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
SequenceString:
KPHRYRPGTV ALRE IRRYQ KSTELLIRKL PFQRLVREIA QDFMTDLRFQ SSAVMALQEA SEAYL VALF EDTNLCAIHA KRVTIMPKDI QLARRIRGER

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
SequenceString:
GGAKRHRKVL RDNIQGITKP AIRRLARRGG VKRISGLI Y EETRGVLKVF LENVIRDAVT YTEHAKRKTV TAMDVVYALK RQGRTLYGFG

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Macromolecule #3: Histone H2A type 1

MacromoleculeName: Histone H2A type 1 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
SequenceString:
AKAKTRSSRA GLQFPVGRVH RLLRKGNYAE RVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAVRND EELNKLLGRV TIAQGGVLP NIQSVLLPK

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Macromolecule #4: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
SequenceString:
TRKESYAIYV YKVLKQVHPD TG ISSKAMS IMNSFVNDVF ERIAGEASRL AHYNKRSTIT SREIQTAVRL LLP GELAKH AVSEGTKAVT KYTSA

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Macromolecule #5: Histone-lysine N-methyltransferase, H3 lysine-79 specific

MacromoleculeName: Histone-lysine N-methyltransferase, H3 lysine-79 specific
type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
SequenceString: SSTFVDWNGP CLRLQYPLFD IEYLR SHEI YSGTPIQSIS LRTTAKLQSI LFSNYMEEYK VDFKRSTAIY NPMSEI GKL IEYSCLVFLP SPYAEQLKET ILPDLNASFD NSDTKGFVNA INLYNKM IR EIPRQRIIDH LETIDKIPRS FIHDFLHIVY TRSIHPQANK ...String:
SSTFVDWNGP CLRLQYPLFD IEYLR SHEI YSGTPIQSIS LRTTAKLQSI LFSNYMEEYK VDFKRSTAIY NPMSEI GKL IEYSCLVFLP SPYAEQLKET ILPDLNASFD NSDTKGFVNA INLYNKM IR EIPRQRIIDH LETIDKIPRS FIHDFLHIVY TRSIHPQANK LKHYKAFS N YVYGELLPNF LSDVYQQCQL KKGDTFMDLG SGVGNCVVQA ALECGCALS FGCEIMDDAS DLTILQYEEL KKRCKLYGMR LNNVEFSLKK SFVDNNRVAE LIPQCDVIL VNNFLFDEDL NKKVEKILQT AKVGCKIISL KSLRSLTYQI N FYNVENIF NRLKVQRYDL KEDSVSWTHS GGEYYISTVM EDVDESLFSP AA RGRRPVK YM

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Macromolecule #6: Polyubiquitin-B

MacromoleculeName: Polyubiquitin-B / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGC

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Macromolecule #7: DNA (146-MER)

MacromoleculeName: DNA (146-MER) / type: dna / ID: 7 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
SequenceString:
TCGAGAATCC CGGTGCCGAG GCCGCTCAAT TGGTCGTAGA CAGCTCTAG CACCGCTTAA ACGCACGTAC GGATTCTCCC CCGCGTTTTA ACCGCCAAGG GGATTACTC CCTAGTCTCC AGGCACGTGT CAGATATATA CATCCGAT

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Macromolecule #8: DNA (146-MER)

MacromoleculeName: DNA (146-MER) / type: dna / ID: 8 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
SequenceString:
ATCGGATGTA TATATCTGAC ACGTGCCTGG AGACTAGGGA GTAATCCCCT TGGCGGTTA AAACGCGGGG GAGAATCCGT ACGTGCGTTT AAGCGGTGCT A GAGCTGTC TACGACCAAT TGAGCGGCCT CGGCACCGGG ATTCTCGA

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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

Concentration0.45 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
20.0 mMTrisTris
50.0 mMKClKCl
1.0 mMMgCl2MgCl2
1.0 mMDTTDTT
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
Details: 3.0 uL of the samples at 0.45 mg/mL concentration were applied Quantifoil gold grids (400 mesh, 1.2 um hole size). The grids were previously glow-discharged 30s. After sample application, ...Details: 3.0 uL of the samples at 0.45 mg/mL concentration were applied Quantifoil gold grids (400 mesh, 1.2 um hole size). The grids were previously glow-discharged 30s. After sample application, the grids were blotted for 3s using Vitrobot Mark IV (FEI Company)at 4o C and 100 percent of humidity. The grids were subsequently plunge-frozen in liquid ethane cooled to liquid nitrogen temperatures.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 297 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 130000
Specialist opticsEnergy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Sampling interval: 5.0 µm / Number grids imaged: 1 / Number real images: 4031 / Average exposure time: 8.0 sec. / Average electron dose: 52.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1673215
CTF correctionSoftware - Name: Gctf
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1u2z


Details: 1U2Z 3TU4 1UBQ
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 2.15) / Details: Ab initio in CryoSparc
Final 3D classificationNumber classes: 3 / Software: (Name: cryoSPARC (ver. 2.15), RELION (ver. 3.0))
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cisTEM (ver. 1.0)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM (ver. 1.0) / Number images used: 142567
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

1u2z

chain_id: A

3tu4


1ubq

chain_id: A
RefinementSpace: REAL / Protocol: OTHER

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