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- EMDB-81902: Cryo-EM structure of canonical human nucleosome in the presence o... -

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Basic information

Entry
Database: EMDB / ID: EMD-81902
TitleCryo-EM structure of canonical human nucleosome in the presence of 1 mM magnesium chloride
Map data
Sample
  • Complex: human canonical nucleosomes under 1mM magnesium ion
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 2-A
    • Protein or peptide: Histone H2B type 1-C/E/F/G/I
    • DNA: DNA (143-MER)
    • DNA: DNA (143-MER)
Keywordshistone / nucleosome / chromatin / NUCLEAR PROTEIN
Function / homology
Function and homology information


ChAHP complex assembly / FXIIa activates plasma kallikrein-kinin system / Interaction of NuRD complexes with transcription factors / NuRD complex assembly / CHD6, CHD7, CHD8, CHD9 subfamily / CHD1 and CHD2 subfamily / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus ...ChAHP complex assembly / FXIIa activates plasma kallikrein-kinin system / Interaction of NuRD complexes with transcription factors / NuRD complex assembly / CHD6, CHD7, CHD8, CHD9 subfamily / CHD1 and CHD2 subfamily / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / telomere organization / Interleukin-7 signaling / 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 / RNA Polymerase I Promoter Opening / Inhibition of DNA recombination at telomere / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / Meiotic synapsis / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Transcriptional regulation by small RNAs / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / epigenetic regulation of gene expression / HDMs demethylate histones / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Negative Regulation of CDH1 Gene Transcription / NoRC negatively regulates rRNA expression / PKMTs methylate histone lysines / G2/M DNA damage checkpoint / Formation of the beta-catenin:TCF transactivating complex / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / nucleosomal DNA binding / RMTs methylate histone arginines / HCMV Early Events / Metalloprotease DUBs / innate immune response in mucosa / structural constituent of chromatin / nucleosome / Regulation of PD-L1(CD274) transcription / nucleosome assembly / UCH proteinases / HATs acetylate histones / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Dengue Virus-Host Interactions / Processing of DNA double-strand break ends / antimicrobial humoral immune response mediated by antimicrobial peptide / Senescence-Associated Secretory Phenotype (SASP) / heterochromatin formation / Oxidative Stress Induced Senescence / antibacterial humoral response / Estrogen-dependent gene expression / chromosome, telomeric region / defense response to Gram-positive bacterium / Ub-specific processing proteases / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / protein-containing complex / DNA binding / RNA binding / extracellular exosome / nucleoplasm / extracellular region / membrane / identical protein binding / nucleus
Similarity search - Function
: / : / Histone H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A ...: / : / Histone H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold
Similarity search - Domain/homology
Histone H4 / Histone H2B type 1-C/E/F/G/I / Histone H3.1 / Histone H2A type 2-A
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.41 Å
AuthorsOkimune KI / Azuma T / Takasuka ET
Funding support Japan, 1 items
OrganizationGrant numberCountry
Other privateG-2025-2-039 Japan
CitationJournal: To Be Published
Title: Cryo-EM structural determination of human nucleosomes reconstituted under near physiological conditions
Authors: Okimune KI / Azuma T / Banko P / Haga J / Terashi G / Morishita R / Kita S / Kihara D / Maenaka K / Takasuka ET
History
DepositionJul 2, 2026-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_81902.png

Downloads & links

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Map

FileDownload / File: emd_81902.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 360 pix.
= 306. Å		0.85 Å/pix.
x 360 pix.
= 306. Å		0.85 Å/pix.
x 360 pix.
= 306. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.16382651 - 0.3846395
Average (Standard dev.)0.0001387696 (±0.010867697)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 306.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_81902_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_81902_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_81902_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 : human canonical nucleosomes under 1mM magnesium ion

EntireName: human canonical nucleosomes under 1mM magnesium ion
Components
  • Complex: human canonical nucleosomes under 1mM magnesium ion
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 2-A
    • Protein or peptide: Histone H2B type 1-C/E/F/G/I
    • DNA: DNA (143-MER)
    • DNA: DNA (143-MER)

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Supramolecule #1: human canonical nucleosomes under 1mM magnesium ion

SupramoleculeName: human canonical nucleosomes under 1mM magnesium ion / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Histone H3.1

MacromoleculeName: Histone H3.1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.437167 KDa
Recombinant expressionOrganism: Triticum aestivum (bread wheat)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEACEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.1

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.394426 KDa
Recombinant expressionOrganism: Triticum aestivum (bread wheat)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A type 2-A

MacromoleculeName: Histone H2A type 2-A / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.125549 KDa
Recombinant expressionOrganism: Triticum aestivum (bread wheat)
SequenceString:
MSGRGKQGGK ARAKAKSRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YMAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIR NDEELNKLLG KVTIAQGGVL PNIQAVLLPK KTESHHKAKG K

UniProtKB: Histone H2A type 2-A

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Macromolecule #4: Histone H2B type 1-C/E/F/G/I

MacromoleculeName: Histone H2B type 1-C/E/F/G/I / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.937213 KDa
Recombinant expressionOrganism: Triticum aestivum (bread wheat)
SequenceString:
MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSV YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSSK

UniProtKB: Histone H2B type 1-C/E/F/G/I

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Macromolecule #5: DNA (143-MER)

MacromoleculeName: DNA (143-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 171.477812 KDa
SequenceString: (DC)(DA)(DA)(DG)(DG)(DA)(DT)(DC)(DC)(DC) (DT)(DG)(DG)(DG)(DA)(DA)(DT)(DT)(DC)(DT) (DC)(DC)(DA)(DG)(DT)(DA)(DC)(DC)(DT) (DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC)(DC)(DC) (DG) (DG)(DT)(DG)(DC)(DC)(DG) ...String:
(DC)(DA)(DA)(DG)(DG)(DA)(DT)(DC)(DC)(DC) (DT)(DG)(DG)(DG)(DA)(DA)(DT)(DT)(DC)(DT) (DC)(DC)(DA)(DG)(DT)(DA)(DC)(DC)(DT) (DG)(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)(DC)(DG) (DT)(DG)(DT)(DC)(DA)(DG)(DA) (DT)(DA) (DT)(DA)(DT)(DA)(DC)(DA)(DT)(DC)(DC)(DT) (DG)(DT)(DG)(DC)(DT)(DC)(DA)(DC) (DA) (DC)(DT)(DG)(DT)(DC)(DG)(DT)(DC)(DC)(DG) (DA)(DA)(DT)(DT)(DC)(DT)(DC)(DC)(DA) (DG)(DT)(DA)(DC)(DC)(DT)(DG)(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)(DC)(DG)(DT)(DG)(DT)(DC) (DA)(DG)(DA)(DT)(DA)(DT) (DA)(DT)(DA) (DC)(DA)(DT)(DC)(DC)(DT)(DG)(DT)(DG)(DC) (DT)(DT)(DC)(DT)(DG)(DA)(DT) (DG)(DG) (DA)(DA)(DC)(DT)(DG)(DG)(DA)(DA)(DT)(DT) (DC)(DT)(DC)(DC)(DA)(DG)(DT)(DA) (DC) (DC)(DT)(DG)(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) (DC)(DG)(DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT) (DA)(DT)(DA)(DT)(DA) (DC)(DA)(DT)(DC) (DC)(DT)(DG)(DT)(DG)(DC)(DC)(DT)(DA)(DA) (DG)(DA)(DG)(DC)(DA)(DG) (DT)(DT)(DA) (DT)(DC)(DT)(DA)(DG)(DA)(DA)(DT)(DA)(DG) (DC)(DC)(DA)(DC)(DC)

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Macromolecule #6: DNA (143-MER)

MacromoleculeName: DNA (143-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 173.243844 KDa
SequenceString: (DG)(DG)(DT)(DG)(DG)(DC)(DT)(DA)(DT)(DT) (DC)(DT)(DA)(DG)(DA)(DT)(DA)(DA)(DC)(DT) (DG)(DC)(DT)(DC)(DT)(DT)(DA)(DG)(DG) (DC)(DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT) (DA) (DT)(DA)(DT)(DA)(DT)(DC) ...String:
(DG)(DG)(DT)(DG)(DG)(DC)(DT)(DA)(DT)(DT) (DC)(DT)(DA)(DG)(DA)(DT)(DA)(DA)(DC)(DT) (DG)(DC)(DT)(DC)(DT)(DT)(DA)(DG)(DG) (DC)(DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT) (DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG) (DA)(DC)(DA)(DC)(DG)(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)(DC)(DA)(DG)(DG)(DT)(DA) (DC) (DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DT)(DC) (DC)(DA)(DG)(DT)(DT)(DC)(DC)(DA)(DT) (DC)(DA)(DG)(DA)(DA)(DG)(DC)(DA)(DC)(DA) (DG)(DG)(DA)(DT)(DG)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DC)(DT)(DG)(DA)(DC)(DA)(DC) (DG)(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)(DC)(DA) (DG)(DG)(DT)(DA)(DC)(DT)(DG) (DG)(DA) (DG)(DA)(DA)(DT)(DT)(DC)(DG)(DG)(DA)(DC) (DG)(DA)(DC)(DA)(DG)(DT)(DG)(DT) (DG) (DA)(DG)(DC)(DA)(DC)(DA)(DG)(DG)(DA)(DT) (DG)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DC) (DT)(DG)(DA)(DC)(DA)(DC)(DG)(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)(DC)(DA)(DG)(DG)(DT)(DA) (DC)(DT)(DG)(DG)(DA)(DG) (DA)(DA)(DT) (DT)(DC)(DC)(DC)(DA)(DG)(DG)(DG)(DA)(DT) (DC)(DC)(DT)(DT)(DG)

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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

Concentration0.05 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
1.0 mMHSCH2CH(OH)CH(OH)CH2SHDTT
1.0 mMMgCl2Magnesium chloride

Details: 20mM HEPES-KOH pH7.5, 1mM DTT, 1mM MgCl2
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 49.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.8 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8jbx

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.7.1) / Number images used: 88640
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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