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- EMDB-10864: OCT4-SOX2-bound nucleosome - SHL+6 -

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Basic information

Entry
Database: EMDB / ID: EMD-10864
TitleOCT4-SOX2-bound nucleosome - SHL+6
Map dataOCT4-SOX2 bound to SHL 6
Sample
  • Complex: Ternary complex of OCT4-SOX2 and SHL+6 nucleosome
    • Complex: HistonesHistone
      • Protein or peptide: Histone H3.1Histone H3
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1-B/E
      • Protein or peptide: Histone H2B type 1-J
      • Protein or peptide: Histone H3.1Histone H3
      • Protein or peptide: Histone H4
    • Complex: DNA
      • DNA: DNA (142-MER)
    • Complex: Green fluorescent protein,POU domain, class 5, transcription factor 1
      • Protein or peptide: Green fluorescent protein,POU domain, class 5, transcription factor 1
    • Complex: SOX2
      • Protein or peptide: Transcription factor SOX-2
  • Ligand: PENTANEDIALGlutaraldehyde
Function / homology
Function and homology information


regulation of heart induction by regulation of canonical Wnt signaling pathway / cell fate commitment involved in formation of primary germ layer / cardiac cell fate determination / POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation / regulation of asymmetric cell division / glial cell fate commitment / BMP signaling pathway involved in heart induction / endodermal cell fate specification / adenohypophysis development / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation ...regulation of heart induction by regulation of canonical Wnt signaling pathway / cell fate commitment involved in formation of primary germ layer / cardiac cell fate determination / POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation / regulation of asymmetric cell division / glial cell fate commitment / BMP signaling pathway involved in heart induction / endodermal cell fate specification / adenohypophysis development / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / Transcriptional regulation of pluripotent stem cells / regulation of cysteine-type endopeptidase activity involved in apoptotic process / pituitary gland development / Transcriptional Regulation by MECP2 / regulation of DNA methylation-dependent heterochromatin assembly / positive regulation of cell-cell adhesion / eye development / neuronal stem cell population maintenance / negative regulation of cell cycle G1/S phase transition / tissue regeneration / response to growth factor / somatic stem cell population maintenance / miRNA binding / negative regulation of miRNA-mediated gene silencing / blastocyst development / negative regulation of megakaryocyte differentiation / CENP-A containing nucleosome / inner ear development / Packaging Of Telomere Ends / Chromatin modifying enzymes / regulation of gene expression, epigenetic / 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 / DNA replication-independent chromatin assembly / negative regulation of tumor necrosis factor-mediated signaling pathway / anatomical structure morphogenesis / negative regulation of neuron differentiation / Cleavage of the damaged pyrimidine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / positive regulation of SMAD protein signal transduction / Inhibition of DNA recombination at telomere / Meiotic synapsis / cell fate commitment / telomere organization / SUMOylation of chromatin organization proteins / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / forebrain development / negative regulation of miRNA transcription / DNA replication-dependent chromatin assembly / Assembly of the ORC complex at the origin of replication / DNA methylation / HCMV Late Events / innate immune response in mucosa / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Condensation of Prophase Chromosomes / heterochromatin assembly / PRC2 methylates histones and DNA / Defective pyroptosis / RNA Polymerase I Promoter Escape / bioluminescence / HDACs deacetylate histones / nuclear chromosome / generation of precursor metabolites and energy / Transcriptional regulation by small RNAs / positive regulation of cell differentiation / NoRC negatively regulates rRNA expression / Nonhomologous End-Joining (NHEJ) / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Deactivation of the beta-catenin transactivating complex / B-WICH complex positively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / lipopolysaccharide binding / Metalloprotease DUBs / DNA Damage/Telomere Stress Induced Senescence / G2/M DNA damage checkpoint / RMTs methylate histone arginines / nucleosome assembly / HDMs demethylate histones / HCMV Early Events / Pre-NOTCH Transcription and Translation / Meiotic recombination / PKMTs methylate histone lysines / osteoblast differentiation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / response to wounding / Transcriptional regulation of granulopoiesis / nucleosome / UCH proteinases / DNA-templated transcription, initiation / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of canonical Wnt signaling pathway / positive regulation of canonical Wnt signaling pathway / negative regulation of epithelial cell proliferation / E3 ubiquitin ligases ubiquitinate target proteins / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks
Similarity search - Function
POU domain-containing protein, class 5 / Transcription factor SOX / Transcription factor SOX-2 / SOX transcription factor / POU-specific (POUs) domain signature 2. / POU domain / POU-specific (POUs) domain signature 1. / Found in Pit-Oct-Unc transcription factors / POU-specific domain / Pou domain - N-terminal to homeobox domain ...POU domain-containing protein, class 5 / Transcription factor SOX / Transcription factor SOX-2 / SOX transcription factor / POU-specific (POUs) domain signature 2. / POU domain / POU-specific (POUs) domain signature 1. / Found in Pit-Oct-Unc transcription factors / POU-specific domain / Pou domain - N-terminal to homeobox domain / POU-specific (POUs) domain profile. / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Lambda repressor-like, DNA-binding domain superfamily / Green fluorescent protein, GFP / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A signature. / Histone H2A conserved site / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / Centromere kinetochore component CENP-T histone fold / CENP-T/Histone H4, histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Core histone H2A/H2B/H3/H4 / Histone H2A/H2B/H3 / Homeobox-like domain superfamily / Histone-fold
Similarity search - Domain/homology
Histone H2A type 1-B/E / Histone H2B type 1-J / Green fluorescent protein / Transcription factor SOX-2 / Histone H4 / Histone H3.1 / POU domain, class 5, transcription factor 1
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.42 Å
AuthorsMichael AK / Kempf G / Cavadini S / Bunker RD / Thoma NH
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science FoundationCRSII3_160734/1 Switzerland
CitationJournal: Science / Year: 2020
Title: Mechanisms of OCT4-SOX2 motif readout on nucleosomes.
Authors: Alicia K Michael / Ralph S Grand / Luke Isbel / Simone Cavadini / Zuzanna Kozicka / Georg Kempf / Richard D Bunker / Andreas D Schenk / Alexandra Graff-Meyer / Ganesh R Pathare / Joscha ...Authors: Alicia K Michael / Ralph S Grand / Luke Isbel / Simone Cavadini / Zuzanna Kozicka / Georg Kempf / Richard D Bunker / Andreas D Schenk / Alexandra Graff-Meyer / Ganesh R Pathare / Joscha Weiss / Syota Matsumoto / Lukas Burger / Dirk Schübeler / Nicolas H Thomä /
Abstract: Transcription factors (TFs) regulate gene expression through chromatin where nucleosomes restrict DNA access. To study how TFs bind nucleosome-occupied motifs, we focused on the reprogramming factors ...Transcription factors (TFs) regulate gene expression through chromatin where nucleosomes restrict DNA access. To study how TFs bind nucleosome-occupied motifs, we focused on the reprogramming factors OCT4 and SOX2 in mouse embryonic stem cells. We determined TF engagement throughout a nucleosome at base-pair resolution in vitro, enabling structure determination by cryo-electron microscopy at two preferred positions. Depending on motif location, OCT4 and SOX2 differentially distort nucleosomal DNA. At one position, OCT4-SOX2 removes DNA from histone H2A and histone H3; however, at an inverted motif, the TFs only induce local DNA distortions. OCT4 uses one of its two DNA-binding domains to engage DNA in both structures, reading out a partial motif. These findings explain site-specific nucleosome engagement by the pluripotency factors OCT4 and SOX2, and they reveal how TFs distort nucleosomes to access chromatinized motifs.
History
DepositionApr 15, 2020-
Header (metadata) releaseMay 6, 2020-
Map releaseMay 6, 2020-
UpdateJul 8, 2020-
Current statusJul 8, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.11
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.11
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6yov
  • Surface level: 0.14
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_10864.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOCT4-SOX2 bound to SHL 6
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 256 pix.
= 220.16 Å
0.86 Å/pix.
x 256 pix.
= 220.16 Å
0.86 Å/pix.
x 256 pix.
= 220.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density
Contour LevelBy AUTHOR: 0.11 / Movie #1: 0.11
Minimum - Maximum-0.3390876 - 0.8904857
Average (Standard dev.)0.004771942 (±0.044493373)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 220.16 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.860.860.86
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z220.160220.160220.160
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.3390.8900.005

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Supplemental data

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Sample components

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Entire : Ternary complex of OCT4-SOX2 and SHL+6 nucleosome

EntireName: Ternary complex of OCT4-SOX2 and SHL+6 nucleosome
Components
  • Complex: Ternary complex of OCT4-SOX2 and SHL+6 nucleosome
    • Complex: HistonesHistone
      • Protein or peptide: Histone H3.1Histone H3
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1-B/E
      • Protein or peptide: Histone H2B type 1-J
      • Protein or peptide: Histone H3.1Histone H3
      • Protein or peptide: Histone H4
    • Complex: DNA
      • DNA: DNA (142-MER)
    • Complex: Green fluorescent protein,POU domain, class 5, transcription factor 1
      • Protein or peptide: Green fluorescent protein,POU domain, class 5, transcription factor 1
    • Complex: SOX2
      • Protein or peptide: Transcription factor SOX-2
  • Ligand: PENTANEDIALGlutaraldehyde

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Supramolecule #1: Ternary complex of OCT4-SOX2 and SHL+6 nucleosome

SupramoleculeName: Ternary complex of OCT4-SOX2 and SHL+6 nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9

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Supramolecule #2: Histones

SupramoleculeName: Histones / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Supramolecule #3: DNA

SupramoleculeName: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #7
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: synthetic construct (others)

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Supramolecule #4: Green fluorescent protein,POU domain, class 5, transcription factor 1

SupramoleculeName: Green fluorescent protein,POU domain, class 5, transcription factor 1
type: complex / ID: 4 / Parent: 1 / Macromolecule list: #8
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

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Supramolecule #5: SOX2

SupramoleculeName: SOX2 / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #9
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

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Macromolecule #1: Histone H3.1

MacromoleculeName: Histone H3.1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.719445 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
GSHMARTKQT ARKSTGGKAP RKQLATKAAR KSAPATGGVK KPHRYRPGTV ALREIRRYQK STELLIRKLP FQRLVREIAQ DFKTDLRFQ SSAVMALQEA CEAYLVGLFE DTNLCAIHAK RVTIMPKDIQ LARRIRGERA

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.547523 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
GSHMSGRGKG GKGLGKGGAK RHRVLRDNIQ GITKPAIRRL ARRGGVKRIS GLIYEETRGV LKVFLENVIR DAVTYTEHAK RKTVTAMDV VYALKRQGRT LYGFGG

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Macromolecule #3: Histone H2A type 1-B/E

MacromoleculeName: Histone H2A type 1-B/E / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.447825 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
GSHMSGRGKQ GGKARAKAKT RSSRAGLQFP VGRVHRLLRK GNYSERVGAG APVYLAAVLE YLTAEILELA GNAARDNKKT RIIPRHLQL AIRNDEELNK LLGRVTIAQG GVLPNIQAVL LPKKTESHHK AKGK

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Macromolecule #4: Histone H2B type 1-J

MacromoleculeName: Histone H2B type 1-J / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.088336 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
GSHMPEPAKS APAPKKGSKK AVTKAQKKDG KKRKRSRKES YSIYVYKVLK QVHPDTGISS KAMGIMNSFV NDIFERIAGE ASRLAHYNK RSTITSREIQ TAVRLLLPGE LAKHAVSEGT KAVTKYTSA

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Macromolecule #5: Histone H3.1

MacromoleculeName: Histone H3.1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.491173 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
GSHMARTKQT ARKSTGGKAP RKQLATKAAR KSAPATGGVK KPHRYRPGTV ALREIRRYQK STELLIRKLP FQRLVREIAQ DFKTDLRFQ SSAVMALQEA CEAYLVGLFE DTNLCAIHAK RVTIMPKDIQ LARRIRGE

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Macromolecule #6: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.676703 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
GSHMSGRGKG GKGLGKGGAK RHRKVLRDNI QGITKPAIRR LARRGGVKRI SGLIYEETRG VLKVFLENVI RDAVTYTEHA KRKTVTAMD VVYALKRQGR TLYGFGG

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Macromolecule #8: Green fluorescent protein,POU domain, class 5, transcription factor 1

MacromoleculeName: Green fluorescent protein,POU domain, class 5, transcription factor 1
type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 69.137789 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDWSHPQFEK SAVDENLYFQ GGMVSKGEEL FTGVVPILVE LDGDVNGHKF SVSGEGEGDA TYGKLTLKFI CTTGKLPVPW PTLVTTLTY GVQCFSRYPD HMKQHDFFKS AMPEGYVQER TIFFKDDGNY KTRAEVKFEG DTLVNRIELK GIDFKEDGNI L GHKLEYNY ...String:
MDWSHPQFEK SAVDENLYFQ GGMVSKGEEL FTGVVPILVE LDGDVNGHKF SVSGEGEGDA TYGKLTLKFI CTTGKLPVPW PTLVTTLTY GVQCFSRYPD HMKQHDFFKS AMPEGYVQER TIFFKDDGNY KTRAEVKFEG DTLVNRIELK GIDFKEDGNI L GHKLEYNY NSHNVYIMAD KQKNGIKVNF KIRHNIEDGS VQLADHYQQN TPIGDGPVLL PDNHYLSTQS KLSKDPNEKR DH MVLLEFV TAAGITLGMD ELYKEAAAKE AAAKMAGHLA SDFAFSPPPG GGGDGPGGPE PGWVDPRTWL SFQGPPGGPG IGP GVGPGS EVWGIPPCPP PYEFCGGMAY CGPQVGVGLV PQGGLETSQP EGEAGVGVES NSDGASPEPC TVTPGAVKLE KEKL EQNPE ESQDIKALQK ELEQFAKLLK QKRITLGYTQ ADVGLTLGVL FGKVFSQTTI CRFEALQLSF KNMCKLRPLL QKWVE EADN NENLQEICKA ETLVQARKRK RTSIENRVRG NLENLFLQCP KPTLQQISHI AQQLGLEKDV VRVWFCNRRQ KGKRSS SDY AQREDFEAAG SPFSGGPVSF PLAPGPHFGT PGYGSPHFTA LYSSVPFPEG EAFPPVSVTT LGSPMHSN

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Macromolecule #9: Transcription factor SOX-2

MacromoleculeName: Transcription factor SOX-2 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.718679 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MDWSHPQFEK SAVDENLYFQ GGMSPDRVKR PMNAFMVWSR GQRRKMAQEN PKMHNSEISK RLGAEWKLLS ETEKRPFIDE AKRLRALHM KEHPDYKYRP RRKTKT

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Macromolecule #7: DNA (142-MER)

MacromoleculeName: DNA (142-MER) / type: dna / ID: 7 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 92.645859 KDa
SequenceString: (DA)(DT)(DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA) (DA)(DT)(DC)(DC)(DC)(DG)(DG)(DT)(DC)(DT) (DG)(DC)(DA)(DG)(DG)(DC)(DC)(DG)(DC) (DT)(DC)(DA)(DA)(DT)(DT)(DG)(DG)(DT)(DC) (DG) (DT)(DA)(DG)(DA)(DC)(DA) ...String:
(DA)(DT)(DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA) (DA)(DT)(DC)(DC)(DC)(DG)(DG)(DT)(DC)(DT) (DG)(DC)(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)(DC)(DT)(DT)(DT)(DG)(DT)(DT)(DA) (DT)(DG)(DC)(DA)(DA)(DA) (DT)(DA)(DC) (DA)(DT)(DC)(DC)(DT)(DG)(DT)(DA)(DC)(DA) (DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DT) (DT)(DG)(DC)(DA)(DT)(DA)(DA)(DC)(DA)(DA) (DA)(DG)(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)(DG)(DC) (DA)(DG)(DA)(DC)(DC)(DG) (DG)(DG)(DA)(DT)(DT)(DC)(DT)(DC)(DC)(DA) (DG)(DG)(DA)(DT)

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Macromolecule #10: PENTANEDIAL

MacromoleculeName: PENTANEDIAL / type: ligand / ID: 10 / Number of copies: 8 / Formula: PTD
Molecular weightTheoretical: 100.116 Da
Chemical component information

ChemComp-PTD:
PENTANEDIAL / medication*YM / Glutaraldehyde

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 45.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Version: gCTF
Startup modelType of model: EMDB MAP
EMDB ID:
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: RANDOM ASSIGNMENT
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v2) / Number images used: 71284

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