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- EMDB-17160: Cryo-EM structure of CLOCK-BMAL1 bound to the native Por enhancer... -

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Basic information

Entry
Database: EMDB / ID: EMD-17160
TitleCryo-EM structure of CLOCK-BMAL1 bound to the native Por enhancer nucleosome (map 2, additional 3D classification and flexible refinement)
Map dataFull-map.
Sample
  • Complex: CLOCK-BMAL1 bound to a nucleosome at SHL -6.2
    • Complex: Nucleosome core particle
      • Complex: Histone octamer
        • Protein or peptide: Histone H3.1
        • Protein or peptide: Histone H4
        • Protein or peptide: Histone H2A type 1-B/E
        • Protein or peptide: Histone H2B type 1-J
      • Complex: Nucleosomal DNA
        • DNA: DNA (147-MER)
        • DNA: DNA (147-MER)
    • Complex: CLOCK-BMAL1 heterodimer
      • Protein or peptide: Circadian locomoter output cycles protein kaput
      • Protein or peptide: Basic helix-loop-helix ARNT-like protein 1
KeywordsE-box / transcription factor / circadian clock / GENE REGULATION
Function / homology
Function and homology information


CLOCK-BMAL transcription complex / positive regulation of skeletal muscle cell differentiation / regulation of hair cycle / positive regulation of protein acetylation / NPAS4 regulates expression of target genes / negative regulation of nuclear receptor-mediated glucocorticoid signaling pathway / maternal process involved in parturition / regulation of type B pancreatic cell development / bHLH transcription factor binding / regulation of cellular senescence ...CLOCK-BMAL transcription complex / positive regulation of skeletal muscle cell differentiation / regulation of hair cycle / positive regulation of protein acetylation / NPAS4 regulates expression of target genes / negative regulation of nuclear receptor-mediated glucocorticoid signaling pathway / maternal process involved in parturition / regulation of type B pancreatic cell development / bHLH transcription factor binding / regulation of cellular senescence / chromatoid body / positive regulation of circadian rhythm / oxidative stress-induced premature senescence / negative regulation of TOR signaling / negative regulation of cold-induced thermogenesis / response to redox state / protein acetylation / negative regulation of fat cell differentiation / histone acetyltransferase activity / regulation of protein catabolic process / E-box binding / regulation of neurogenesis / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / CENP-A containing nucleosome / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / histone acetyltransferase / Packaging Of Telomere Ends / energy homeostasis / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Deposition of new CENPA-containing nucleosomes at the centromere / telomere organization / Inhibition of DNA recombination at telomere / Meiotic synapsis / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / regulation of insulin secretion / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / innate immune response in mucosa / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / DNA damage checkpoint signaling / HCMV Late Events / SIRT1 negatively regulates rRNA expression / epigenetic regulation of gene 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 / cellular response to ionizing radiation / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / transcription coregulator activity / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / Transcriptional regulation by small RNAs / circadian regulation of gene expression / 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 / HDMs demethylate histones / regulation of circadian rhythm / NoRC negatively regulates rRNA expression / PML body / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / chromatin DNA binding / Pre-NOTCH Transcription and Translation / autophagy / Metalloprotease DUBs / RMTs methylate histone arginines
Similarity search - Function
: / : / Nuclear translocator / Helix-loop-helix DNA-binding domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. ...: / : / Nuclear translocator / Helix-loop-helix DNA-binding domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / : / Histone H2B signature. / Histone H2B / Histone H2B / PAS domain / Histone H2A conserved site / Histone H2A signature. / PAS domain superfamily / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / 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 / Histone-fold
Similarity search - Domain/homology
Circadian locomoter output cycles protein kaput / Histone H2A type 1-B/E / Histone H2B type 1-J / Histone H4 / Histone H3.1 / Basic helix-loop-helix ARNT-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsMichael AK / Stoos L / Kempf G / Cavadini S / Thoma N
Funding supportEuropean Union, France, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)884331European Union
Human Frontier Science Program (HFSP)LT000646/2018-L5 France
CitationJournal: Nature / Year: 2023
Title: Cooperation between bHLH transcription factors and histones for DNA access.
Authors: Alicia K Michael / Lisa Stoos / Priya Crosby / Nikolas Eggers / Xinyu Y Nie / Kristina Makasheva / Martina Minnich / Kelly L Healy / Joscha Weiss / Georg Kempf / Simone Cavadini / Lukas ...Authors: Alicia K Michael / Lisa Stoos / Priya Crosby / Nikolas Eggers / Xinyu Y Nie / Kristina Makasheva / Martina Minnich / Kelly L Healy / Joscha Weiss / Georg Kempf / Simone Cavadini / Lukas Kater / Jan Seebacher / Luca Vecchia / Deyasini Chakraborty / Luke Isbel / Ralph S Grand / Florian Andersch / Jennifer L Fribourgh / Dirk Schübeler / Johannes Zuber / Andrew C Liu / Peter B Becker / Beat Fierz / Carrie L Partch / Jerome S Menet / Nicolas H Thomä /
Abstract: The basic helix-loop-helix (bHLH) family of transcription factors recognizes DNA motifs known as E-boxes (CANNTG) and includes 108 members. Here we investigate how chromatinized E-boxes are engaged ...The basic helix-loop-helix (bHLH) family of transcription factors recognizes DNA motifs known as E-boxes (CANNTG) and includes 108 members. Here we investigate how chromatinized E-boxes are engaged by two structurally diverse bHLH proteins: the proto-oncogene MYC-MAX and the circadian transcription factor CLOCK-BMAL1 (refs. ). Both transcription factors bind to E-boxes preferentially near the nucleosomal entry-exit sites. Structural studies with engineered or native nucleosome sequences show that MYC-MAX or CLOCK-BMAL1 triggers the release of DNA from histones to gain access. Atop the H2A-H2B acidic patch, the CLOCK-BMAL1 Per-Arnt-Sim (PAS) dimerization domains engage the histone octamer disc. Binding of tandem E-boxes at endogenous DNA sequences occurs through direct interactions between two CLOCK-BMAL1 protomers and histones and is important for circadian cycling. At internal E-boxes, the MYC-MAX leucine zipper can also interact with histones H2B and H3, and its binding is indirectly enhanced by OCT4 elsewhere on the nucleosome. The nucleosomal E-box position and the type of bHLH dimerization domain jointly determine the histone contact, the affinity and the degree of competition and cooperativity with other nucleosome-bound factors.
History
DepositionApr 19, 2023-
Header (metadata) releaseMay 24, 2023-
Map releaseMay 24, 2023-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17160.png

Downloads & links

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Map

FileDownload / File: emd_17160.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull-map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.68 Å/pix.
x 220 pix.
= 369.6 Å		1.68 Å/pix.
x 220 pix.
= 369.6 Å		1.68 Å/pix.
x 220 pix.
= 369.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.68 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.166
Minimum - Maximum-0.60664886 - 1.6577255
Average (Standard dev.)-0.0026346731 (±0.05494682)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 369.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Flexible refinement.

Fileemd_17160_additional_1.map
AnnotationFlexible refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B.

Fileemd_17160_half_map_1.map
AnnotationHalf map B.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A.

Fileemd_17160_half_map_2.map
AnnotationHalf map A.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CLOCK-BMAL1 bound to a nucleosome at SHL -6.2

EntireName: CLOCK-BMAL1 bound to a nucleosome at SHL -6.2
Components
  • Complex: CLOCK-BMAL1 bound to a nucleosome at SHL -6.2
    • Complex: Nucleosome core particle
      • Complex: Histone octamer
        • Protein or peptide: Histone H3.1
        • Protein or peptide: Histone H4
        • Protein or peptide: Histone H2A type 1-B/E
        • Protein or peptide: Histone H2B type 1-J
      • Complex: Nucleosomal DNA
        • DNA: DNA (147-MER)
        • DNA: DNA (147-MER)
    • Complex: CLOCK-BMAL1 heterodimer
      • Protein or peptide: Circadian locomoter output cycles protein kaput
      • Protein or peptide: Basic helix-loop-helix ARNT-like protein 1

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Supramolecule #1: CLOCK-BMAL1 bound to a nucleosome at SHL -6.2

SupramoleculeName: CLOCK-BMAL1 bound to a nucleosome at SHL -6.2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7

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Supramolecule #2: Nucleosome core particle

SupramoleculeName: Nucleosome core particle / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#5

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Supramolecule #3: Histone octamer

SupramoleculeName: Histone octamer / type: complex / ID: 3 / Parent: 2 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: Nucleosomal DNA

SupramoleculeName: Nucleosomal DNA / type: complex / ID: 4 / Parent: 2 / Macromolecule list: #5-#6
Source (natural)Organism: synthetic construct (others)

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Supramolecule #5: CLOCK-BMAL1 heterodimer

SupramoleculeName: CLOCK-BMAL1 heterodimer / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #7-#8
Source (natural)Organism: Mus musculus (house mouse)

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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: 15.719445 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMARTKQT ARKSTGGKAP RKQLATKAAR KSAPATGGVK KPHRYRPGTV ALREIRRYQK STELLIRKLP FQRLVREIAQ DFKTDLRFQ SSAVMALQEA CEAYLVGLFE DTNLCAIHAK RVTIMPKDIQ LARRIRGERA

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: 11.676703 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMSGRGKG GKGLGKGGAK RHRKVLRDNI QGITKPAIRR LARRGGVKRI SGLIYEETRG VLKVFLENVI RDAVTYTEHA KRKTVTAMD VVYALKRQGR TLYGFGG

UniProtKB: Histone H4

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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 (E. coli)
SequenceString:
GSHMSGRGKQ GGKARAKAKT RSSRAGLQFP VGRVHRLLRK GNYSERVGAG APVYLAAVLE YLTAEILELA GNAARDNKKT RIIPRHLQL AIRNDEELNK LLGRVTIAQG GVLPNIQAVL LPKKTESHHK AKGK

UniProtKB: Histone H2A type 1-B/E

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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 (E. coli)
SequenceString:
GSHMPEPAKS APAPKKGSKK AVTKAQKKDG KKRKRSRKES YSIYVYKVLK QVHPDTGISS KAMGIMNSFV NDIFERIAGE ASRLAHYNK RSTITSREIQ TAVRLLLPGE LAKHAVSEGT KAVTKYTSA

UniProtKB: Histone H2B type 1-J

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Macromolecule #7: Circadian locomoter output cycles protein kaput

MacromoleculeName: Circadian locomoter output cycles protein kaput / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO / EC number: histone acetyltransferase
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 43.768355 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GAMNPVEEDD KDKAKRVSRN KSEKKRRDQF NVLIKELGSM LPGNARKMDK STVLQKSIDF LRKHKETTAQ SDASEIRQDW KPTFLSNEE FTQLMLEALD GFFLAIMTDG SIIYVSESVT SLLEHLPSDL VDQSIFNFIP EGEHSEVYKI LSTHLLESDS L TPEYLKSK ...String:
GAMNPVEEDD KDKAKRVSRN KSEKKRRDQF NVLIKELGSM LPGNARKMDK STVLQKSIDF LRKHKETTAQ SDASEIRQDW KPTFLSNEE FTQLMLEALD GFFLAIMTDG SIIYVSESVT SLLEHLPSDL VDQSIFNFIP EGEHSEVYKI LSTHLLESDS L TPEYLKSK NQLEFCCHML RGTIDPKEPS TYEYVRFIGN FKSLTSVSTS THNGFEGTIQ RTHRPSYEDR VCFVATVRLA TP QFIKEMC TVEEPNEEFT SRHSLEWKFL FLDHRAPPII GYLPFEVLGT SGYDYYHVDD LENLAKCHEH LMQYGKGKSC YYR FLTKGQ QWIWLQTHYY ITYHQWNSRP EFIVCTHTVV SYAEVRAERR RELGIEESL

UniProtKB: Circadian locomoter output cycles protein kaput

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Macromolecule #8: Basic helix-loop-helix ARNT-like protein 1

MacromoleculeName: Basic helix-loop-helix ARNT-like protein 1 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 43.821207 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GAMNPEYAEH QGRIKNAREA HSQIEKRRRD KMNSFIDELA SLVPTCNAMS RKLDKLTVLR MAVQHMKTLR GATNPYTEAN YKPTFLSDD ELKHLILRAA DGFLFVVGCD RGKILFVSES VFKILNYSQN DLIGQSLFDY LHPKDIAKVK EQLSSSDTAP R ERLIDAKT ...String:
GAMNPEYAEH QGRIKNAREA HSQIEKRRRD KMNSFIDELA SLVPTCNAMS RKLDKLTVLR MAVQHMKTLR GATNPYTEAN YKPTFLSDD ELKHLILRAA DGFLFVVGCD RGKILFVSES VFKILNYSQN DLIGQSLFDY LHPKDIAKVK EQLSSSDTAP R ERLIDAKT GLPVKTDITP GPSRLCSGAR RSFFCRMKCN RPSVKVEDKD FASTCSKKKD RKSFCTIHST GYLKSWPPTK MG LDEDNEP DNEGCNLSCL VAIGRLHSHM VPQPANGEIR VKSMEYVSRH AIDGKFVFVD QRATAILAYL PQELLGTSCY EYF HQDDIG HLAECHRQVL QTREKITTNC YKFKIKDGSF ITLRSRWFSF MNPWTKEVEY IVSTNTVV

UniProtKB: Basic helix-loop-helix ARNT-like protein 1

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Macromolecule #5: DNA (147-MER)

MacromoleculeName: DNA (147-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.051621 KDa
SequenceString: (DC)(DC)(DC)(DC)(DC)(DA)(DC)(DC)(DC)(DC) (DG)(DA)(DC)(DT)(DT)(DT)(DG)(DT)(DT)(DC) (DC)(DT)(DG)(DG)(DA)(DT)(DC)(DC)(DG) (DT)(DT)(DA)(DT)(DG)(DC)(DA)(DA)(DC)(DC) (DC) (DA)(DA)(DG)(DC)(DT)(DT) ...String:
(DC)(DC)(DC)(DC)(DC)(DA)(DC)(DC)(DC)(DC) (DG)(DA)(DC)(DT)(DT)(DT)(DG)(DT)(DT)(DC) (DC)(DT)(DG)(DG)(DA)(DT)(DC)(DC)(DG) (DT)(DT)(DA)(DT)(DG)(DC)(DA)(DA)(DC)(DC) (DC) (DA)(DA)(DG)(DC)(DT)(DT)(DC)(DA) (DA)(DC)(DT)(DC)(DT)(DG)(DG)(DG)(DT)(DT) (DT)(DG) (DT)(DA)(DG)(DT)(DG)(DT)(DG) (DT)(DC)(DC)(DA)(DG)(DG)(DA)(DC)(DC)(DT) (DT)(DG)(DA) (DG)(DG)(DG)(DG)(DA)(DG) (DA)(DG)(DG)(DG)(DA)(DC)(DT)(DT)(DT)(DG) (DA)(DA)(DA)(DG) (DC)(DC)(DA)(DC)(DG) (DC)(DC)(DT)(DT)(DT)(DC)(DC)(DT)(DC)(DC) (DA)(DG)(DC)(DC)(DT) (DC)(DA)(DC)(DC) (DC)(DT)(DT)(DC)(DA)(DC)(DG)(DT)(DT)(DT) (DG)(DT)(DG)(DG)(DT)(DC) (DC)(DA)(DC) (DG)(DT)(DG)(DC)

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Macromolecule #6: DNA (147-MER)

MacromoleculeName: DNA (147-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.698188 KDa
SequenceString: (DG)(DC)(DA)(DC)(DG)(DT)(DG)(DG)(DA)(DC) (DC)(DA)(DC)(DA)(DA)(DA)(DC)(DG)(DT)(DG) (DA)(DA)(DG)(DG)(DG)(DT)(DG)(DA)(DG) (DG)(DC)(DT)(DG)(DG)(DA)(DG)(DG)(DA)(DA) (DA) (DG)(DG)(DC)(DG)(DT)(DG) ...String:
(DG)(DC)(DA)(DC)(DG)(DT)(DG)(DG)(DA)(DC) (DC)(DA)(DC)(DA)(DA)(DA)(DC)(DG)(DT)(DG) (DA)(DA)(DG)(DG)(DG)(DT)(DG)(DA)(DG) (DG)(DC)(DT)(DG)(DG)(DA)(DG)(DG)(DA)(DA) (DA) (DG)(DG)(DC)(DG)(DT)(DG)(DG)(DC) (DT)(DT)(DT)(DC)(DA)(DA)(DA)(DG)(DT)(DC) (DC)(DC) (DT)(DC)(DT)(DC)(DC)(DC)(DC) (DT)(DC)(DA)(DA)(DG)(DG)(DT)(DC)(DC)(DT) (DG)(DG)(DA) (DC)(DA)(DC)(DA)(DC)(DT) (DA)(DC)(DA)(DA)(DA)(DC)(DC)(DC)(DA)(DG) (DA)(DG)(DT)(DT) (DG)(DA)(DA)(DG)(DC) (DT)(DT)(DG)(DG)(DG)(DT)(DT)(DG)(DC)(DA) (DT)(DA)(DA)(DC)(DG) (DG)(DA)(DT)(DC) (DC)(DA)(DG)(DG)(DA)(DA)(DC)(DA)(DA)(DA) (DG)(DT)(DC)(DG)(DG)(DG) (DG)(DT)(DG) (DG)(DG)(DG)(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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 14988
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

4f3l

source_name: PDB, initial_model_type: experimental model

4h10

source_name: PDB, initial_model_type: experimental model

6t93

source_name: PDB, initial_model_type: experimental model
Output model

PDB-8osl:
Cryo-EM structure of CLOCK-BMAL1 bound to the native Por enhancer nucleosome (map 2, additional 3D classification and flexible refinement)

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