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- EMDB-20512: Cryo-EM structure of MLL1 in complex with RbBP5 and WDR5 bound to... -

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Basic information

Entry
Database: EMDB / ID: EMD-20512
TitleCryo-EM structure of MLL1 in complex with RbBP5 and WDR5 bound to the nucleosome
Map dataMLL1 in complex with RbBP5 and WDR5
Sample
  • Complex: Human MLL1 complex bound to the nucleosome
    • Protein or peptide: x 9 types
    • DNA: x 2 types
  • Ligand: x 2 types
KeywordsMixed-Lineage Leukemia / MLL1 / nucleosome / histone H3 Lys4 methyltransferase / RbBP5 / WDR5 / HISTONE BINDING-DNA BINDING-DNA complex
Function / homology
Function and homology information


negative regulation of DNA methylation-dependent heterochromatin formation / protein-cysteine methyltransferase activity / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / response to potassium ion / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / histone H3Q5ser reader activity / histone H3K4me1 reader activity / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes ...negative regulation of DNA methylation-dependent heterochromatin formation / protein-cysteine methyltransferase activity / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / response to potassium ion / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / histone H3Q5ser reader activity / histone H3K4me1 reader activity / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / definitive hemopoiesis / ATAC complex / regulation of short-term neuronal synaptic plasticity / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / anterior/posterior pattern specification / embryonic hemopoiesis / T-helper 2 cell differentiation / endosomal transport / Formation of WDR5-containing histone-modifying complexes / exploration behavior / histone methyltransferase complex / minor groove of adenine-thymine-rich DNA binding / regulation of cell division / hemopoiesis / MLL1 complex / regulation of embryonic development / histone acetyltransferase complex / membrane depolarization / cellular response to transforming growth factor beta stimulus / negative regulation of fibroblast proliferation / spleen development / positive regulation of gluconeogenesis / homeostasis of number of cells within a tissue / transcription initiation-coupled chromatin remodeling / Transferases; Transferring one-carbon groups; Methyltransferases / gluconeogenesis / post-embryonic development / skeletal system development / Deactivation of the beta-catenin transactivating complex / circadian regulation of gene expression / trans-Golgi network / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / beta-catenin binding / visual learning / protein modification process / PKMTs methylate histone lysines / response to estrogen / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / mitotic spindle / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / Neddylation / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / protein-containing complex assembly / fibroblast proliferation / histone binding / methylation / transcription cis-regulatory region binding / regulation of cell cycle / protein heterodimerization activity / positive regulation of cell population proliferation / apoptotic process / DNA damage response / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / nucleolus / negative regulation of transcription by RNA polymerase II / Golgi apparatus / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
: / Sdc1/DPY30 / : / : / Set1/Ash2 histone methyltransferase complex subunit ASH2-like, WH / ASH2, PHD zinc finger / Dpy-30 motif / Dpy-30 motif / Histone methyltransferase complex subunit ASH2 / Retinoblastoma-binding protein 5/Swd1 ...: / Sdc1/DPY30 / : / : / Set1/Ash2 histone methyltransferase complex subunit ASH2-like, WH / ASH2, PHD zinc finger / Dpy-30 motif / Dpy-30 motif / Histone methyltransferase complex subunit ASH2 / Retinoblastoma-binding protein 5/Swd1 / KMT2A, ePHD domain / KMT2A, PHD domain 1 / KMT2A, PHD domain 2 / KMT2A, PHD domain 3 / Methyltransferase, trithorax / : / FY-rich, N-terminal / F/Y-rich N-terminus / PHD-like zinc-binding domain / FYR domain FYRN motif profile. / "FY-rich" domain, N-terminal region / FY-rich, C-terminal / F/Y rich C-terminus / FYR domain FYRC motif profile. / "FY-rich" domain, C-terminal region / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / WDR5 beta-propeller domain / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / : / Zinc finger, PHD-type / PHD zinc finger / Histone H2B signature. / Histone H2A conserved site / Histone H2A 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 / Zinc finger, FYVE/PHD-type / 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 / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / WD domain, G-beta repeat / Concanavalin A-like lectin/glucanase domain superfamily / Zinc finger, RING/FYVE/PHD-type / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Histone H2B 1.1 / Histone H2A type 1 / WD repeat-containing protein 5 / Histone H4 / Histone H3.2 / Histone-lysine N-methyltransferase 2A / Retinoblastoma-binding protein 5 / Protein dpy-30 homolog / Set1/Ash2 histone methyltransferase complex subunit ASH2
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog) / Homo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.2 Å
AuthorsPark SH / Ayoub A
Funding support United States, Korea, Republic Of, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR)DK111465 United States
National Research Foundation (NRF, Korea)NRF-2015M3D3A1A01064876 Korea, Republic Of
CitationJournal: Nat Commun / Year: 2019
Title: Cryo-EM structure of the human MLL1 core complex bound to the nucleosome.
Authors: Sang Ho Park / Alex Ayoub / Young-Tae Lee / Jing Xu / Hanseong Kim / Wei Zheng / Biao Zhang / Liang Sha / Sojin An / Yang Zhang / Michael A Cianfrocco / Min Su / Yali Dou / Uhn-Soo Cho /
Abstract: Mixed lineage leukemia (MLL) family histone methyltransferases are enzymes that deposit histone H3 Lys4 (K4) mono-/di-/tri-methylation and regulate gene expression in mammals. Despite extensive ...Mixed lineage leukemia (MLL) family histone methyltransferases are enzymes that deposit histone H3 Lys4 (K4) mono-/di-/tri-methylation and regulate gene expression in mammals. Despite extensive structural and biochemical studies, the molecular mechanisms whereby the MLL complexes recognize histone H3K4 within nucleosome core particles (NCPs) remain unclear. Here we report the single-particle cryo-electron microscopy (cryo-EM) structure of the NCP-bound human MLL1 core complex. We show that the MLL1 core complex anchors to the NCP via the conserved RbBP5 and ASH2L, which interact extensively with nucleosomal DNA and the surface close to the N-terminal tail of histone H4. Concurrent interactions of RbBP5 and ASH2L with the NCP uniquely align the catalytic MLL1 domain at the nucleosome dyad, thereby facilitating symmetrical access to both H3K4 substrates within the NCP. Our study sheds light on how the MLL1 complex engages chromatin and how chromatin binding promotes MLL1 tri-methylation activity.
History
DepositionJul 23, 2019-
Header (metadata) releaseAug 28, 2019-
Map releaseDec 18, 2019-
UpdateAug 16, 2023-
Current statusAug 16, 2023Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6pwv
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20512.png

Downloads & links

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Map

FileDownload / File: emd_20512.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMLL1 in complex with RbBP5 and WDR5
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 350 pix.
= 353.5 Å		1.01 Å/pix.
x 350 pix.
= 353.5 Å		1.01 Å/pix.
x 350 pix.
= 353.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.01 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.023706937 - 0.06282161
Average (Standard dev.)0.00016996978 (±0.0017959245)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 353.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.011.011.01
M x/y/z350350350
origin x/y/z0.0000.0000.000
length x/y/z353.500353.500353.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS350350350
D min/max/mean-0.0240.0630.000

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Supplemental data

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Sample components

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Entire : Human MLL1 complex bound to the nucleosome

EntireName: Human MLL1 complex bound to the nucleosome
Components
  • Complex: Human MLL1 complex bound to the nucleosome
    • Protein or peptide: Retinoblastoma-binding protein 5
    • Protein or peptide: WD repeat-containing protein 5
    • Protein or peptide: Histone-lysine N-methyltransferase 2A
    • 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
    • DNA: DNA (147-MER)
    • DNA: DNA (147-MER)
    • Protein or peptide: Protein dpy-30 homolog
    • Protein or peptide: Set1/Ash2 histone methyltransferase complex subunit ASH2
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE
  • Ligand: ZINC ION

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Supramolecule #1: Human MLL1 complex bound to the nucleosome

SupramoleculeName: Human MLL1 complex bound to the nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Macromolecule #1: Retinoblastoma-binding protein 5

MacromoleculeName: Retinoblastoma-binding protein 5 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 59.179359 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SNLELLESFG QNYPEEADGT LDCISMALTC TFNRWGTLLA VGCNDGRIVI WDFLTRGIAK IISAHIHPVC SLCWSRDGHK LVSASTDNI VSQWDVLSGD CDQRFRFPSP ILKVQYHPRD QNKVLVCPMK SAPVMLTLSD SKHVVLPVDD DSDLNVVASF D RRGEYIYT ...String:
SNLELLESFG QNYPEEADGT LDCISMALTC TFNRWGTLLA VGCNDGRIVI WDFLTRGIAK IISAHIHPVC SLCWSRDGHK LVSASTDNI VSQWDVLSGD CDQRFRFPSP ILKVQYHPRD QNKVLVCPMK SAPVMLTLSD SKHVVLPVDD DSDLNVVASF D RRGEYIYT GNAKGKILVL KTDSQDLVAS FRVTTGTSNT TAIKSIEFAR KGSCFLINTA DRIIRVYDGR EILTCGRDGE PE PMQKLQD LVNRTPWKKC CFSGDGEYIV AGSARQHALY IWEKSIGNLV KILHGTRGEL LLDVAWHPVR PIIASISSGV VSI WAQNQV ENWSAFAPDF KELDENVEYE ERESEFDIED EDKSEPEQTG ADAAEDEEVD VTSVDPIAAF CSSDEELEDS KALL YLPIA PEVEDPEENP YGPPPDAVQT SLMDEGASSE KKRQSSADGS QPPKKKPKTT NIELQGVPND EVHPLLGVKG DGKSK KKQA GRPKGSKGKE KDSPFKPKLY KGDRGLPLEG SAKGKVQAEL SQPLTAGGAI SELL

UniProtKB: Retinoblastoma-binding protein 5

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Macromolecule #2: WD repeat-containing protein 5

MacromoleculeName: WD repeat-containing protein 5 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.390992 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SATQSKPTPV KPNYALKFTL AGHTKAVSSV KFSPNGEWLA SSSADKLIKI WGAYDGKFEK TISGHKLGIS DVAWSSDSNL LVSASDDKT LKIWDVSSGK CLKTLKGHSN YVFCCNFNPQ SNLIVSGSFD ESVRIWDVKT GKCLKTLPAH SDPVSAVHFN R DGSLIVSS ...String:
SATQSKPTPV KPNYALKFTL AGHTKAVSSV KFSPNGEWLA SSSADKLIKI WGAYDGKFEK TISGHKLGIS DVAWSSDSNL LVSASDDKT LKIWDVSSGK CLKTLKGHSN YVFCCNFNPQ SNLIVSGSFD ESVRIWDVKT GKCLKTLPAH SDPVSAVHFN R DGSLIVSS SYDGLCRIWD TASGQCLKTL IDDDNPPVSF VKFSPNGKYI LAATLDNTLK LWDYSKGKCL KTYTGHKNEK YC IFANFSV TGGKWIVSGS EDNLVYIWNL QTKEIVQKLQ GHTDVVISTA CHPTENIIAS AALENDKTIK LWKSDC

UniProtKB: WD repeat-containing protein 5

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Macromolecule #3: Histone-lysine N-methyltransferase 2A

MacromoleculeName: Histone-lysine N-methyltransferase 2A / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: histone-lysine N-methyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.141732 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SGSARAEVHL RKSAFDMFNF LASKHRQPPE YNPNDEEEEE VQLKSARRAT SMDLPMPMRF RHLKKTSKEA VGVYRSPIHG RGLFCKRNI DAGEMVIEYA GIVIRSILTD KREKYYDSKG IGCYMFRIDD SEVVDATMHG NAARFINHSC EPNCYSRVIN I DGQKHIVI ...String:
SGSARAEVHL RKSAFDMFNF LASKHRQPPE YNPNDEEEEE VQLKSARRAT SMDLPMPMRF RHLKKTSKEA VGVYRSPIHG RGLFCKRNI DAGEMVIEYA GIVIRSILTD KREKYYDSKG IGCYMFRIDD SEVVDATMHG NAARFINHSC EPNCYSRVIN I DGQKHIVI FAMRKIYRGE ELTYDYKFPI EDASNKLPCN CGAKKCRKFL N

UniProtKB: Histone-lysine N-methyltransferase 2A

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Macromolecule #4: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.435126 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEASEA YLVALFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.2

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Macromolecule #5: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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Macromolecule #6: Histone H2A type 1

MacromoleculeName: Histone H2A type 1 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.978241 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKQGGKT RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAVRN DEELNKLLGR VTIAQGGVLP NIQSVLLPKK TESSKSAKSK

UniProtKB: Histone H2A type 1

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Macromolecule #7: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.524752 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AKSAPAPKKG SKKAVTKTQK KDGKKRRKTR KESYAIYVYK VLKQVHPDTG ISSKAMSIMN SFVNDVFERI AGEASRLAHY NKRSTITSR EIQTAVRLLL PGELAKHAVS EGTKAVTKYT SAK

UniProtKB: Histone H2B 1.1

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Macromolecule #10: Protein dpy-30 homolog

MacromoleculeName: Protein dpy-30 homolog / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.492876 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGSMEPEQML EGQTQVAENP HSEYGLTDNV ERIVENEKIN AEKSSKQKVD LQSLPTRAYL DQTVVPILLQ GLAVLAKERP PNPIEFLAS YLLKNKAQFE DRN

UniProtKB: Protein dpy-30 homolog

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Macromolecule #11: Set1/Ash2 histone methyltransferase complex subunit ASH2

MacromoleculeName: Set1/Ash2 histone methyltransferase complex subunit ASH2
type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.244641 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SDTQAGSVDE ENGRQLGEVE LQCGICTKWF TADTFGIDTS SCLPFMTNYS FHCNVCHHSG NTYFLRKQAN LKEMCLSALA NLTWQSRTQ DEHPKTMFSK DKDIIPFIDK YWECMTTRQR PGKMTWPNNI VKTMSKERDV FLVKEHPDPG SKDPEEDYPK F GLLDQDLS ...String:
SDTQAGSVDE ENGRQLGEVE LQCGICTKWF TADTFGIDTS SCLPFMTNYS FHCNVCHHSG NTYFLRKQAN LKEMCLSALA NLTWQSRTQ DEHPKTMFSK DKDIIPFIDK YWECMTTRQR PGKMTWPNNI VKTMSKERDV FLVKEHPDPG SKDPEEDYPK F GLLDQDLS NIGPAYDNQK QSSAVSTSGN LNGGIAAGSS GKGRGAKRKQ QDGGTTGTTK KARSDPLFSA QRLPPHGYPL EH PFNKDGY RYILAEPDPH APDPEKLELD CWAGKPIPGD LYRACLYERV LLALHDRAPQ LKISDDRLTV VGEKGYSMVR ASH GVRKGA WYFEITVDEM PPDTAARLGW SQPLGNLQAP LGYDKFSYSW RSKKGTKFHQ SIGKHYSSGY GQGDVLGFYI NLPE DTETA KSLPDTYKDK ALIKFKSYLY FEEKDFVDKA EKSLKQTPHS EIIFYKNGVN QGVAYKDIFE GVYFPAISLY KSCTV SINF GPCFKYPPKD LTYRPMSDMG WGAVVEHTLA DVLYHVETEV DGRRSPPWEP

UniProtKB: Set1/Ash2 histone methyltransferase complex subunit ASH2

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Macromolecule #8: DNA (147-MER)

MacromoleculeName: DNA (147-MER) / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 45.13877 KDa
SequenceString: (DA)(DT)(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) ...String:
(DA)(DT)(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) (DC)(DG)(DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DC) (DA)(DT)(DC) (DC)(DG)(DA)(DT)

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Macromolecule #9: DNA (147-MER)

MacromoleculeName: DNA (147-MER) / type: dna / ID: 9 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 45.610043 KDa
SequenceString: (DA)(DT)(DC)(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) ...String:
(DA)(DT)(DC)(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)(DG)(DA)(DT)

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Macromolecule #12: S-ADENOSYL-L-HOMOCYSTEINE

MacromoleculeName: S-ADENOSYL-L-HOMOCYSTEINE / type: ligand / ID: 12 / Number of copies: 2 / Formula: SAH
Molecular weightTheoretical: 384.411 Da
Chemical component information

ChemComp-SAH:
S-ADENOSYL-L-HOMOCYSTEINE

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Macromolecule #13: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 13 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: 7.5
GridDetails: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 64.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 8433
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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