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- EMDB-0695: Cryo-EM structure of human MLL1-NCP complex, binding mode2 -

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Basic information

Entry
Database: EMDB / ID: EMD-0695
TitleCryo-EM structure of human MLL1-NCP complex, binding mode2
Map dataMain map of human MLL1-NCP complex, binding mode2
Sample
  • Complex: Human MLL1 complex associated with an unmodified nucleosome, binding mode 2
    • Complex: Human MLL1 complexKMT2A
      • Protein or peptide: x 8 types
      • DNA: x 2 types
    • Complex: unmodified nucleosome
  • Ligand: x 2 types
Keywordshistone modification / nucleosome / MLL / TRANSCRIPTION / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


protein-cysteine methyltransferase activity / response to potassium ion / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / negative regulation of DNA methylation-dependent heterochromatin formation / regulation of short-term neuronal synaptic plasticity / MLL3/4 complex / Set1C/COMPASS complex ...protein-cysteine methyltransferase activity / response to potassium ion / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / negative regulation of DNA methylation-dependent heterochromatin formation / regulation of short-term neuronal synaptic plasticity / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / definitive hemopoiesis / NSL complex / histone H3K4 methyltransferase activity / T-helper 2 cell differentiation / : / Cardiogenesis / embryonic hemopoiesis / exploration behavior / anterior/posterior pattern specification / histone methyltransferase complex / regulation of tubulin deacetylation / : / regulation of cell division / Formation of WDR5-containing histone-modifying complexes / minor groove of adenine-thymine-rich DNA binding / membrane depolarization / MLL1 complex / regulation of embryonic development / hemopoiesis / histone acetyltransferase complex / negative regulation of fibroblast proliferation / homeostasis of number of cells within a tissue / positive regulation of gluconeogenesis / spleen development / transcription initiation-coupled chromatin remodeling / cellular response to transforming growth factor beta stimulus / methylated histone binding / Transferases; Transferring one-carbon groups; Methyltransferases / post-embryonic development / skeletal system development / Deactivation of the beta-catenin transactivating complex / gluconeogenesis / Formation of the beta-catenin:TCF transactivating complex / circadian regulation of gene expression / protein modification process / lysine-acetylated histone binding / euchromatin / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / visual learning / mitotic spindle / PKMTs methylate histone lysines / RMTs methylate histone arginines / beta-catenin binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / response to estrogen / nucleosome / Neddylation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / histone binding / fibroblast proliferation / protein-containing complex assembly / transcription cis-regulatory region binding / regulation of cell cycle / protein heterodimerization activity / apoptotic process / DNA damage response / chromatin binding / positive regulation of cell population proliferation / nucleolus / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol
Similarity search - Function
ASH2, PHD zinc finger / Set1/Ash2 histone methyltransferase complex subunit ASH2-like, WH / 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 / : ...ASH2, PHD zinc finger / Set1/Ash2 histone methyltransferase complex subunit ASH2-like, WH / 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. / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / PHD-finger / Zinc finger PHD-type signature. / 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 / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Histone H3 signature 1. / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Zinc finger, FYVE/PHD-type / Histone-fold / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Concanavalin A-like lectin/glucanase domain superfamily / G-protein beta WD-40 repeat / Zinc finger, RING/FYVE/PHD-type / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Histone H3 / 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 / Histone H2A / Set1/Ash2 histone methyltransferase complex subunit ASH2
Similarity search - Component
Biological speciesHomo sapiens (human) / Xenopus laevis (African clawed frog) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsHuang J / Xue H
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (China) China
CitationJournal: Nature / Year: 2019
Title: Structural basis of nucleosome recognition and modification by MLL methyltransferases.
Authors: Han Xue / Tonghui Yao / Mi Cao / Guanjun Zhu / Yan Li / Guiyong Yuan / Yong Chen / Ming Lei / Jing Huang /
Abstract: Methyltransferases of the mixed-lineage leukaemia (MLL) family-which include MLL1, MLL2, MLL3, MLL4, SET1A and SET1B-implement methylation of histone H3 on lysine 4 (H3K4), and have critical and ...Methyltransferases of the mixed-lineage leukaemia (MLL) family-which include MLL1, MLL2, MLL3, MLL4, SET1A and SET1B-implement methylation of histone H3 on lysine 4 (H3K4), and have critical and distinct roles in the regulation of transcription in haematopoiesis, adipogenesis and development. The C-terminal catalytic SET (Su(var.)3-9, enhancer of zeste and trithorax) domains of MLL proteins are associated with a common set of regulatory factors (WDR5, RBBP5, ASH2L and DPY30) to achieve specific activities. Current knowledge of the regulation of MLL activity is limited to the catalysis of histone H3 peptides, and how H3K4 methyl marks are deposited on nucleosomes is poorly understood. H3K4 methylation is stimulated by mono-ubiquitination of histone H2B on lysine 120 (H2BK120ub1), a prevalent histone H2B mark that disrupts chromatin compaction and favours open chromatin structures, but the underlying mechanism remains unknown. Here we report cryo-electron microscopy structures of human MLL1 and MLL3 catalytic modules associated with nucleosome core particles that contain H2BK120ub1 or unmodified H2BK120. These structures demonstrate that the MLL1 and MLL3 complexes both make extensive contacts with the histone-fold and DNA regions of the nucleosome; this allows ease of access to the histone H3 tail, which is essential for the efficient methylation of H3K4. The H2B-conjugated ubiquitin binds directly to RBBP5, orienting the association between MLL1 or MLL3 and the nucleosome. The MLL1 and MLL3 complexes display different structural organizations at the interface between the WDR5, RBBP5 and MLL1 (or the corresponding MLL3) subunits, which accounts for the opposite roles of WDR5 in regulating the activity of the two enzymes. These findings transform our understanding of the structural basis for the regulation of MLL activity at the nucleosome level, and highlight the pivotal role of nucleosome regulation in histone-tail modification.
History
DepositionJul 20, 2019-
Header (metadata) releaseSep 11, 2019-
Map releaseSep 11, 2019-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.007
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.007
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6kiz
  • Surface level: 0.007
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0695.png

Downloads & links

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Map

FileDownload / File: emd_0695.map.gz / Format: CCP4 / Size: 75.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map of human MLL1-NCP complex, binding mode2
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.005 / Movie #1: 0.007
Minimum - Maximum-0.018888574 - 0.043704677
Average (Standard dev.)-0.000027539041 (±0.0018504456)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions270270270
Spacing270270270
CellA=B=C: 297.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z270270270
origin x/y/z0.0000.0000.000
length x/y/z297.000297.000297.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS270270270
D min/max/mean-0.0190.044-0.000

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Supplemental data

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Additional map: Additional map shows good density of RBBP5 WD40 domain.

Fileemd_0695_additional.map
AnnotationAdditional map shows good density of RBBP5 WD40 domain.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Additional map shows good density of RBBP5 WD40 domain.

Fileemd_0695_additional_1.map
AnnotationAdditional map shows good density of RBBP5 WD40 domain.
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 MLL1 complex associated with an unmodified nucleosome, bind...

EntireName: Human MLL1 complex associated with an unmodified nucleosome, binding mode 2
Components
  • Complex: Human MLL1 complex associated with an unmodified nucleosome, binding mode 2
    • Complex: Human MLL1 complexKMT2A
      • Protein or peptide: Histone H3
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B 1.1
      • DNA: DNA (145-MER)
      • DNA: DNA (145-MER)
      • Protein or peptide: Retinoblastoma-binding protein 5
      • Protein or peptide: Histone-lysine N-methyltransferase 2A
      • Protein or peptide: WD repeat-containing protein 5
      • Protein or peptide: Set1/Ash2 histone methyltransferase complex subunit ASH2
    • Complex: unmodified nucleosome
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE
  • Ligand: ZINC ION

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Supramolecule #1: Human MLL1 complex associated with an unmodified nucleosome, bind...

SupramoleculeName: Human MLL1 complex associated with an unmodified nucleosome, binding mode 2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10

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Supramolecule #2: Human MLL1 complex

SupramoleculeName: Human MLL1 complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#10
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: unmodified nucleosome

SupramoleculeName: unmodified nucleosome / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#10
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Macromolecule #1: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.30393 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEASEAY LVALFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3

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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: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.263231 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 3 / 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

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Macromolecule #4: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.498715 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AKSAPAPKKG SKKAVTKTQK KDGKKRRKTR KESYAIYVYK VLKQVHPDTG ISSKAMSIMN SFVNDVFERI AGEASRLAHY NKRSTITSR EIQTAVRLLL PGELAKHAVS EGTKAVTCYT SAK

UniProtKB: Histone H2B 1.1

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Macromolecule #7: Retinoblastoma-binding protein 5

MacromoleculeName: Retinoblastoma-binding protein 5 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 59.223477 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNLELLESFG QNYPEEADGT LDCISMALTC TFNRWGTLLA VGCNDGRIVI WDFLTRGIAK IISAHIHPVC SLCWSRDGHK LVSASTDNI VSQWDVLSGD CDQRFRFPSP ILKVQYHPRD QNKVLVCPMK SAPVMLTLSD SKHVVLPVDD DSDLNVVASF D RRGEYIYT ...String:
MNLELLESFG 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 #8: Histone-lysine N-methyltransferase 2A

MacromoleculeName: Histone-lysine N-methyltransferase 2A / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO / EC number: histone-lysine N-methyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.970539 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: NEPPLNPHGS ARAEVHLRKS AFDMFNFLAS KHRQPPEYNP NDEEEEEVQL KSARRATSMD LPMPMRFRHL KKTSKEAVGV YRSPIHGRG LFCKRNIDAG EMVIEYAGNV IRSIQTDKRE KYYDSKGIGC YMFRIDDSEV VDATMHGNAA RFINHSCEPN C YSRVINID ...String:
NEPPLNPHGS ARAEVHLRKS AFDMFNFLAS KHRQPPEYNP NDEEEEEVQL KSARRATSMD LPMPMRFRHL KKTSKEAVGV YRSPIHGRG LFCKRNIDAG EMVIEYAGNV IRSIQTDKRE KYYDSKGIGC YMFRIDDSEV VDATMHGNAA RFINHSCEPN C YSRVINID GQKHIVIFAM RKIYRGEELT YDYKFPIEDA SNKLPCNCGA KKCRKFLN

UniProtKB: Histone-lysine N-methyltransferase 2A

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Macromolecule #9: WD repeat-containing protein 5

MacromoleculeName: WD repeat-containing protein 5 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.635438 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MATEEKKPET EAARAQPTPS SSATQSKPTP VKPNYALKFT LAGHTKAVSS VKFSPNGEWL ASSSADKLIK IWGAYDGKFE KTISGHKLG ISDVAWSSDS NLLVSASDDK TLKIWDVSSG KCLKTLKGHS NYVFCCNFNP QSNLIVSGSF DESVRIWDVK T GKCLKTLP ...String:
MATEEKKPET EAARAQPTPS SSATQSKPTP VKPNYALKFT LAGHTKAVSS VKFSPNGEWL ASSSADKLIK IWGAYDGKFE KTISGHKLG ISDVAWSSDS NLLVSASDDK TLKIWDVSSG KCLKTLKGHS NYVFCCNFNP QSNLIVSGSF DESVRIWDVK T GKCLKTLP AHSDPVSAVH FNRDGSLIVS SSYDGLCRIW DTASGQCLKT LIDDDNPPVS FVKFSPNGKY ILAATLDNTL KL WDYSKGK CLKTYTGHKN EKYCIFANFS VTGGKWIVSG SEDNLVYIWN LQTKEIVQKL QGHTDVVIST ACHPTENIIA SAA LENDKT IKLWKSDC

UniProtKB: WD repeat-containing protein 5

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Macromolecule #10: Set1/Ash2 histone methyltransferase complex subunit ASH2

MacromoleculeName: Set1/Ash2 histone methyltransferase complex subunit ASH2
type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.288758 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDTQAGSVDE ENGRQLGEVE LQCGICTKWF TADTFGIDTS SCLPFMTNYS FHCNVCHHSG NTYFLRKQAN LKEMCLSALA NLTWQSRTQ DEHPKTMFSK DKDIIPFIDK YWECMTTRQR PGKMTWPNNI VKTMSKERDV FLVKEHPDPG SKDPEEDYPK F GLLDQDLS ...String:
MDTQAGSVDE 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 #5: DNA (145-MER)

MacromoleculeName: DNA (145-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 44.521367 KDa
SequenceString: (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) ...String:
(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)

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Macromolecule #6: DNA (145-MER)

MacromoleculeName: DNA (145-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 44.992648 KDa
SequenceString: (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) ...String:
(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)

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Macromolecule #11: S-ADENOSYL-L-HOMOCYSTEINE

MacromoleculeName: S-ADENOSYL-L-HOMOCYSTEINE / type: ligand / ID: 11 / Number of copies: 1 / Formula: SAH
Molecular weightTheoretical: 384.411 Da
Chemical component information

ChemComp-SAH:
S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine

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Macromolecule #12: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 12 / Number of copies: 1 / 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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 45.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 31882

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