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- EMDB-21544: Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ... -

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Basic information

Entry
Database: EMDB / ID: EMD-21544
TitleCryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class05)
Map dataMLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class05)
Sample
  • Complex: MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome
    • Complex: Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Histone-lysine N-methyltransferase 2A, Set1/Ash2 histone methyltransferase complex subunit ASH2
      • 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: Set1/Ash2 histone methyltransferase complex subunit ASH2
    • Complex: Histone H3.2, Histone H4, Histone H2A type 1, Histone H2B 1.1
      • 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
    • Complex: DNA
      • DNA: DNA (147-MER)
      • DNA: DNA (147-MER)
KeywordsMLL1-NCP / H3K4 methylation / TRANSFERASE / TRANSFERASE-STRUCTURAL PROTEIN-DNA complex
Function / homology
Function and homology information


negative regulation of DNA methylation-dependent heterochromatin formation / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / protein-cysteine methyltransferase activity / response to potassium ion / histone H3K4 trimethyltransferase activity / T-helper 2 cell differentiation / unmethylated CpG binding / Phosphorylation of CLOCK, acetylation of BMAL1 (ARNTL) at target gene promoters / histone H3Q5ser reader activity ...negative regulation of DNA methylation-dependent heterochromatin formation / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / protein-cysteine methyltransferase activity / response to potassium ion / histone H3K4 trimethyltransferase activity / T-helper 2 cell differentiation / unmethylated CpG binding / Phosphorylation of CLOCK, acetylation of BMAL1 (ARNTL) at target gene promoters / histone H3Q5ser reader activity / definitive hemopoiesis / histone H3K4me1 reader activity / Loss of Function of KMT2D in MLL4 Complex Formation in Kabuki Syndrome / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / The CRY:PER:kinase complex represses transactivation by the BMAL:CLOCK (ARNTL:CLOCK) complex / MLL3/4 complex / embryonic hemopoiesis / Set1C/COMPASS complex / ATAC complex / histone H3K4 methyltransferase activity / Cardiogenesis / Phosphorylated BMAL1:CLOCK (ARNTL:CLOCK) activates expression of core clock genes / regulation of tubulin deacetylation / Formation of WDR5-containing histone-modifying complexes / hemopoiesis / histone methyltransferase complex / minor groove of adenine-thymine-rich DNA binding / MLL1 complex / histone acetyltransferase complex / regulation of cell division / cellular response to transforming growth factor beta stimulus / membrane depolarization / Transferases; Transferring one-carbon groups; Methyltransferases / regulation of embryonic development / transcription initiation-coupled chromatin remodeling / circadian regulation of gene expression / Deactivation of the beta-catenin transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / response to estrogen / mitotic spindle / beta-catenin binding / PKMTs methylate histone lysines / Formation of the beta-catenin:TCF transactivating complex / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / nucleosomal DNA binding / RMTs methylate histone arginines / innate immune response in mucosa / structural constituent of chromatin / nucleosome / Regulation of PD-L1(CD274) transcription / nucleosome assembly / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / protein-containing complex assembly / methylation / antimicrobial humoral immune response mediated by antimicrobial peptide / heterochromatin formation / histone binding / antibacterial humoral response / chromatin organization / regulation of cell cycle / transcription cis-regulatory region binding / protein heterodimerization activity / apoptotic process / positive regulation of cell population proliferation / chromatin binding / regulation of transcription by RNA polymerase II / DNA damage response / nucleolus / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / DNA binding / : / nucleoplasm / zinc ion binding / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
: / : / Set1/Ash2 histone methyltransferase complex subunit ASH2-like, WH / ASH2, PHD zinc finger / 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 ...: / : / Set1/Ash2 histone methyltransferase complex subunit ASH2-like, WH / ASH2, PHD zinc finger / 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 profile. / SET domain superfamily / 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 H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / Zinc finger, FYVE/PHD-type / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Histone-fold / Concanavalin A-like lectin/glucanase domain superfamily / WD domain, G-beta repeat / 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 / 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: 6.0 Å
AuthorsPark SH / Lee YT
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR)DK111465 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA250329 United States
CitationJournal: Nat Commun / Year: 2021
Title: Mechanism for DPY30 and ASH2L intrinsically disordered regions to modulate the MLL/SET1 activity on chromatin.
Authors: Young-Tae Lee / Alex Ayoub / Sang-Ho Park / Liang Sha / Jing Xu / Fengbiao Mao / Wei Zheng / Yang Zhang / Uhn-Soo Cho / Yali Dou /
Abstract: Recent cryo-EM structures show the highly dynamic nature of the MLL1-NCP (nucleosome core particle) interaction. Functional implication and regulation of such dynamics remain unclear. Here we show ...Recent cryo-EM structures show the highly dynamic nature of the MLL1-NCP (nucleosome core particle) interaction. Functional implication and regulation of such dynamics remain unclear. Here we show that DPY30 and the intrinsically disordered regions (IDRs) of ASH2L work together in restricting the rotational dynamics of the MLL1 complex on the NCP. We show that DPY30 binding to ASH2L leads to stabilization and integration of ASH2L IDRs into the MLL1 complex and establishes new ASH2L-NCP contacts. The significance of ASH2L-DPY30 interactions is demonstrated by requirement of both ASH2L IDRs and DPY30 for dramatic increase of processivity and activity of the MLL1 complex. This DPY30 and ASH2L-IDR dependent regulation is NCP-specific and applies to all members of the MLL/SET1 family of enzymes. We further show that DPY30 is causal for de novo establishment of H3K4me3 in ESCs. Our study provides a paradigm of how H3K4me3 is regulated on chromatin and how H3K4me3 heterogeneity can be modulated by ASH2L IDR interacting proteins.
History
DepositionMar 13, 2020-
Header (metadata) releaseMar 31, 2021-
Map releaseMar 31, 2021-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing 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 cylindrical radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6w5n
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21544.png

Downloads & links

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Map

FileDownload / File: emd_21544.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class05)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 300 pix.
= 300. Å		1 Å/pix.
x 300 pix.
= 300. Å		1 Å/pix.
x 300 pix.
= 300. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0078 / Movie #1: 0.01
Minimum - Maximum-0.017511481 - 0.05429599
Average (Standard dev.)0.00025798933 (±0.0020596227)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 300.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z300.000300.000300.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0180.0540.000

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Supplemental data

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Sample components

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Entire : MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nu...

EntireName: MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome
Components
  • Complex: MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome
    • Complex: Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Histone-lysine N-methyltransferase 2A, Set1/Ash2 histone methyltransferase complex subunit ASH2
      • 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: Set1/Ash2 histone methyltransferase complex subunit ASH2
    • Complex: Histone H3.2, Histone H4, Histone H2A type 1, Histone H2B 1.1
      • 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
    • Complex: DNA
      • DNA: DNA (147-MER)
      • DNA: DNA (147-MER)

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Supramolecule #1: MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nu...

SupramoleculeName: MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 380 KDa

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Supramolecule #2: Retinoblastoma-binding protein 5, WD repeat-containing protein 5,...

SupramoleculeName: Retinoblastoma-binding protein 5, WD repeat-containing protein 5, Histone-lysine N-methyltransferase 2A, Set1/Ash2 histone methyltransferase complex subunit ASH2
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Histone H3.2, Histone H4, Histone H2A type 1, Histone H2B 1.1

SupramoleculeName: Histone H3.2, Histone H4, Histone H2A type 1, Histone H2B 1.1
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#8
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Supramolecule #4: DNA

SupramoleculeName: DNA / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #9-#10
Source (natural)Organism: synthetic construct (others)

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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 H3]-lysine4 N-trimethyltransferase
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: Set1/Ash2 histone methyltransferase complex subunit ASH2

MacromoleculeName: Set1/Ash2 histone methyltransferase complex subunit ASH2
type: protein_or_peptide / ID: 4 / 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 #5: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 5 / 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 #6: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 6 / 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 #7: Histone H2A type 1

MacromoleculeName: Histone H2A type 1 / type: protein_or_peptide / ID: 7 / 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 #8: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.655948 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAKSAPAPKK GSKKAVTKTQ KKDGKKRRKT RKESYAIYVY KVLKQVHPDT GISSKAMSIM NSFVNDVFER IAGEASRLAH YNKRSTITS REIQTAVRLL LPGELAKHAV SEGTKAVTKY TSAK

UniProtKB: Histone H2B 1.1

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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: 45.13877 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 #10: DNA (147-MER)

MacromoleculeName: DNA (147-MER) / type: dna / ID: 10 / 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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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 / 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: 6.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 23236
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-6w5n:
Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class05)

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