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- EMDB-23738: Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode01 -

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Basic information

Entry
Database: EMDB / ID: EMD-23738
TitleCryo-EM structure of MLL1-NCP (H3K4M) complex, mode01
Map dataMode01
Sample
  • Complex: MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Mode01)
    • Complex: RbBP5, WDR5, SET1, and ASH2L
      • 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: nucleosome
      • 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)
KeywordsMLL1-NCP / H3K4 methylation / TRANSFERASE / TRANSFERASE-DNA BINDING PROTEIN-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 / regulation of short-term neuronal synaptic plasticity / ATAC complex / NSL complex / definitive hemopoiesis / histone H3K4 methyltransferase activity / Cardiogenesis / anterior/posterior pattern specification / embryonic hemopoiesis / T-helper 2 cell differentiation / 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 / Deactivation of the beta-catenin transactivating complex / Transferases; Transferring one-carbon groups; Methyltransferases / gluconeogenesis / skeletal system development / post-embryonic development / circadian regulation of gene expression / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / visual learning / beta-catenin binding / PKMTs methylate histone lysines / protein modification process / 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 / Neddylation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / nucleosome assembly / HATs acetylate histones / 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 transcription by RNA polymerase II / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / nucleolus / 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 / nucleus / 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 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 / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Zinc finger, PHD-type / PHD zinc finger / 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 / 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 H3 / Histone H2B 1.1 / WD repeat-containing protein 5 / Histone H4 / 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: 4.76 Å
AuthorsPark SH / Ayoub A
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM082856 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA250329 United States
CitationJournal: Biochemistry / Year: 2022
Title: Regulation of MLL1 Methyltransferase Activity in Two Distinct Nucleosome Binding Modes.
Authors: Ayoub A / Park SH / Lee YT / Cho US / Dou Y
History
DepositionApr 1, 2021-
Header (metadata) releaseDec 29, 2021-
Map releaseDec 29, 2021-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0082
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0082
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7mbm
  • Surface level: 0.0082
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol

Downloads & links

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Map

FileDownload / File: emd_23738.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMode01
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.0082 / Movie #1: 0.0082
Minimum - Maximum-0.024043888 - 0.051229615
Average (Standard dev.)0.000085523454 (±0.0012700394)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 370.99997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z350350350
origin x/y/z0.0000.0000.000
length x/y/z371.000371.000371.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS350350350
D min/max/mean-0.0240.0510.000

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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 (Mode01)
Components
  • Complex: MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Mode01)
    • Complex: RbBP5, WDR5, SET1, and ASH2L
      • 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: nucleosome
      • 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)

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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 (Mode01)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: RbBP5, WDR5, SET1, and ASH2L

SupramoleculeName: RbBP5, WDR5, SET1, and ASH2L / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: nucleosome

SupramoleculeName: nucleosome / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#10
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 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

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.437144 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTMQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEASEA YLVALFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3

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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

MacromoleculeName: Histone H2A / 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

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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 (145-MER)

MacromoleculeName: DNA (145-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 #10: DNA (145-MER)

MacromoleculeName: DNA (145-MER) / type: dna / ID: 10 / 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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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 / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 53.4 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

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.76 Å / Number images used: 30322
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-7mbm:
Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode01

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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