EMD-9998

Single-particle
3.2 Å
EMD-9998
3D View Gallery
Deposition: 20/07/2019
Map released: 11/09/2019
Last modified: 27/03/2024
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Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-9998
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Map-only Validation report (pdf.gz) Map-only Validation report (cif.gz) Map-only Validation report (xml.gz)
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EMICSS annotations (xml)

Cryo-EM structure of human MLL1-ubNCP complex (3.2 angstrom)

EMD-9998

Single-particle
3.2 Å
EMD-9998
3D View Gallery
Deposition: 20/07/2019
Map released: 11/09/2019
Last modified: 27/03/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Name: Human MLL1 complex associated with an H2B-monoubiquitinated nucleosome (3.2 angstrom)
Complex [3]
Name: Human MLL1 complex associated with an H2B-monoubiquitinated nucleosome (3.2 angstrom)
Name: Human MLL1
Natural source [1]
Organism: Homo sapiens
Name: H2B-monoubiquitinated nucleosome
Natural source [1]
Organism: Xenopus laevis
Protein [9]
LEVO
Name: Histone H3
Number of copies: 2
UniProtKB UniProtKB PDBe-KB PDBe-KB AlphaFold DB AlphaFold DB
Domains
Gene Ontology [5]

Molecular function:
structural constituent of chromatin protein heterodimerization activity DNA binding
Cellular location:
nucleoplasm nucleosome
Natural source
Organism: Xenopus laevis
Molecular weight
Experimental Theoretical Method
- 15 kDa -
Recombinant Expression
Organism Strain Cell Plasmid
Escherichia coli - - -
LEVO
Name: Histone H4
Number of copies: 2
UniProtKB UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [6]
Biological process:
DNA-templated transcription, initiation
Molecular function:
structural constituent of chromatin protein heterodimerization activity DNA binding
Cellular location:
nucleosome nucleus
Natural source
Organism: Xenopus laevis
Molecular weight
Experimental Theoretical Method
- 11 kDa -
Recombinant Expression
Organism Strain Cell Plasmid
Escherichia coli - - -
LEVO
Name: Histone H2A
Number of copies: 2
UniProtKB UniProtKB PDBe-KB PDBe-KB AlphaFold DB AlphaFold DB
Domains
Gene Ontology [5]

Molecular function:
structural constituent of chromatin protein heterodimerization activity DNA binding
Cellular location:
nucleosome nucleus
Natural source
Organism: Xenopus laevis
Molecular weight
Experimental Theoretical Method
- 13 kDa -
Recombinant Expression
Organism Strain Cell Plasmid
Escherichia coli - - -
LEVO
Name: Histone H2B 1.1
Number of copies: 2
UniProtKB UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [5]

Molecular function:
structural constituent of chromatin protein heterodimerization activity DNA binding
Cellular location:
nucleus nucleosome
Natural source
Organism: Xenopus laevis
Molecular weight
Experimental Theoretical Method
- 13 kDa -
Recombinant Expression
Organism Strain Cell Plasmid
Escherichia coli - - -
LEVO
Name: Histone-lysine N-methyltransferase 2A
EC number: 2.1.1.43
Number of copies: 1
UniProtKB UniProtKB PDBe-KB
Domains
Natural source
Organism: Homo sapiens
Molecular weight
Experimental Theoretical Method
- 24 kDa -
Recombinant Expression
Organism Strain Cell Plasmid
Escherichia coli - - -
LEVO
Name: Retinoblastoma-binding protein 5
Number of copies: 1
UniProtKB UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [17]
Biological process:
chromatin organization DNA damage response transcription initiation-coupled chromatin remodeling response to estrogen histone H3-K4 methylation cellular response to DNA damage stimulus
Molecular function:
histone binding transcription cis-regulatory region binding methylated histone binding
Cellular location:
MLL1/2 complex MLL3/4 complex nucleolus MLL1 complex nucleoplasm nucleus Set1C/COMPASS complex histone methyltransferase complex
Natural source
Organism: Homo sapiens
Molecular weight
Experimental Theoretical Method
- 59 kDa -
Recombinant Expression
Organism Strain Cell Plasmid
Escherichia coli - - -
LEVO
Name: WD repeat-containing protein 5
Number of copies: 1
UniProtKB UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [40]
Biological process:
negative regulation of transcription by RNA polymerase II transcription initiation-coupled chromatin remodeling regulation of DNA-templated transcription positive regulation of DNA-templated transcription gluconeogenesis positive regulation of transcription, DNA-templated histone H4-K16 acetylation regulation of cell division regulation of cell cycle regulation of embryonic development neuron projection development skeletal system development regulation of histone deacetylation regulation of transcription by RNA polymerase II histone H4-K8 acetylation regulation of dosage compensation by inactivation of X chromosome negative regulation of histone H3-K4 methylation histone H3 acetylation chromatin organization regulation of tubulin deacetylation regulation of transcription, DNA-templated histone H4-K5 acetylation positive regulation of histone H3-K4 methylation positive regulation of gluconeogenesis histone H3-K14 acetylation histone H3-K4 methylation
Molecular function:
histone H3K4 methyltransferase activity methylated histone binding histone binding
Cellular location:
mitotic spindle MLL1/2 complex ATAC complex nucleus NSL complex histone acetyltransferase complex histone methyltransferase complex MLL1 complex MLL3/4 complex nucleoplasm Set1C/COMPASS complex
Natural source
Organism: Homo sapiens
Molecular weight
Experimental Theoretical Method
- 36 kDa -
Recombinant Expression
Organism Strain Cell Plasmid
Escherichia coli - - -
LEVO
Name: Set1/Ash2 histone methyltransferase complex subunit ASH2
Number of copies: 1
UniProtKB UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [2]
Biological process:
histone H3-K4 methylation

Cellular location:
Set1C/COMPASS complex
Natural source
Organism: Homo sapiens
Molecular weight
Experimental Theoretical Method
- 60 kDa -
Recombinant Expression
Organism Strain Cell Plasmid
Escherichia coli - - -
LEVO
Name: Ubiquitin
Number of copies: 1
UniProtKB UniProtKB PDBe-KB AlphaFold DB
Domains
Natural source
Organism: Homo sapiens
Molecular weight
Experimental Theoretical Method
- 8 kDa -
Recombinant Expression
Organism Strain Cell Plasmid
Escherichia coli - - -
DNA [2]
DNA
Name: DNA (145-MER)
Number of copies: 1
Natural source
Organism: synthetic construct
Molecular weight
Experimental Theoretical Method
- 44 kDa -
DNA
Name: DNA (145-MER)
Number of copies: 1
Natural source
Organism: synthetic construct
Molecular weight
Experimental Theoretical Method
- 44 kDa -
Ligand [4]
Name: S-ADENOSYL-L-HOMOCYSTEINE
HET code: SAH
Number of copies: 1
ChEMBL ChEBI DrugBank
Molecular weight
Experimental Theoretical Method
- 384 Da -
Name: ZINC ION
HET code: ZN
Number of copies: 1
ChEMBL ChEBI DrugBank
Molecular weight
Experimental Theoretical Method
- 65 Da -
Name: LYSINE
HET code: LYS
Number of copies: 1
ChEBI
Molecular weight
Experimental Theoretical Method
- 147 Da -
Name: GLUTAMINE
HET code: GLN
Number of copies: 1
ChEMBL ChEBI DrugBank
Molecular weight
Experimental Theoretical Method
- 146 Da -