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- EMDB-34055: histone methyltransferase -

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Basic information

Entry
Database: EMDB / ID: EMD-34055
Titlehistone methyltransferase
Map data
Sample
  • Complex: histone methyltransferase and nucleosome complex
    • Complex: Histone
      • Protein or peptide: Histone H3.2
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A.Z
    • Complex: Histone,SUV420H1
      • DNA: DNA (146-MER)
      • Protein or peptide: Histone H2B 1.1
      • Protein or peptide: [histone H4]-N-methyl-L-lysine20 N-methyltransferase KMT5B
  • Ligand: ZINC ION
  • Ligand: S-ADENOSYLMETHIONINES-Adenosyl methionine
Keywordshistone methyltransferase / GENE REGULATION
Function / homology
Function and homology information


histone H4K20me methyltransferase activity / [histone H4]-N-methyl-L-lysine20 N-methyltransferase / histone H4K20 monomethyltransferase activity / [histone H4]-lysine20 N-methyltransferase / muscle organ development / heterochromatin organization / nucleosomal DNA binding / RNA polymerase II core promoter sequence-specific DNA binding / heterochromatin / cellular response to estradiol stimulus ...histone H4K20me methyltransferase activity / [histone H4]-N-methyl-L-lysine20 N-methyltransferase / histone H4K20 monomethyltransferase activity / [histone H4]-lysine20 N-methyltransferase / muscle organ development / heterochromatin organization / nucleosomal DNA binding / RNA polymerase II core promoter sequence-specific DNA binding / heterochromatin / cellular response to estradiol stimulus / euchromatin / chromatin DNA binding / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / Amyloid fiber formation / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / nucleoplasm / nucleus
Similarity search - Function
KMT5B , SET domain / Suv4-20 family, animal / Histone-lysine N-methyltransferase Suv4-20/Set9 / Histone-lysine N-methyltransferase, N-terminal domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain ...KMT5B , SET domain / Suv4-20 family, animal / Histone-lysine N-methyltransferase Suv4-20/Set9 / Histone-lysine N-methyltransferase, N-terminal domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / 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 / 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
Similarity search - Domain/homology
[histone H4]-N-methyl-L-lysine20 N-methyltransferase KMT5B / Histone H2B 1.1 / Histone H2A.Z / Histone H4 / Histone H3.2
Similarity search - Component
Biological speciesHomo sapiens (human) / Xenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsLi H / Wang WY
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)XDB37010100 China
CitationJournal: Mol Cell / Year: 2023
Title: Structural insight into H4K20 methylation on H2A.Z-nucleosome by SUV420H1.
Authors: Li Huang / Youwang Wang / Haizhen Long / Haoqiang Zhu / Zengqi Wen / Liwei Zhang / Wenhao Zhang / Zhenqian Guo / Longge Wang / Fangyi Tang / Jie Hu / Keyan Bao / Ping Zhu / Guohong Li / Zheng Zhou /
Abstract: DNA replication ensures the accurate transmission of genetic information during the cell cycle. Histone variant H2A.Z is crucial for early replication origins licensing and activation in which ...DNA replication ensures the accurate transmission of genetic information during the cell cycle. Histone variant H2A.Z is crucial for early replication origins licensing and activation in which SUV420H1 preferentially recognizes H2A.Z-nucleosome and deposits H4 lysine 20 dimethylation (H4K20me2) on replication origins. Here, we report the cryo-EM structures of SUV420H1 bound to H2A.Z-nucleosome or H2A-nucleosome and demonstrate that SUV420H1 directly interacts with H4 N-terminal tail, the DNA, and the acidic patch in the nucleosome. The H4 (1-24) forms a lasso-shaped structure that stabilizes the SUV420H1-nucleosome complex and precisely projects the H4K20 residue into the SUV420H1 catalytic center. In vitro and in vivo analyses reveal a crucial role of the SUV420H1 KR loop (residues 214-223), which lies close to the H2A.Z-specific residues D97/S98, in H2A.Z-nucleosome preferential recognition. Together, our findings elucidate how SUV420H1 recognizes nucleosomes to ensure site-specific H4K20me2 modification and provide insights into how SUV420H1 preferentially recognizes H2A.Z nucleosome.
History
DepositionAug 9, 2022-
Header (metadata) releaseDec 13, 2023-
Map releaseDec 13, 2023-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34055.png

Downloads & links

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Map

FileDownload / File: emd_34055.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1 Å
Density
Contour LevelBy AUTHOR: 0.013
Minimum - Maximum-0.053254995 - 0.07293621
Average (Standard dev.)0.0007043704 (±0.0042832857)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 200.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_34055_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_34055_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : histone methyltransferase and nucleosome complex

EntireName: histone methyltransferase and nucleosome complex
Components
  • Complex: histone methyltransferase and nucleosome complex
    • Complex: Histone
      • Protein or peptide: Histone H3.2
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A.Z
    • Complex: Histone,SUV420H1
      • DNA: DNA (146-MER)
      • Protein or peptide: Histone H2B 1.1
      • Protein or peptide: [histone H4]-N-methyl-L-lysine20 N-methyltransferase KMT5B
  • Ligand: ZINC ION
  • Ligand: S-ADENOSYLMETHIONINES-Adenosyl methionine

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Supramolecule #1: histone methyltransferase and nucleosome complex

SupramoleculeName: histone methyltransferase and nucleosome complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6

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Supramolecule #2: Histone

SupramoleculeName: Histone / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2, #4
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Histone,SUV420H1

SupramoleculeName: Histone,SUV420H1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3, #5-#6
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Macromolecule #1: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 12.046091 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
GEVKKPHRYR PGTVALREIR RYQKSTELLI RKLPFQRLVR EIAQDFKTDL RFQSSAVMAL QEASEAYLVA LFEDTNLCAI HAKRVTIMP KDIQLARRIR GERA

UniProtKB: Histone H3.2

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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: 11.265247 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
SGRGKGGKGL GKGGAKRHR(ECX) VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHA KRK TVTAMDVVYA LKRQGRTLYG FGG

UniProtKB: Histone H4

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Macromolecule #4: Histone H2A.Z

MacromoleculeName: Histone H2A.Z / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.091093 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
GKAKTKAVSR SQRAGLQFPV GRIHRHLKSR TTSHGRVGAT AAVYSAAILE YLTAEVLELA GNASKDLKVK RITPRHLQLA IRGDEELDS LIKATIAGGG VIPHIHKSLI GKKG

UniProtKB: Histone H2A.Z

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Macromolecule #5: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 10.607212 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
KTRKESYAIY VYKVLKQVHP DTGISSKAMS IMNSFVNDVF ERIAGEASRL AHYNKRSTIT SREIQTAVRL LLPGELAKHA VSEGTKAVT KYTSAK

UniProtKB: Histone H2B 1.1

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Macromolecule #6: [histone H4]-N-methyl-L-lysine20 N-methyltransferase KMT5B

MacromoleculeName: [histone H4]-N-methyl-L-lysine20 N-methyltransferase KMT5B
type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO / EC number: [histone H4]-lysine20 N-methyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.214787 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: GQSRYVPSSG MSAKELCEND DLATSLVLDP YLGFQTHKMN TRFRPIKGRQ EELKEVIERF KKDEHLEKAF KCLTSGEWAR HYFLNKNKM QEKLFKEHVF IYLRMFATDS GFEILPCNRY SSEQNGAKIV ATKEWKRNDK IELLVGCIAE LSEIEENMLL R HGENDFSV ...String:
GQSRYVPSSG MSAKELCEND DLATSLVLDP YLGFQTHKMN TRFRPIKGRQ EELKEVIERF KKDEHLEKAF KCLTSGEWAR HYFLNKNKM QEKLFKEHVF IYLRMFATDS GFEILPCNRY SSEQNGAKIV ATKEWKRNDK IELLVGCIAE LSEIEENMLL R HGENDFSV MYSTRKNCAQ LWLGPAAFIN HDCRPNCKFV STGRDTACVK ALRDIEPGEE ISCYYGDGFF GENNEFCECY TC ERRGTGA FKSRVGLPAP APVINSKYGL RETDKRLNRL KK

UniProtKB: [histone H4]-N-methyl-L-lysine20 N-methyltransferase KMT5B

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Macromolecule #3: DNA (146-MER)

MacromoleculeName: DNA (146-MER) / type: dna / ID: 3 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.054844 KDa
SequenceString: (DA)(DT)(DC)(DA)(DA)(DT)(DA)(DT)(DC)(DC) (DA)(DC)(DC)(DT)(DG)(DC)(DA)(DG)(DA)(DT) (DT)(DC)(DT)(DA)(DC)(DC)(DA)(DA)(DA) (DA)(DG)(DT)(DG)(DT)(DA)(DT)(DT)(DT)(DG) (DG) (DA)(DA)(DA)(DC)(DT)(DG) ...String:
(DA)(DT)(DC)(DA)(DA)(DT)(DA)(DT)(DC)(DC) (DA)(DC)(DC)(DT)(DG)(DC)(DA)(DG)(DA)(DT) (DT)(DC)(DT)(DA)(DC)(DC)(DA)(DA)(DA) (DA)(DG)(DT)(DG)(DT)(DA)(DT)(DT)(DT)(DG) (DG) (DA)(DA)(DA)(DC)(DT)(DG)(DC)(DT) (DC)(DC)(DA)(DT)(DC)(DA)(DA)(DA)(DA)(DG) (DG)(DC) (DA)(DT)(DG)(DT)(DT)(DC)(DA) (DG)(DC)(DG)(DG)(DA)(DA)(DT)(DT)(DC)(DC) (DG)(DC)(DT) (DG)(DA)(DA)(DC)(DA)(DT) (DG)(DC)(DC)(DT)(DT)(DT)(DT)(DG)(DA)(DT) (DG)(DG)(DA)(DG) (DC)(DA)(DG)(DT)(DT) (DT)(DC)(DC)(DA)(DA)(DA)(DT)(DA)(DC)(DA) (DC)(DT)(DT)(DT)(DT) (DG)(DG)(DT)(DA) (DG)(DA)(DA)(DT)(DC)(DT)(DG)(DC)(DA)(DG) (DG)(DT)(DG)(DG)(DA)(DT) (DA)(DT)(DT) (DG)(DA)(DT)

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Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #8: S-ADENOSYLMETHIONINE

MacromoleculeName: S-ADENOSYLMETHIONINE / type: ligand / ID: 8 / Number of copies: 2 / Formula: SAM
Molecular weightTheoretical: 398.437 Da
Chemical component information

ChemComp-SAM:
S-ADENOSYLMETHIONINE / S-Adenosyl methionine

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.8 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 77000
FSC plot (resolution estimation)

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