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- PDB-7yrg: histone methyltransferase -

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Basic information

Entry
Database: PDB / ID: 7yrg
Titlehistone methyltransferase
Components
  • DNA (146-MER)
  • Histone H2A.Z
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
  • [histone H4]-N-methyl-L-lysine20 N-methyltransferase KMT5B
KeywordsGENE REGULATION / histone methyltransferase
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
S-ADENOSYLMETHIONINE / DNA / DNA (> 10) / DNA (> 100) / [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 speciesXenopus laevis (African clawed frog)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsLi, H. / Wang, W.Y.
Funding support China, 1items
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, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H3.2
B: Histone H4
I: DNA (146-MER)
J: DNA (146-MER)
C: Histone H2A.Z
D: Histone H2B 1.1
E: Histone H3.2
F: Histone H4
G: Histone H2A.Z
H: Histone H2B 1.1
K: [histone H4]-N-methyl-L-lysine20 N-methyltransferase KMT5B
L: [histone H4]-N-methyl-L-lysine20 N-methyltransferase KMT5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,48616
Polymers246,55912
Non-polymers9284
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 5 types, 10 molecules AEBFCGDHKL

#1: Protein Histone H3.2


Mass: 12046.091 Da / Num. of mol.: 2 / Mutation: G2E,G70A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P84233
#2: Protein Histone H4 /


Mass: 11265.247 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P62799
#4: Protein Histone H2A.Z / / H2A/z


Mass: 12091.093 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2AZ1, H2AFZ, H2AZ
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0C0S5
#5: Protein Histone H2B 1.1 / H2B1.1


Mass: 10607.212 Da / Num. of mol.: 2 / Mutation: S33T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P02281
#6: Protein [histone H4]-N-methyl-L-lysine20 N-methyltransferase KMT5B / [histone H4]-lysine20 N-methyltransferase KMT5B


Mass: 32214.787 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KMT5B
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: B7WNX0, [histone H4]-lysine20 N-methyltransferase, [histone H4]-N-methyl-L-lysine20 N-methyltransferase

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DNA chain , 1 types, 2 molecules IJ

#3: DNA chain DNA (146-MER)


Mass: 45054.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Non-polymers , 2 types, 4 molecules

#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#8: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1histone methyltransferase and nucleosome complexCOMPLEX#1-#60RECOMBINANT
2HistoneCOMPLEX#1-#2, #41RECOMBINANT
3Histone,SUV420H1COMPLEX#3, #5-#61RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Xenopus laevis (African clawed frog)8355
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2300 nm / Nominal defocus min: 1800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 77000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00515116
ELECTRON MICROSCOPYf_angle_d0.67721635
ELECTRON MICROSCOPYf_dihedral_angle_d30.6994108
ELECTRON MICROSCOPYf_chiral_restr0.0392436
ELECTRON MICROSCOPYf_plane_restr0.0051731

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