+Open data
-Basic information
Entry | Database: PDB / ID: 7yrd | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | histone methyltransferase | |||||||||
Components |
| |||||||||
Keywords | GENE 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 / RNA polymerase II core promoter sequence-specific DNA binding / heterochromatin / nucleosomal DNA binding / cellular response to estradiol stimulus / euchromatin ...histone H4K20me methyltransferase activity / [histone H4]-N-methyl-L-lysine20 N-methyltransferase / histone H4K20 monomethyltransferase activity / [histone H4]-lysine20 N-methyltransferase / muscle organ development / RNA polymerase II core promoter sequence-specific DNA binding / heterochromatin / nucleosomal DNA binding / cellular response to estradiol stimulus / euchromatin / heterochromatin formation / chromatin DNA binding / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / methylation / 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 | |||||||||
Biological species | Xenopus laevis (African clawed frog) Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Li, H. / Wang, W.Y. | |||||||||
Funding support | China, 1items
| |||||||||
Citation | Journal: 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7yrd.cif.gz | 334.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7yrd.ent.gz | 253 KB | Display | PDB format |
PDBx/mmJSON format | 7yrd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yrd_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7yrd_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7yrd_validation.xml.gz | 44.4 KB | Display | |
Data in CIF | 7yrd_validation.cif.gz | 67.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yr/7yrd ftp://data.pdbj.org/pub/pdb/validation_reports/yr/7yrd | HTTPS FTP |
-Related structure data
Related structure data | 34053MC 7yrgC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Protein , 5 types, 9 molecules AEBFCGDHK
#1: Protein | 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 | 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 | 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 | Mass: 10607.212 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: P02281 #6: Protein | [ | Mass: 32214.787 Da / Num. of mol.: 1 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 |
---|
-DNA chain , 1 types, 2 molecules IJ
#3: DNA chain | 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) |
---|
-Non-polymers , 2 types, 2 molecules
#7: Chemical | ChemComp-ZN / |
---|---|
#8: Chemical | ChemComp-SAM / |
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: histone methyltransferase and nucleosome complex / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2300 nm / Nominal defocus min: 1800 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 223000 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|