Download MendeleyCryo-EM structure of activation/inactivation forms of UPS7 bound to DNMT1
Nakamura, N., Yoshimi, S., Kikuchi, A., Kori, S., Onoda, H., Nakanishi, M., Nishiyama, A., Arita, K.To be published.
9K2W | pdb_00009k2w
Cryo-EM structure of USP7:DNMT1 complex; closed conformation
- PDB DOI: https://doi.org/10.2210/pdb9K2W/pdb
- EM Map EMD-61999: EMDB EMDataResource
- Classification: STRUCTURAL PROTEIN
- Organism(s): Homo sapiens
- Expression System: Escherichia coli, Spodoptera frugiperda
- Mutation(s): No
- Deposited: 2024-10-18 Released: 2025-06-25
- Funding Organization(s): Japan Society for the Promotion of Science (JSPS)
Experimental Data Snapshot
- Method: ELECTRON MICROSCOPY
- Resolution: 3.54 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
wwPDB Validation 3D Report Full Report
This is version 1.0 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Ubiquitin carboxyl-terminal hydrolase 7 | 1,107 | Homo sapiens | Mutation(s): 0 Gene Names: USP7, HAUSP EC: 3.4.19.12 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q93009 (Homo sapiens) Explore Q93009 Go to UniProtKB: Q93009 | |||||
PHAROS: Q93009 GTEx: ENSG00000187555 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q93009 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| DNA (cytosine-5)-methyltransferase 1 | 1,271 | Homo sapiens | Mutation(s): 0 Gene Names: DNMT1, AIM, CXXC9, DNMT EC: 2.1.1.37 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P26358 (Homo sapiens) Explore P26358 Go to UniProtKB: P26358 | |||||
PHAROS: P26358 GTEx: ENSG00000130816 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P26358 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ZN (Subject of Investigation/LOI) Query on ZN | C [auth B], D [auth B] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: ELECTRON MICROSCOPY
- Resolution: 3.54 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
| Task | Software Package | Version |
|---|---|---|
| MODEL REFINEMENT | PHENIX | |
Entry History & Funding Information
Deposition Data
- Released Date: 2025-06-25 Deposition Author(s): Nakamura, N., Arita, K.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Japan Society for the Promotion of Science (JSPS) | Japan | JP18H02392 |
| Japan Society for the Promotion of Science (JSPS) | Japan | JP19H05294 |
| Japan Society for the Promotion of Science (JSPS) | Japan | JP19H05741 |
| Japan Society for the Promotion of Science (JSPS) | Japan | 24K01967 |
| Japan Society for the Promotion of Science (JSPS) | Japan | 19H05285 |
| Japan Society for the Promotion of Science (JSPS) | Japan | 21H00272 |
| Japan Society for the Promotion of Science (JSPS) | Japan | 24K02001 |
Revision History (Full details and data files)
- Version 1.0: 2025-06-25
Type: Initial release
