9JL6 | pdb_00009jl6

Cryo-EM structure of chalcone synthase (CHS) from Physcomitrella patens in the presence of CHIL

PDB DOI: https://doi.org/10.2210/pdb9JL6/pdb
EM Map EMD-61579: EMDB EMDataResource

Classification: TRANSFERASE
Organism(s): Physcomitrium patens
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2024-09-18 Released: 2025-10-01
Deposition Author(s): Sato, K., Yokoyama, T., Tanaka, Y., Imaizumi, R., Yasuda, A., Yanai, T., Yamashita, S., Waki, T., Tsunashima, M., Nakayama, T.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.18 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9JL6

This is version 1.0 of the entry. See complete history.

Literature

Cryo-EM structure of chalcone synthase (CHS) from Physcomitrella patens in the presence of CHIL

Sato, K., Yokoyama, T., Tanaka, Y., Imaizumi, R., Yasuda, A., Yanai, T., Yamashita, S., Waki, T., Tsunashima, M., Nakayama, T.

To be published.

Macromolecule Content

Total Structure Weight: 85.23 kDa
Atom Count: 5,790
Modeled Residue Count: 764
Deposited Residue Count: 794
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chalcone synthase	A, B	397	Physcomitrium patens	Mutation(s): 0 Gene Names: PHYPA_029015 EC: 2.3.1.74
UniProt
Find proteins for Q2VAZ3 (Physcomitrium patens) Explore Q2VAZ3 Go to UniProtKB: Q2VAZ3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2VAZ3
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.18 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-10-01

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History (Full details and data files)

Version 1.0: 2025-10-01
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.