9L5D | pdb_00009l5d

CryoEM structure of Arabidopsis thaliana M309I Rubisco with D4 symmetry

• PDB DOI: https://doi.org/10.2210/pdb9L5D/pdb
• EM Map EMD-62829: EMDB EMDataResource

• Classification: PHOTOSYNTHESIS
• Organism(s): Arabidopsis thaliana
• Mutation(s): Yes 


• Deposited: 2024-12-23 Released: 2026-05-20 
• Deposition Author(s): Yamori, W., Nakazato, I., Yuchen, Q., Sanga, Y., Miyata, T., Uehara, R., Noto, Y., Namba, K., Fukayama, H., Matsumura, H., Arimura, S.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED), Japan Science and Technology

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 1.75 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

CryoEM structure of Arabidopsis thaliana M309I Rubisco with D4 symmetry

Yamori, W., Nakazato, I., Yuchen, Q., Sanga, Y., Miyata, T., Uehara, R., Noto, Y., Namba, K., Fukayama, H., Matsumura, H., Arimura, S.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Hetero 16-mer - A8B8 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 586.69 kDa 
• Atom Count: 35,688 
• Modeled Residue Count: 4,320 
• Deposited Residue Count: 5,320 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribulose bisphosphate carboxylase large chain	A, C [auth B], E [auth D], G [auth F], I [auth H], K [auth J], M [auth L], O [auth N]	479	Arabidopsis thaliana	Mutation(s): 1  EC: 4.1.1.39
UniProt
Find proteins for O03042 (Arabidopsis thaliana) Explore O03042  Go to UniProtKB:  O03042

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribulose bisphosphate carboxylase small subunit 1A, chloroplastic	B [auth S], D [auth C], F [auth E], H [auth G], J [auth I], L [auth K], N [auth M], P [auth O]	180	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P10795 (Arabidopsis thaliana) Explore P10795  Go to UniProtKB:  P10795

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4 (Subject of Investigation/LOI)	Q [auth A], R [auth B], S [auth D], T [auth F], U [auth H], V [auth J], W [auth L], X [auth N]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 1.75 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487
RECONSTRUCTION	RELION	4

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-05-20 
Deposition Author(s): Yamori, W., Nakazato, I., Yuchen, Q., Sanga, Y., Miyata, T., Uehara, R., Noto, Y., Namba, K., Fukayama, H., Matsumura, H., Arimura, S.

---

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	24H02277
Japan Society for the Promotion of Science (JSPS)	Japan	24K01994
Japan Society for the Promotion of Science (JSPS)	Japan	23K18033
Japan Agency for Medical Research and Development (AMED)	Japan	JP21am0101117
Japan Agency for Medical Research and Development (AMED)	Japan	JP22ama121003
Japan Agency for Medical Research and Development (AMED)	Japan	JP23ama121001
Japan Agency for Medical Research and Development (AMED)	Japan	JP17pc0101020
Japan Science and Technology	Japan	JPMJOP1861

Revision History  

• Version 1.0: 2026-05-20
  Type: Initial release