9TL9 | pdb_00009tl9

Cryo-EM Structure of the LPOR:Chlide:NADPH Complexes (RD-25) - improved resolution of a dimer building block form RF-25

PDB DOI: https://doi.org/10.2210/pdb9TL9/pdb
EM Map EMD-56046: EMDB EMDataResource

Classification: PHOTOSYNTHESIS
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-12-10 Released: 2026-08-12
Deposition Author(s): Gabruk, M., Desfosses, A., Estrozi, L.F., Pintscher, S., Rawski, M.
Funding Organization(s): Polish National Science Centre

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.58 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

wwPDB Validation 3D Report Full Report

Validation slider image for 9TL9

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

Literature

Structures of LPOR-Chlide complexes reveal the structural basis of membrane remodeling and photocatalysis

Gabruk, M., Desfosses, A., Estrozi, L.F., Pintscher, S., Rawski, M., Wazny, G., Garbacz, A., Zbyradowski, M., Kruk, J., Fiedor, L.

(2026) Nat Commun

DOI: https://doi.org/10.1038/s41467-026-76316-7

Macromolecule Content

Total Structure Weight: 80.77 kDa
Atom Count: 5,110
Modeled Residue Count: 636
Deposited Residue Count: 706
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protochlorophyllide reductase B, chloroplastic	A, B	353	Arabidopsis thaliana	Mutation(s): 0 Gene Names: PORB, At4g27440, F27G19.40 EC: 1.3.1.33
UniProt
Find proteins for P21218 (Arabidopsis thaliana) Explore P21218 Go to UniProtKB: P21218
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P21218
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LMG (Subject of Investigation/LOI) Query on LMG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C₄₅ H₈₆ O₁₀ DCLTVZLYPPIIID-CVELTQQQSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
NDP (Subject of Investigation/LOI) Query on NDP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
A1JWG (Subject of Investigation/LOI) Query on A1JWG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	Chlorophyllide a C₃₅ H₃₄ Mg N₄ O₅ LRLVQWDKYFMPKX-NYABAGMLSA-L		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.58 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC	4.3

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-08-12

Deposition Author(s):

Funding Organization	Location	Grant Number
Polish National Science Centre	Poland	2019/35/D/NZ1/00295

Revision History (Full details and data files)

Version 1.0: 2026-08-12
Type: Initial release

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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.