9TLH | pdb_00009tlh

Cryo-EM Structure of the oligomeric LPOR:Chlide:NADPH Complexes HF-23


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.03 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 

wwPDB Validation 3D Report Full Report

Validation slider image for 9TLH

This is version 1.1 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 17

  • DOI: https://doi.org/10.1038/s41467-026-76316-7
  • Primary Citation Related Structures: 
    9TL6, 9TL7, 9TL8, 9TL9, 9TLA, 9TLB, 9TLC, 9TLH, 9TLK

  • PubMed Abstract: 

    Light-dependent protochlorophyllide oxidoreductase (LPOR) is a light-driven enzyme in flowering plants. It is involved in chlorophyll biosynthesis while also reorganizing membrane lipids into the cubic membrane network that supports chloroplast development. However, the structural basis of these two activities and their relationship have remained unclear. Here, cryo-electron microscopy of chlorophyllide-bound LPOR oligomers reveals nine distinct assembly states, including helical filaments, stacked rings and segmented strings of dimers. We find that strings of LPOR dimers reshape lipid bilayers into a range of membrane architectures through combinations of three inter-string interfaces, providing a structural explanation for the flexibility of these assemblies. The highest-resolution map (2.55 Å), shows the pigment-binding region in sufficient detail to reveal a solvent-accessible channel near the pigment and a conformation of the propionate group may support hydride transfer from NADPH. Together, these findings establish a structural framework linking LPOR oligomerization, membrane remodeling and photocatalysis, and suggest that chlorophyllide-bound LPOR assemblies may have a regulatory function in mature leaves.


  • Organizational Affiliation
    • Department of Plant Physiology and Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Kraków, Poland. michal.gabruk@uj.edu.pl.

Macromolecule Content 

  • Total Structure Weight: 1,776.89 kDa 
  • Atom Count: 112,359 
  • Modeled Residue Count: 13,994 
  • Deposited Residue Count: 15,532 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protochlorophyllide reductase B, chloroplastic353Arabidopsis thalianaMutation(s): 0 
Gene Names: PORBAt4g27440F27G19.40
EC: 1.3.1.33
UniProt
Find proteins for P21218 (Arabidopsis thaliana)
Explore P21218 
Go to UniProtKB:  P21218
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21218
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LMG
(Subject of Investigation/LOI)

Query on LMG



Download:Ideal Coordinates CCD File
AE [auth CE]
BD [auth BI]
BE [auth CF]
BF [auth DB]
CB [auth AD]
AE [auth CE],
BD [auth BI],
BE [auth CF],
BF [auth DB],
CB [auth AD],
DC [auth BA],
DD [auth BJ],
EF [auth DC],
FE [auth CG],
GB [auth AE],
GC [auth BB],
GD [auth BK],
GF [auth DD],
IB [auth AF],
IE [auth CH],
KC [auth BC],
KE [auth CI],
KF [auth DE],
LB [auth AG],
LC [auth BD],
LD [auth BL],
LF [auth DF],
ND [auth CA],
OB [auth AH],
OE [auth CJ],
PC [auth BE],
QF [auth DG],
RB [auth AI],
RD [auth CB],
SC [auth BF],
SD [auth CC],
SE [auth CK],
SF [auth DH],
TA [auth AA],
TB [auth AJ],
UE [auth CL],
VD [auth CD],
WC [auth BG],
XA [auth AB],
XB [auth AK],
YA [auth AC],
YE [auth DA],
ZB [auth AL],
ZC [auth BH]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
NDP
(Subject of Investigation/LOI)

Query on NDP



Download:Ideal Coordinates CCD File
AB [auth AC]
AF [auth DB]
BB [auth AD]
BC [auth AL]
CC [auth BA]
AB [auth AC],
AF [auth DB],
BB [auth AD],
BC [auth AL],
CC [auth BA],
CD [auth BI],
CE [auth CF],
DF [auth DC],
EE [auth CG],
FB [auth AE],
FC [auth BB],
FD [auth BJ],
HB [auth AF],
HD [auth BK],
HE [auth CH],
HF [auth DD],
IC [auth BC],
JF [auth DE],
KD [auth BL],
MB [auth AG],
MC [auth BD],
ME [auth CI],
NE [auth CJ],
NF [auth DF],
OC [auth BE],
OD [auth CA],
OF [auth DG],
PB [auth AH],
PD [auth CB],
QB [auth AI],
QE [auth CK],
RC [auth BF],
RF [auth DH],
SA [auth AA],
TD [auth CC],
TE [auth CL],
UC [auth BG],
VA [auth AB],
VB [auth AJ],
WB [auth AK],
WD [auth CD],
WE [auth DA],
YC [auth BH],
YD [auth CE]
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
A1JWG
(Subject of Investigation/LOI)

Query on A1JWG



Download:Ideal Coordinates CCD File
AC [auth AL]
AD [auth BI]
CF [auth DC]
DB [auth AD]
DE [auth CF]
AC [auth AL],
AD [auth BI],
CF [auth DC],
DB [auth AD],
DE [auth CF],
EB [auth AE],
EC [auth BA],
ED [auth BJ],
FF [auth DD],
GE [auth CG],
HC [auth BB],
ID [auth BK],
IF [auth DE],
JB [auth AF],
JC [auth BC],
JD [auth BL],
JE [auth CH],
KB [auth AG],
LE [auth CI],
MD [auth CA],
MF [auth DF],
NB [auth AH],
NC [auth BD],
PE [auth CJ],
PF [auth DG],
QC [auth BE],
QD [auth CB],
RE [auth CK],
SB [auth AI],
TC [auth BF],
TF [auth DH],
UA [auth AA],
UB [auth AJ],
UD [auth CC],
VC [auth BG],
VE [auth CL],
WA [auth AB],
XC [auth BH],
XD [auth CD],
XE [auth DA],
YB [auth AK],
ZA [auth AC],
ZD [auth CE],
ZE [auth DB]
Chlorophyllide a
C35 H34 Mg N4 O5
LRLVQWDKYFMPKX-NYABAGMLSA-L

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.03 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONcryoSPARC4.3

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Polish National Science CentrePoland2019/35/D/NZ1/00295

Revision History  (Full details and data files)

  • Version 1.0: 2026-08-12
    Type: Initial release
  • Version 1.1: 2026-09-16
    Changes: Data collection, Database references