[English] 日本語
Yorodumi
- EMDB-56051: Cryo-EM Structure of the oligomeric LPOR:Chlide:NADPH Complexes HF-29 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-56051
TitleCryo-EM Structure of the oligomeric LPOR:Chlide:NADPH Complexes HF-29
Map dataprimary
Sample
  • Complex: Cryo-EM Structure of the oligomeric LPOR:Chlide:NADPH Complexes HF-29
    • Protein or peptide: Light-dependent protochlorophyllide oxidoreductase, isoform B of Arabidopsis thaliana
Keywordsphotoenzyme / chlorophyllide / oligomer / PHOTOSYNTHESIS
Function / homology
Function and homology information


protochlorophyllide reductase / protochlorophyllide reductase activity / response to ethylene / chloroplast outer membrane / chlorophyll biosynthetic process / chloroplast thylakoid / chloroplast envelope / chloroplast thylakoid membrane / photosynthesis / chloroplast ...protochlorophyllide reductase / protochlorophyllide reductase activity / response to ethylene / chloroplast outer membrane / chlorophyll biosynthetic process / chloroplast thylakoid / chloroplast envelope / chloroplast thylakoid membrane / photosynthesis / chloroplast / protein domain specific binding / mRNA binding / cytosol
Similarity search - Function
Light-dependent protochlorophyllide reductase / short chain dehydrogenase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Protochlorophyllide reductase B, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodhelical reconstruction / cryo EM / Resolution: 3.87 Å
AuthorsGabruk M / Desfosses A / Estrozi LF / Pintscher S / Rawski M
Funding support Poland, 1 items
OrganizationGrant numberCountry
Polish National Science Centre2019/35/D/NZ1/00295 Poland
CitationJournal: Nat Commun / Year: 2026
Title: Structures of LPOR-Chlide complexes reveal the structural basis of membrane remodeling and photocatalysis.
Authors: Michał Gabruk / Ambroise Desfosses / Leandro Farias Estrozi / Sebastian Pintscher / Michał Rawski / Grzegorz Ważny / Agnieszka Garbacz / Mateusz Zbyradowski / Jerzy Kruk / Leszek Fiedor /
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 ...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.
History
DepositionDec 10, 2025-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_56051.png

Downloads & links

-
Map

FileDownload / File: emd_56051.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationprimary
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 640 pix.
= 550.4 Å		0.86 Å/pix.
x 640 pix.
= 550.4 Å		0.86 Å/pix.
x 640 pix.
= 550.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0816
Minimum - Maximum-0.11042068 - 0.25882617
Average (Standard dev.)0.0018410096 (±0.017458323)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 550.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: sharpened

Fileemd_56051_additional_1.map
Annotationsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half A

Fileemd_56051_half_map_1.map
Annotationhalf A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half B

Fileemd_56051_half_map_2.map
Annotationhalf B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Cryo-EM Structure of the oligomeric LPOR:Chlide:NADPH Complexes HF-29

EntireName: Cryo-EM Structure of the oligomeric LPOR:Chlide:NADPH Complexes HF-29
Components
  • Complex: Cryo-EM Structure of the oligomeric LPOR:Chlide:NADPH Complexes HF-29
    • Protein or peptide: Light-dependent protochlorophyllide oxidoreductase, isoform B of Arabidopsis thaliana

-
Supramolecule #1: Cryo-EM Structure of the oligomeric LPOR:Chlide:NADPH Complexes HF-29

SupramoleculeName: Cryo-EM Structure of the oligomeric LPOR:Chlide:NADPH Complexes HF-29
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)

-
Macromolecule #1: Light-dependent protochlorophyllide oxidoreductase, isoform B of ...

MacromoleculeName: Light-dependent protochlorophyllide oxidoreductase, isoform B of Arabidopsis thaliana
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: protochlorophyllide reductase
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGS T AATSSPTV TK SVDGKKT LRK GNVVVT GASS GLGLA TAKAL AETG KWNVIM ACR DFLKAER AA KSVGMPKD S YTVMHLDLA SLDSVRQFVD NFRRTETPL D VLVCNAAV YF PTAKEPT YSA EGFELS VATN HLGHF ...String:
MGSSHHHHHH SSGLVPRGS T AATSSPTV TK SVDGKKT LRK GNVVVT GASS GLGLA TAKAL AETG KWNVIM ACR DFLKAER AA KSVGMPKD S YTVMHLDLA SLDSVRQFVD NFRRTETPL D VLVCNAAV YF PTAKEPT YSA EGFELS VATN HLGHF LLARL LLDD LKKSDY PSK RLIIVGS IT GNTNTLAG N VPPKANLGD LRGLAGGLNG LNSSAMIDG G DFDGAKAY KD SKVCNML TMQ EFHRRF HEET GVTFA SLYPG CIAS TGLFRE HIP LFRALFP PF QKYITKGY V SETESGKRL AQVVSDPSLT KSGVYWSWN N ASASFENQ LS EEASDVE KAR KVWEIS EKLV GLA

UniProtKB: Protochlorophyllide reductase B, chloroplastic

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

-
Sample preparation

BufferpH: 7.1
Component:
ConcentrationFormulaName
37.0 mMNa2HPO4sodium phosphate
225.0 mMNaClsodium chloride
150.0 mMimidazoleimidazole
5.0 mM2-mercaptoethanol2-mercaptoethanol
25.0 %glycerolglycerol
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 294 K / Instrument: FEI VITROBOT MARK III
Details28 uM AtPORB, 40 uM Chlorophyllide, 600 uM NADPH, 230 uM lipids (50mol% MGDG, 35mol% DGDG, 15mol% PG)

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 15.75 Å
Applied symmetry - Helical parameters - Δ&Phi: -22.240 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3) / Number images used: 176014
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7jk9

Final angle assignmentType: NOT APPLICABLE

-
Atomic model buiding 1

Initial modelPDB ID:

7jk9


Chain - Source name: PDB / Chain - Initial model type: experimental model / Details: initial model

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more