[English] 日本語
Yorodumi
- EMDB-22364: Helical filaments of plant light-dependent protochlorophyllide ox... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-22364
TitleHelical filaments of plant light-dependent protochlorophyllide oxidoreductase (LPOR) bound to NADPH, Pchlide, and membrane
Map dataRELION sharpened map (B factor -97) with local symmetry and then helical symmetry applied to the entire map
Sample
  • Complex: light-dependent protochlorophyllide oxidoreductase bound to NADPH, Pchlide, and lipid membrane
    • Protein or peptide: Protochlorophyllide reductase B, chloroplastic
  • Ligand: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: Protochlorophyllide
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
Keywordsreductase / light-activated / ligand-protein complex / PHOTOSYNTHESIS
Function / homology
Function and homology information


protochlorophyllide reductase / protochlorophyllide reductase activity / chloroplast outer membrane / response to ethylene / chlorophyll biosynthetic process / chloroplast thylakoid / chloroplast envelope / chloroplast thylakoid membrane / photosynthesis / chloroplast ...protochlorophyllide reductase / protochlorophyllide reductase activity / chloroplast outer membrane / response to ethylene / 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: 3.1 Å
AuthorsNguyen HC / Gabruk M
Funding support Poland, United States, 3 items
OrganizationGrant numberCountry
Foundation for Polish Science024.2018 Poland
Ministry of Science and Higher Education (Poland)PPN/BEK/2018/1/00105 Poland
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1DP2GM110772-01 United States
CitationJournal: Nat Plants / Year: 2021
Title: Photocatalytic LPOR forms helical lattices that shape membranes for chlorophyll synthesis.
Authors: Henry C Nguyen / Arthur A Melo / Jerzy Kruk / Adam Frost / Michal Gabruk /
Abstract: Chlorophyll biosynthesis, crucial to life on Earth, is tightly regulated because its precursors are phototoxic. In flowering plants, the enzyme light-dependent protochlorophyllide oxidoreductase ...Chlorophyll biosynthesis, crucial to life on Earth, is tightly regulated because its precursors are phototoxic. In flowering plants, the enzyme light-dependent protochlorophyllide oxidoreductase (LPOR) captures photons to catalyse the penultimate reaction: the reduction of a double bond within protochlorophyllide (Pchlide) to generate chlorophyllide (Chlide). In darkness, LPOR oligomerizes to facilitate photon energy transfer and catalysis. However, the complete three-dimensional structure of LPOR, the higher-order architecture of LPOR oligomers and the implications of these self-assembled states for catalysis, including how LPOR positions Pchlide and the co-factor NADPH, remain unknown. Here, we report the atomic structure of LPOR assemblies by electron cryo-microscopy. LPOR polymerizes with its substrates into helical filaments around constricted lipid bilayer tubes. Portions of LPOR and Pchlide insert into the outer membrane leaflet, targeting the product, Chlide, to the membrane for the final reaction site of chlorophyll biosynthesis. In addition to its crucial photocatalytic role, we show that in darkness LPOR filaments directly shape membranes into high-curvature tubules with the spectral properties of the prolamellar body, whose light-triggered disassembly provides lipids for thylakoid assembly. Moreover, our structure of the catalytic site challenges previously proposed reaction mechanisms. Together, our results reveal a new and unexpected synergy between photosynthetic membrane biogenesis and chlorophyll synthesis in plants, orchestrated by LPOR.
History
DepositionJul 28, 2020-
Header (metadata) releaseMar 17, 2021-
Map releaseMar 17, 2021-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.005
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.005
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7jk9
  • Surface level: 0.005
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7jk9
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22364.png

Downloads & links

-
Map

FileDownload / File: emd_22364.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRELION sharpened map (B factor -97) with local symmetry and then helical symmetry applied to the entire map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 384 pix.
= 427.52 Å		1.11 Å/pix.
x 384 pix.
= 427.52 Å		1.11 Å/pix.
x 384 pix.
= 427.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.11333 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005 / Movie #1: 0.005
Minimum - Maximum-0.012325817 - 0.021030618
Average (Standard dev.)0.000017081938 (±0.0013632152)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 427.51987 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11333333333331.11333333333331.1133333333333
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z427.520427.520427.520
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0120.0210.000

-
Supplemental data

-
Mask #1

Fileemd_22364_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: RELION sharpened map (B factor -97) with central Z of 40%

Fileemd_22364_additional_1.map
AnnotationRELION sharpened map (B factor -97) with central Z of 40%
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: RELION Refine3D summed and filtered map with central Z of 40%

Fileemd_22364_additional_2.map
AnnotationRELION Refine3D summed and filtered map with central Z of 40%
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: RELION Refine3D unfiltered half map with central Z of 40%

Fileemd_22364_half_map_1.map
AnnotationRELION Refine3D unfiltered half map with central Z of 40%
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: RELION Refine3D unfiltered half map with central Z of 40%

Fileemd_22364_half_map_2.map
AnnotationRELION Refine3D unfiltered half map with central Z of 40%
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : light-dependent protochlorophyllide oxidoreductase bound to NADPH...

EntireName: light-dependent protochlorophyllide oxidoreductase bound to NADPH, Pchlide, and lipid membrane
Components
  • Complex: light-dependent protochlorophyllide oxidoreductase bound to NADPH, Pchlide, and lipid membrane
    • Protein or peptide: Protochlorophyllide reductase B, chloroplastic
  • Ligand: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: Protochlorophyllide
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

-
Supramolecule #1: light-dependent protochlorophyllide oxidoreductase bound to NADPH...

SupramoleculeName: light-dependent protochlorophyllide oxidoreductase bound to NADPH, Pchlide, and lipid membrane
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)

-
Macromolecule #1: Protochlorophyllide reductase B, chloroplastic

MacromoleculeName: Protochlorophyllide reductase B, chloroplastic / type: protein_or_peptide / ID: 1 / Number of copies: 40 / Enantiomer: LEVO / EC number: protochlorophyllide reductase
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 43.415199 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MALQAASLVS SAFSVRKDAK LNASSSSFKD SSLFGASITD QIKSEHGSSS LRFKREQSLR NLAIRAQTAA TSSPTVTKSV DGKKTLRKG NVVVTGASSG LGLATAKALA ETGKWNVIMA CRDFLKAERA AKSVGMPKDS YTVMHLDLAS LDSVRQFVDN F RRTETPLD ...String:
MALQAASLVS SAFSVRKDAK LNASSSSFKD SSLFGASITD QIKSEHGSSS LRFKREQSLR NLAIRAQTAA TSSPTVTKSV DGKKTLRKG NVVVTGASSG LGLATAKALA ETGKWNVIMA CRDFLKAERA AKSVGMPKDS YTVMHLDLAS LDSVRQFVDN F RRTETPLD VLVCNAAVYF PTAKEPTYSA EGFELSVATN HLGHFLLARL LLDDLKKSDY PSKRLIIVGS ITGNTNTLAG NV PPKANLG DLRGLAGGLN GLNSSAMIDG GDFDGAKAYK DSKVCNMLTM QEFHRRFHEE TGVTFASLYP GCIASTGLFR EHI PLFRAL FPPFQKYITK GYVSETESGK RLAQVVSDPS LTKSGVYWSW NNASASFENQ LSEEASDVEK ARKVWEISEK LVGL A

UniProtKB: Protochlorophyllide reductase B, chloroplastic

-
Macromolecule #2: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

MacromoleculeName: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
type: ligand / ID: 2 / Number of copies: 40 / Formula: NDP
Molecular weightTheoretical: 745.421 Da
Chemical component information

ChemComp-NDP:
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

-
Macromolecule #3: Protochlorophyllide

MacromoleculeName: Protochlorophyllide / type: ligand / ID: 3 / Number of copies: 40 / Formula: PMR
Molecular weightTheoretical: 612.957 Da
Chemical component information

ChemComp-PMR:
Protochlorophyllide

-
Macromolecule #4: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 4 / Number of copies: 40 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

ChemComp-LMG:
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 7.1
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 73.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 43.1 Å
Applied symmetry - Helical parameters - Δ&Phi: 50.34 °
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 17898
Segment selectionNumber selected: 294156 / Software - Name: crYOLO
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

+
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