[English] 日本語
Yorodumi
- EMDB-47669: CryoEM structure of BchN-BchB bound to Pchlide from the DPOR unde... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-47669
TitleCryoEM structure of BchN-BchB bound to Pchlide from the DPOR under turnover complex dataset
Map data
Sample
  • Complex: CryoEM structure of BchN-BchB bound to Pchlide from the DPOR under turnover complex dataset
    • Protein or peptide: Light-independent protochlorophyllide reductase subunit N
    • Protein or peptide: Light-independent protochlorophyllide reductase subunit B
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: Protochlorophyllide
  • Ligand: COPPER (II) ION
KeywordsPlant Protein / Electron transfer Enzymes / Photosynthesis / Oxidoreductase
Function / homology
Function and homology information


ferredoxin:protochlorophyllide reductase (ATP-dependent) / photosynthesis, dark reaction / light-independent bacteriochlorophyll biosynthetic process / oxidoreductase activity, acting on iron-sulfur proteins as donors / oxidoreductase activity, acting on the CH-CH group of donors, iron-sulfur protein as acceptor / 4 iron, 4 sulfur cluster binding / ATP binding / metal ion binding
Similarity search - Function
Light-independent protochlorophyllide reductase, N subunit / : / Light-independent protochlorophyllide reductase, B subunit / Protochlorophyllide reductase, ChlB, light independent / Light-independent protochlorophyllide reductase subunit B-like, C-terminal / Proto-chlorophyllide reductase, C-terminal / Proto-chlorophyllide reductase 57 kD subunit / : / Nitrogenase/oxidoreductase, component 1 / Nitrogenase component 1 type Oxidoreductase
Similarity search - Domain/homology
Light-independent protochlorophyllide reductase subunit N / Light-independent protochlorophyllide reductase subunit B
Similarity search - Component
Biological speciesCereibacter sphaeroides (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.29 Å
AuthorsKashyap R / Antony E
Funding support United States, 1 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0020965 United States
CitationJournal: Nat Commun / Year: 2025
Title: Cryo-EM captures the coordination of asymmetric electron transfer through a di-copper site in DPOR.
Authors: Rajnandani Kashyap / Natalie Walsh / Jaigeeth Deveryshetty / Monika Tokmina-Lukaszewska / Kewei Zhao / Yunqiao J Gan / Brian M Hoffman / Ritimukta Sarangi / Brian Bothner / Brian Bennett / Edwin Antony /
Abstract: Enzymes that catalyze long-range electron transfer (ET) reactions often function as higher order complexes that possess two structurally symmetrical halves. The functional advantages for such an ...Enzymes that catalyze long-range electron transfer (ET) reactions often function as higher order complexes that possess two structurally symmetrical halves. The functional advantages for such an architecture remain a mystery. Using cryoelectron microscopy we capture snapshots of the nitrogenase-like dark-operative protochlorophyllide oxidoreductase (DPOR) during substrate binding and turnover. DPOR catalyzes reduction of the C17 = C18 double bond in protochlorophyllide during the dark chlorophyll biosynthetic pathway. DPOR is composed of electron donor (L-protein) and acceptor (NB-protein) component proteins that transiently form a complex in the presence of ATP to facilitate ET. NB-protein is an αβ heterotetramer with two structurally identical halves. However, our structures reveal that NB-protein becomes functionally asymmetric upon substrate binding. Asymmetry results in allosteric inhibition of L-protein engagement and ET in one half. Residues that form a conduit for ET are aligned in one half while misaligned in the other. An ATP hydrolysis-coupled conformational switch is triggered once ET is accomplished in one half. These structural changes are then relayed to the other half through a di-nuclear copper center at the tetrameric interface of the NB-protein and leads to activation of ET and substrate reduction. These findings provide a mechanistic blueprint for regulation of long-range electron transfer reactions.
History
DepositionNov 1, 2024-
Header (metadata) releaseMay 7, 2025-
Map releaseMay 7, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_47669.png

Downloads & links

-
Map

FileDownload / File: emd_47669.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 480 pix.
= 393.6 Å		0.82 Å/pix.
x 480 pix.
= 393.6 Å		0.82 Å/pix.
x 480 pix.
= 393.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0954
Minimum - Maximum-0.6888451 - 1.459746
Average (Standard dev.)-0.00015222064 (±0.015922023)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 393.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_47669_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_47669_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : CryoEM structure of BchN-BchB bound to Pchlide from the DPOR unde...

EntireName: CryoEM structure of BchN-BchB bound to Pchlide from the DPOR under turnover complex dataset
Components
  • Complex: CryoEM structure of BchN-BchB bound to Pchlide from the DPOR under turnover complex dataset
    • Protein or peptide: Light-independent protochlorophyllide reductase subunit N
    • Protein or peptide: Light-independent protochlorophyllide reductase subunit B
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: Protochlorophyllide
  • Ligand: COPPER (II) ION

-
Supramolecule #1: CryoEM structure of BchN-BchB bound to Pchlide from the DPOR unde...

SupramoleculeName: CryoEM structure of BchN-BchB bound to Pchlide from the DPOR under turnover complex dataset
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Cereibacter sphaeroides (bacteria)
Molecular weightTheoretical: 236 KDa

-
Macromolecule #1: Light-independent protochlorophyllide reductase subunit N

MacromoleculeName: Light-independent protochlorophyllide reductase subunit N
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
EC number: ferredoxin:protochlorophyllide reductase (ATP-dependent)
Source (natural)Organism: Cereibacter sphaeroides (bacteria)
Molecular weightTheoretical: 46.188773 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSLDLPPPPA RGCRSTEVLK ERGQREVFCG LTGIIWLHRK MQDAFFLVVG SRTCAHLLQS AAGVMIFAEP RFGTAVLEEK DLAGLADAN AELDREVDRL LARRPDIRQL FLVGSCPSEV IKLDLHRAAE RLSAHHGPAV RVYNFSGSGI ETTFTQGEDA C LASIVPTL ...String:
MSLDLPPPPA RGCRSTEVLK ERGQREVFCG LTGIIWLHRK MQDAFFLVVG SRTCAHLLQS AAGVMIFAEP RFGTAVLEEK DLAGLADAN AELDREVDRL LARRPDIRQL FLVGSCPSEV IKLDLHRAAE RLSAHHGPAV RVYNFSGSGI ETTFTQGEDA C LASIVPTL PATEARELLL VGALPDVVED QAVSLLTQLG IGPVRCLPAH HAAEAPGVGP NTVFALVQPF LGDTHGALTR RG ARHIAAP FPFGEEGTTL WLKAIADEFG VSAETFEAVT AAPRARARKA VAAASEGLRG KSVFFLPDSQ LEPSLARFLT REC GMSAVE VGTPFLHRGI LGPDLDLLAE GPVLSEGQDV ERQLDRVRAA RPDLTVCGLG LANPLEAEGF TTKWAIELVF TPVH FYEQA GDLAGLFSRP VRRRAILRRE AAE

UniProtKB: Light-independent protochlorophyllide reductase subunit N

-
Macromolecule #2: Light-independent protochlorophyllide reductase subunit B

MacromoleculeName: Light-independent protochlorophyllide reductase subunit B
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
EC number: ferredoxin:protochlorophyllide reductase (ATP-dependent)
Source (natural)Organism: Cereibacter sphaeroides (bacteria)
Molecular weightTheoretical: 58.374266 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKLTLWTYEG PPHVGAMRVA TGMTGMHYVL HAPQGDTYAD LLFTMIERRG KRPPVSYTTF QARDLGSDTA ELFQSACRDA YERFQPQAI MVGSSCTAEL IQDDTGGLAD ALSLPVPVVH LELPSYQRKE NFGADESFLQ ICRKLARPME RTEKVSCNLL G PTALGFRH ...String:
MKLTLWTYEG PPHVGAMRVA TGMTGMHYVL HAPQGDTYAD LLFTMIERRG KRPPVSYTTF QARDLGSDTA ELFQSACRDA YERFQPQAI MVGSSCTAEL IQDDTGGLAD ALSLPVPVVH LELPSYQRKE NFGADESFLQ ICRKLARPME RTEKVSCNLL G PTALGFRH RDDILEVTRL LEGMGIAVNA VAPMGASPAD IARLGAAHFN VLLYPETGES AARWAEKTLK QPYTKTVPIG VG ATRDFVA EVAALAGVAP VADDSRLRQP WWSASVDSTY LTGKRVFLFG DATHVIAAAR VARDEMGFEV VGMGCYNREF ARP MRAAAK GYGLEALVTD DYLEVEEAIQ ALAPELILGT QMERHIAKRL GIPCAVISAP VHVQDFPARY SPQMGFEGAN VLFD TWIHP LTMGLEEHLL TMFREDFEFH DEAGPSHHGG KAVPASAPRA DEAAEALPAT GAETAEGGSI PPEAVPPAAA AAAEA PAGE IVWLTDAERE LKKIPFFVRG KARRNTEKFA AEKGLTRISI ETLYEAKAHY AR

UniProtKB: Light-independent protochlorophyllide reductase subunit B

-
Macromolecule #3: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 3 / Number of copies: 2 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

-
Macromolecule #4: Protochlorophyllide

MacromoleculeName: Protochlorophyllide / type: ligand / ID: 4 / Number of copies: 2 / Formula: PMR
Molecular weightTheoretical: 612.957 Da
Chemical component information

ChemComp-PMR:
Protochlorophyllide

-
Macromolecule #5: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 69816
Initial angle assignmentType: NOT APPLICABLE
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