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- EMDB-44913: CryoEM structure of DPOR in the presence of ADP-AlF3 -

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Basic information

Entry
Database: EMDB / ID: EMD-44913
TitleCryoEM structure of DPOR in the presence of ADP-AlF3
Map data
Sample
  • Complex: CryoEM structure of DPOR in the presence of ADP-AlF3
    • Protein or peptide: Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein
    • 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, iron-sulphur ATP-binding protein / 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 / NifH/frxC family / NifH/chlL conserved site ...Light-independent protochlorophyllide reductase, iron-sulphur ATP-binding protein / 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 / NifH/frxC family / NifH/chlL conserved site / 4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family / NifH/frxC family signature 2. / NifH/frxC family signature 1. / NIFH_FRXC family profile. / Nitrogenase/oxidoreductase, component 1 / : / Nitrogenase component 1 type Oxidoreductase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Light-independent protochlorophyllide reductase subunit N / Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / Light-independent protochlorophyllide reductase subunit B
Similarity search - Component
Biological speciesCereibacter sphaeroides (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.68 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
DepositionMay 17, 2024-
Header (metadata) releaseMay 7, 2025-
Map releaseMay 7, 2025-
UpdateMay 7, 2025-
Current statusMay 7, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44913.png

Downloads & links

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Map

FileDownload / File: emd_44913.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

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0635
Minimum - Maximum-0.30777338 - 0.7845346
Average (Standard dev.)0.00008371582 (±0.012476651)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Half map: #2

Fileemd_44913_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_44913_half_map_2.map
Projections & Slices
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Sample components

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Entire : CryoEM structure of DPOR in the presence of ADP-AlF3

EntireName: CryoEM structure of DPOR in the presence of ADP-AlF3
Components
  • Complex: CryoEM structure of DPOR in the presence of ADP-AlF3
    • Protein or peptide: Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein
    • 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

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Supramolecule #1: CryoEM structure of DPOR in the presence of ADP-AlF3

SupramoleculeName: CryoEM structure of DPOR in the presence of ADP-AlF3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Cereibacter sphaeroides (bacteria)
Molecular weightTheoretical: 347.8 KDa

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Macromolecule #1: Light-independent protochlorophyllide reductase iron-sulfur ATP-b...

MacromoleculeName: Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
EC number: ferredoxin:protochlorophyllide reductase (ATP-dependent)
Source (natural)Organism: Cereibacter sphaeroides (bacteria)
Molecular weightTheoretical: 34.85034 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SQDPENLYFQ SMSPKDLTIP TGADGEGSVQ VHLDEADKIT GAKVFAVYGK GGIGKSTTSS NLSAAFSILG KRVLQIGCD PKHDSTFTLT GSLVPTVIDV LKDVDFHPEE LRPEDFVFEG FNGVMCVEAG GPPAGTGCGG YVVGQTVKLL K QHHLLDDT ...String:
MGSSHHHHHH SQDPENLYFQ SMSPKDLTIP TGADGEGSVQ VHLDEADKIT GAKVFAVYGK GGIGKSTTSS NLSAAFSILG KRVLQIGCD PKHDSTFTLT GSLVPTVIDV LKDVDFHPEE LRPEDFVFEG FNGVMCVEAG GPPAGTGCGG YVVGQTVKLL K QHHLLDDT DVVIFDVLGD VVCGGFAAPL QHADQAVVVT ANDFDSIYAM NRIIAAVQAK SKNYKVRLAG CVANRSRATD EV DRFCKET NFRRLAHMPD LDAIRRSRLK KKTLFEMDED QDVLAARAEY IRLAESLWRG LDPIDPHSLP DREIFELLGF D

UniProtKB: Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein

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Macromolecule #2: Light-independent protochlorophyllide reductase subunit N

MacromoleculeName: Light-independent protochlorophyllide reductase subunit N
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: 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

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Macromolecule #3: Light-independent protochlorophyllide reductase subunit B

MacromoleculeName: Light-independent protochlorophyllide reductase subunit B
type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
EC number: ferredoxin:protochlorophyllide reductase (ATP-dependent)
Source (natural)Organism: Cereibacter sphaeroides (bacteria)
Molecular weightTheoretical: 58.302234 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 DEAAEALPLT GAETAEGGSI PPEAVPPAEA AAVPA GEIV WLTDAERELK KIPFFVRGKA RRNTEKFAAE KGLTRISLET LYEAKAHYAR

UniProtKB: Light-independent protochlorophyllide reductase subunit B

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Macromolecule #4: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 4 / Number of copies: 4 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #5: Protochlorophyllide

MacromoleculeName: Protochlorophyllide / type: ligand / ID: 5 / Number of copies: 2 / Formula: PMR
Molecular weightTheoretical: 612.957 Da
Chemical component information

ChemComp-PMR:
Protochlorophyllide

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Macromolecule #6: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

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

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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

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.68 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 20571
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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