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- EMDB-43443: CryoEM structure of BchN-BchB electron acceptor component protein... -

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Basic information

Entry
Database: EMDB / ID: EMD-43443
TitleCryoEM structure of BchN-BchB electron acceptor component protein of DPOR
Map data
Sample
  • Complex: CryoEM structure of BchN-BchB electron acceptor component protein of DPOR
    • Protein or peptide: Light-independent protochlorophyllide reductase subunit N
    • Protein or peptide: Light-independent protochlorophyllide reductase subunit B
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: COPPER (II) ION
  • Ligand: water
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 / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors ...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 / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / SUMOylation of transcription cofactors / Postmitotic nuclear pore complex (NPC) reformation / septin ring / SUMOylation of DNA damage response and repair proteins / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of DNA replication proteins / SUMOylation of SUMOylation proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SUMOylation of RNA binding proteins / SUMOylation of chromatin organization proteins / ubiquitin-like protein ligase binding / protein sumoylation / condensed nuclear chromosome / protein tag activity / 4 iron, 4 sulfur cluster binding / ATP binding / metal ion binding / identical protein binding / nucleus
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 ...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 / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Light-independent protochlorophyllide reductase subunit N / Ubiquitin-like protein SMT3 / Light-independent protochlorophyllide reductase subunit B
Similarity search - Component
Biological speciesCereibacter sphaeroides (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 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
DepositionJan 18, 2024-
Header (metadata) releaseApr 30, 2025-
Map releaseApr 30, 2025-
UpdateMay 7, 2025-
Current statusMay 7, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43443.png

Downloads & links

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Map

FileDownload / File: emd_43443.map.gz / Format: CCP4 / Size: 244.1 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 400 pix.
= 328. Å		0.82 Å/pix.
x 400 pix.
= 328. Å		0.82 Å/pix.
x 400 pix.
= 328. 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: 0.204
Minimum - Maximum-1.2022455 - 1.8073447
Average (Standard dev.)-0.00023640023 (±0.031445097)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 328.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_43443_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_43443_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : CryoEM structure of BchN-BchB electron acceptor component protein...

EntireName: CryoEM structure of BchN-BchB electron acceptor component protein of DPOR
Components
  • Complex: CryoEM structure of BchN-BchB electron acceptor component protein of DPOR
    • Protein or peptide: Light-independent protochlorophyllide reductase subunit N
    • Protein or peptide: Light-independent protochlorophyllide reductase subunit B
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: COPPER (II) ION
  • Ligand: water

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Supramolecule #1: CryoEM structure of BchN-BchB electron acceptor component protein...

SupramoleculeName: CryoEM structure of BchN-BchB electron acceptor component protein of DPOR
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Cereibacter sphaeroides (bacteria)
Molecular weightTheoretical: 236 KDa

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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 BL21(DE3) (bacteria)
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 #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: 69.448922 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSDSEVNQEA KPEVKPEVKP ETHINLKVSD GSSEIFFKIK KTTPLRRLME AFAKRQGKEM DSLRFLYDGI RIQADQTPED LDMEDNDII EAHREQIMKL TLWTYEGPPH VGAMRVATGM TGMHYVLHAP QGDTYADLLF TMIERRGKRP PVSYTTFQAR D LGSDTAEL ...String:
MSDSEVNQEA KPEVKPEVKP ETHINLKVSD GSSEIFFKIK KTTPLRRLME AFAKRQGKEM DSLRFLYDGI RIQADQTPED LDMEDNDII EAHREQIMKL TLWTYEGPPH VGAMRVATGM TGMHYVLHAP QGDTYADLLF TMIERRGKRP PVSYTTFQAR D LGSDTAEL FQSACRDAYE RFQPQAIMVG SSCTAELIQD DTGGLADALS LPVPVVHLEL PSYQRKENFG ADESFLQICR KL ARPMERT EKVSCNLLGP TALGFRHRDD ILEVTRLLEG MGIAVNAVAP MGASPADIAR LGAAHFNVLL YPETGESAAR WAE KTLKQP YTKTVPIGVG ATRDFVAEVA ALAGVAPVAD DSRLRQPWWS ASVDSTYLTG KRVFLFGDAT HVIAAARVAR DEMG FEVVG MGCYNREFAR PMRAAAKGYG LEALVTDDYL EVEEAIQALA PELILGTQME RHIAKRLGIP CAVISAPVHV QDFPA RYSP QMGFEGANVL FDTWIHPLTM GLEEHLLTMF REDFEFHDEA GPSHHGGKAV PASAPRADEA AEALPLTGAE TAEGGS IPP EAVPPAEAAA VPAGEIVWLT DAERELKKIP FFVRGKARRN TEKFAAEKGL TRISLETLYE AKAHYAR

UniProtKB: Ubiquitin-like protein SMT3, Light-independent protochlorophyllide reductase subunit B

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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

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Macromolecule #4: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 160048
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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