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- EMDB-46680: Rhodospirillum rubrum Nitrogenase-like Methylthio-alkane Reductas... -

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Basic information

Entry
Database: EMDB / ID: EMD-46680
TitleRhodospirillum rubrum Nitrogenase-like Methylthio-alkane Reductase Complex with an Oxidized P-cluster
Map data
Sample
  • Complex: Complex of marDK heterotetramer under dithionite reduced conditions
    • Protein or peptide: Nitrogenase
    • Protein or peptide: Nitrogenase
  • Ligand: FE(8)-S(7) CLUSTER
KeywordsMethylthio-alkane reductase / Carbon-Sulfur lyase / dimethylsulfide / methane / methanethiol / OXIDOREDUCTASE
Function / homology: / : / Nitrogenase/oxidoreductase, component 1 / Nitrogenase component 1 type Oxidoreductase / nitrogenase / nitrogenase activity / Nitrogenase / Nitrogenase
Function and homology information
Biological speciesRhodospirillum rubrum ATCC 11170 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.35 Å
AuthorsKreitler DF / Hu G / North JA
Funding support United States, 3 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)KP1607011 United States
Department of Energy (DOE, United States)DE-SC0022091 United States
Department of Energy (DOE, United States)DE-SC0024125 United States
CitationJournal: Nat Catal / Year: 2025
Title: Architecture, catalysis and regulation of methylthio-alkane reductase for bacterial sulfur acquisition from volatile organic compounds
Authors: Murali S / Hu GB / Kreitler DF / Carriedo AA / Lewis LC / Fosu SA / Weaver OG / Buzas EM / Byerly KM / Yoshikuni Y / McSweeney S / Shafaat HS / North JA
History
DepositionAug 21, 2024-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46680.png

Downloads & links

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Map

FileDownload / File: emd_46680.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.)
0.83 Å/pix.
x 400 pix.
= 330. Å		0.83 Å/pix.
x 400 pix.
= 330. Å		0.83 Å/pix.
x 400 pix.
= 330. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.3234393 - 0.7405876
Average (Standard dev.)0.00020965458 (±0.014414871)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 330.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_46680_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_46680_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of marDK heterotetramer under dithionite reduced conditions

EntireName: Complex of marDK heterotetramer under dithionite reduced conditions
Components
  • Complex: Complex of marDK heterotetramer under dithionite reduced conditions
    • Protein or peptide: Nitrogenase
    • Protein or peptide: Nitrogenase
  • Ligand: FE(8)-S(7) CLUSTER

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Supramolecule #1: Complex of marDK heterotetramer under dithionite reduced conditions

SupramoleculeName: Complex of marDK heterotetramer under dithionite reduced conditions
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Rhodospirillum rubrum ATCC 11170 (bacteria)
Molecular weightTheoretical: 228 KDa

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Macromolecule #1: Nitrogenase

MacromoleculeName: Nitrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: nitrogenase
Source (natural)Organism: Rhodospirillum rubrum ATCC 11170 (bacteria)
Molecular weightTheoretical: 57.613164 KDa
Recombinant expressionOrganism: Rhodospirillum rubrum ATCC 11170 (bacteria)
SequenceString: MPIHHHHHHQ HNLKTSVVES REQRLGTIIA WDGKASDLSK ESAYARSEGC GSACGAKARR VCEMRSPFSQ GSVCSEQMVE CQAGNVRGA VLVQHSPIGC GAGQVIYNSI FRNGLAIRGL PVENLHLIST NLRERDMVYG GLDKLERTIR DAWERHHPQA I FIATSCPT ...String:
MPIHHHHHHQ HNLKTSVVES REQRLGTIIA WDGKASDLSK ESAYARSEGC GSACGAKARR VCEMRSPFSQ GSVCSEQMVE CQAGNVRGA VLVQHSPIGC GAGQVIYNSI FRNGLAIRGL PVENLHLIST NLRERDMVYG GLDKLERTIR DAWERHHPQA I FIATSCPT AIIGDDIESV ASQLEAEFGI PVIPLHCEGF KSKHWSTGFD ATQHGILRQI VRKNPERKQE DLVNVINLWG SD VFGPMLG ELGLRVNYVV DLATVEDLAQ MSEAAATVGF CYTLSTYMAA ALEQEFGVPE VKAPMPYGFA GTDAWLREIA RVT HREEQA EAYIAREHAR VKPQLEALRE KLKGIKGFVS TGSAYAHGMI QVLRELGVTV DGSLVFHHDP VYDSQDPRQD SLAH LVDNY GDVGHFSVGN RQQFQFYGLL QRVKPDFIII RHNGLAPLAS RLGIPAIPLG DEHIAVGYQG ILNLGESILD VLAHR KFHE DIAAHVRLPY RQDWLARDPF DLARQSAGQP RRPAE

UniProtKB: Nitrogenase

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Macromolecule #2: Nitrogenase

MacromoleculeName: Nitrogenase / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: nitrogenase
Source (natural)Organism: Rhodospirillum rubrum ATCC 11170 (bacteria)
Molecular weightTheoretical: 50.856289 KDa
Recombinant expressionOrganism: Rhodospirillum rubrum ATCC 11170 (bacteria)
SequenceString: MPDAESRSQV TAKAAPPPAP KTNSIEQVRY ICSIGAMHSA SAIPRVIPIT HCGPGCADKQ FMNVAFYNGF QGGGYGGGAV VPSTNATER EVVFGGAERL DELIGASLQV LDADLFVVLT GCIPDLVGDD IGSVVGPYQK RGVPIVYAET GGFRGNNFTG H ELVTKAII ...String:
MPDAESRSQV TAKAAPPPAP KTNSIEQVRY ICSIGAMHSA SAIPRVIPIT HCGPGCADKQ FMNVAFYNGF QGGGYGGGAV VPSTNATER EVVFGGAERL DELIGASLQV LDADLFVVLT GCIPDLVGDD IGSVVGPYQK RGVPIVYAET GGFRGNNFTG H ELVTKAII DQFVGDYDAE RDGAREPHTV NVWSLLPYHN TFWRGDLTEI KRLLEGIGLK VNILFGPQSA GVAEWKAIPR AG FNLVLSP WLGLDTARHL DRKYGQPTLH RPIIPIGAKE TGAFLREVAA FAGLDSAVVE AFITAEEAVY YRYLEDFTDF YAE YWWGLP AKFAVIGDSA YNLALTKFLV NQLGLIPGLQ IITDNPPEEV REDIRAHYHA IADDVATDVS FEEDSYTIHQ KIRA TDFGH KAPILFGTTW ERDLAKELKG AIVEVGFPAS YEVVLSRSYL GYRGALTLLE KIYTTTVSAS A

UniProtKB: Nitrogenase

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Macromolecule #3: FE(8)-S(7) CLUSTER

MacromoleculeName: FE(8)-S(7) CLUSTER / type: ligand / ID: 3 / Number of copies: 2 / Formula: CLF
Molecular weightTheoretical: 671.215 Da
Chemical component information

ChemComp-CLF:
FE(8)-S(7) CLUSTER

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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

Concentration1.9 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
25.0 mMC4H11NO3Tris
100.0 mMNaClsodium chloride
2.0 mMNa2S2O4sodium dithionite
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 50 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Pressure: 4.0000000000000003e-07 kPa / Details: 30 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: 3.5ul sample was applied to a glow discharged UltrAuFoil grid, blotted for 3 or 4 seconds before plunged in liquid ethane cooled with liquid nitrogen..
DetailsThe sample was monodisperse, diluted with buffer from 7.5 mg/mL stock solution.

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 79.8 K / Max: 79.8 K
Specialist opticsSpherical aberration corrector: N/A. / Chromatic aberration corrector: N/A. / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 15 eV
DetailsSample was screened using negative staining and Cryo-EM on a screening microscope for sample readiness assessment before automated high-throughput and high-resolution data collection on Titan Krios. Multiple batches of Cryo-EM specimen were prepared in order to deal with the orientation preference. The calibrated minimum/maximum defocus were the calculated minimum and maximum of images that with contaminants or broken ice.
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 4840 / Average exposure time: 2.26 sec. / Average electron dose: 50.0 e/Å2
Details: Data was collected on a ThermoScientific Titan Krios G3i Cryo-TEM operated at 300kV and at a nominal 105,000 magnification using ThermoScientific EPU program with the defocus range of -1.0 ...Details: Data was collected on a ThermoScientific Titan Krios G3i Cryo-TEM operated at 300kV and at a nominal 105,000 magnification using ThermoScientific EPU program with the defocus range of -1.0 to -2.0 um . Image stack files were filtered with a BioQuantum energy filter at 15eV slit width and acquired with a Gatan K3 Direct Electron Detector and (Gatan, Pleasanton, CA, USA) in COunted Super-Resolution mode resulting pixel size 0.4125 angstrom. Total electron dose was 50 electrons. And each stack file consists of 40 frames.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.0100000000000002 µm / Calibrated defocus min: 0.214 µm / Calibrated magnification: 109454 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 6195342
CTF correctionSoftware - Name: cryoSPARC (ver. 4.2.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: SIMULTANEOUS ITERATIVE (SIRT) / Resolution.type: BY AUTHOR / Resolution: 2.35 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1)
Details: Final step was actually Non-uniform Refinement of two classes of an Ab Initio reconstruction.
Number images used: 149015
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 3 / Avg.num./class: 52958 / Software - Name: cryoSPARC (ver. 4.2.1)
Details: Ab Initio reconstructions and 3D classification had been performed prior to the final classification.

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model / Details: AlphaFold multimer
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9d9u:
Rhodospirillum rubrum Nitrogenase-like Methylthio-alkane Reductase Complex with an Oxidized P-cluster

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