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- EMDB-50553: Methylthio-alkane reductase complex -

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Basic information

Entry
Database: EMDB / ID: EMD-50553
TitleMethylthio-alkane reductase complex
Map datasharpened main map
Sample
  • Complex: Methylthio-alkane reductase complex
    • Protein or peptide: Nitrogenase
    • Protein or peptide: Nitrogenase
    • Protein or peptide: Nitrogenase iron protein
  • Ligand: FeFe cofactor
  • Ligand: FE(8)-S(7) CLUSTER
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ALUMINUM FLUORIDE
  • Ligand: IRON/SULFUR CLUSTER
KeywordsMethylthioethanol / dimethyl sulfide / ethylmethyl sulfide / methanethiol / ethylene / methane / ethane / metalloenzyme / OXIDOREDUCTASE
Function / homology
Function and homology information


nitrogenase / nitrogenase activity / 4 iron, 4 sulfur cluster binding / ATP binding / metal ion binding
Similarity search - Function
: / Nitrogenase iron protein NifH / 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 iron protein NifH / 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
Nitrogenase iron protein / Nitrogenase / Nitrogenase
Similarity search - Component
Biological speciesRhodospirillum rubrum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.71 Å
AuthorsLago-Maciel A / Zarzycki J / Prinz S / Reif-Trauttmansdorff T / Rebelein JG
Funding support Germany, 3 items
OrganizationGrant numberCountry
German Research Foundation (DFG)446841743 Germany
Max Planck Society Germany
Max Planck SocietyIMPRS - Principles of microbial life Germany
CitationJournal: To Be Published
Title: Structural characterization of the methylthio-alkane reductase from the nitrogenase family
Authors: Lago-Maciel A / Soares J / Zarzycki J / Prinz S / Reif-Trattmansdorff T / Schuller JM / Paczia N / Pierik AJ / Rebelein JG
History
DepositionJun 6, 2024-
Header (metadata) releaseSep 17, 2025-
Map releaseSep 17, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50553.png

Downloads & links

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Map

FileDownload / File: emd_50553.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened main map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.84 Å/pix.
x 380 pix.
= 318.06 Å		0.84 Å/pix.
x 380 pix.
= 318.06 Å		0.84 Å/pix.
x 380 pix.
= 318.06 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.837 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.75
Minimum - Maximum-19.061373 - 40.229908000000002
Average (Standard dev.)0.000877918 (±1.0002756)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 318.06 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map B

Fileemd_50553_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_50553_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Methylthio-alkane reductase complex

EntireName: Methylthio-alkane reductase complex
Components
  • Complex: Methylthio-alkane reductase complex
    • Protein or peptide: Nitrogenase
    • Protein or peptide: Nitrogenase
    • Protein or peptide: Nitrogenase iron protein
  • Ligand: FeFe cofactor
  • Ligand: FE(8)-S(7) CLUSTER
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ALUMINUM FLUORIDE
  • Ligand: IRON/SULFUR CLUSTER

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Supramolecule #1: Methylthio-alkane reductase complex

SupramoleculeName: Methylthio-alkane reductase complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / Details: 1:1 complex of catalytic core and reductase dimer
Source (natural)Organism: Rhodospirillum rubrum (bacteria)
Molecular weightTheoretical: 280 KDa

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Macromolecule #1: Nitrogenase

MacromoleculeName: Nitrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: nitrogenase
Source (natural)Organism: Rhodospirillum rubrum (bacteria)
Molecular weightTheoretical: 57.560164 KDa
Recombinant expressionOrganism: Rhodobacter capsulatus (bacteria)
SequenceString: MPINLKTSVV ESREQRLGTI IAWDGKASDL SKESAYARSE GCGSACGAKA RRVCEMRSPF SQGSVCSEQM VECQAGNVRG AVLVQHSPI GCGAGQVIYN SIFRNGLAIR GLPVENLHLI STNLRERDMV YGGLDKLERT IRDAWERHHP QAIFIATSCP T AIIGDDIE ...String:
MPINLKTSVV ESREQRLGTI IAWDGKASDL SKESAYARSE GCGSACGAKA RRVCEMRSPF SQGSVCSEQM VECQAGNVRG AVLVQHSPI GCGAGQVIYN SIFRNGLAIR GLPVENLHLI STNLRERDMV YGGLDKLERT IRDAWERHHP QAIFIATSCP T AIIGDDIE SVASQLEAEF GIPVIPLHCE GFKSKHWSTG FDATQHGILR QIVRKNPERK QEDLVNVINL WGSDVFGPML GE LGLRVNY VVDLATVEDL AQMSEAAATV GFCYTLSTYM AAALEQEFGV PEVKAPMPYG FAGTDAWLRE IARVTHREEQ AEA YIAREH ARVKPQLEAL REKLKGIKGF VSTGSAYAHG MIQVLRELGV TVDGSLVFHH DPVYDSQDPR QDSLAHLVDN YGDV GHFSV GNRQQFQFYG LLQRVKPDFI IIRHNGLAPL ASRLGIPAIP LGDEHIAVGY QGILNLGESI LDVLAHRKFH EDIAA HVRL PYRQDWLARD PFDLARQSAG QPRRPAEWSH PQFEK

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 (bacteria)
Molecular weightTheoretical: 50.856289 KDa
Recombinant expressionOrganism: Rhodobacter capsulatus (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: Nitrogenase iron protein

MacromoleculeName: Nitrogenase iron protein / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: nitrogenase
Source (natural)Organism: Rhodospirillum rubrum (bacteria)
Molecular weightTheoretical: 31.914785 KDa
Recombinant expressionOrganism: Rhodobacter capsulatus (bacteria)
SequenceString: MHHHHHHAKS PKQIAIYGKG GIGKSTTTSN ISAALAEAGY KVMQFGCDPK SDSTNTLRGG DYIPSVLDLL RENARVDAHE AIFQGFGGI YCVEAGGPAP GVGCAGRGII TAVELLKQQN VFEELDLDYV IFDVLGDVVC GGFAVPIREG IAEHVFTVSS S DFMAIYAA ...String:
MHHHHHHAKS PKQIAIYGKG GIGKSTTTSN ISAALAEAGY KVMQFGCDPK SDSTNTLRGG DYIPSVLDLL RENARVDAHE AIFQGFGGI YCVEAGGPAP GVGCAGRGII TAVELLKQQN VFEELDLDYV IFDVLGDVVC GGFAVPIREG IAEHVFTVSS S DFMAIYAA NNLFKGIQKY SNAGGALLGG VIANSINTDF HRDIIDDFVA RTQTQVVQYV PRSLTVTQAE LQGRTTIEAA PE SAQAEIY RTLARSIADH TDSKVPTPLN AQELRDWSAS WANQLIEIER ASQPIPALAS

UniProtKB: Nitrogenase iron protein

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Macromolecule #4: FeFe cofactor

MacromoleculeName: FeFe cofactor / type: ligand / ID: 4 / Number of copies: 1 / Formula: S5Q
Molecular weightTheoretical: 747.356 Da
Chemical component information

ChemComp-S5Q:
FeFe cofactor

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Macromolecule #5: FE(8)-S(7) CLUSTER

MacromoleculeName: FE(8)-S(7) CLUSTER / type: ligand / ID: 5 / Number of copies: 1 / Formula: CLF
Molecular weightTheoretical: 671.215 Da
Chemical component information

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

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Macromolecule #6: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #8: ALUMINUM FLUORIDE

MacromoleculeName: ALUMINUM FLUORIDE / type: ligand / ID: 8 / Number of copies: 2 / Formula: AF3
Molecular weightTheoretical: 83.977 Da
Chemical component information

ChemComp-AF3:
ALUMINUM FLUORIDE

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Macromolecule #9: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 9 / Number of copies: 1 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR 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

BufferpH: 7.8
GridModel: C-flat-2/1 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 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 opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.71 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4) / Number images used: 116370
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 4.4)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 4.4)
Final 3D classificationNumber classes: 25 / Software - Name: cryoSPARC (ver. 4.4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9fmg:
Methylthio-alkane reductase complex

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