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- EMDB-16890: Iron Nitrogenase Complex from Rhodobacter capsulatus -

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Basic information

Entry
Database: EMDB / ID: EMD-16890
TitleIron Nitrogenase Complex from Rhodobacter capsulatus
Map data
Sample
  • Complex: Iron Nitrogenase Complex from Rhodobacter capsulatus
    • Protein or peptide: x 4 types
  • Ligand: x 8 types
Keywordsnitrogen fixation / Fe nitrogenase / OXIDOREDUCTASE
Function / homology
Function and homology information


nitrogenase / nitrogenase activity / iron-sulfur cluster binding / 4 iron, 4 sulfur cluster binding / iron ion binding / ATP binding / metal ion binding
Similarity search - Function
Nitrogenase iron-iron, delta subunit / Nitrogenase iron-iron protein, alpha chain / Nitrogenase iron-iron, beta subunit / Vanadium/alternative nitrogenase delta subunit / Vanadium/alternative nitrogenase delta subunit / Nitrogenase alpha chain / Nitrogenase iron protein NifH / NifH/frxC family / NifH/chlL conserved site / 4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family ...Nitrogenase iron-iron, delta subunit / Nitrogenase iron-iron protein, alpha chain / Nitrogenase iron-iron, beta subunit / Vanadium/alternative nitrogenase delta subunit / Vanadium/alternative nitrogenase delta subunit / Nitrogenase alpha chain / 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 component 1, alpha chain / Nitrogenase component 1, conserved site / Nitrogenases component 1 alpha and beta subunits signature 2. / Nitrogenases component 1 alpha and beta subunits signature 1. / : / Nitrogenase/oxidoreductase, component 1 / Nitrogenase component 1 type Oxidoreductase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Nitrogenase iron protein / Nitrogenase protein alpha chain / Nitrogenase iron-iron protein delta chain / Nitrogenase iron-iron protein, beta subunit
Similarity search - Component
Biological speciesRhodobacter capsulatus SB 1003 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.35 Å
AuthorsSchmidt FV / Schulz L / Zarzycki J / Prinz S / Erb TJ / Rebelein JG
Funding support Germany, 2 items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research Foundation (DFG)446841743 Germany
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Structural insights into the iron nitrogenase complex.
Authors: Frederik V Schmidt / Luca Schulz / Jan Zarzycki / Simone Prinz / Niels N Oehlmann / Tobias J Erb / Johannes G Rebelein /
Abstract: Nitrogenases are best known for catalyzing the reduction of dinitrogen to ammonia at a complex metallic cofactor. Recently, nitrogenases were shown to reduce carbon dioxide (CO) and carbon monoxide ...Nitrogenases are best known for catalyzing the reduction of dinitrogen to ammonia at a complex metallic cofactor. Recently, nitrogenases were shown to reduce carbon dioxide (CO) and carbon monoxide to hydrocarbons, offering a pathway to recycle carbon waste into hydrocarbon products. Among the three nitrogenase isozymes, the iron nitrogenase has the highest wild-type activity for the reduction of CO, but the molecular architecture facilitating these activities has remained unknown. Here, we report a 2.35-Å cryogenic electron microscopy structure of the ADP·AlF-stabilized iron nitrogenase complex from Rhodobacter capsulatus, revealing an [FeSC-(R)-homocitrate] cluster in the active site. The enzyme complex suggests that the iron nitrogenase G subunit is involved in cluster stabilization and substrate channeling and confers specificity between nitrogenase reductase and catalytic component proteins. Moreover, the structure highlights a different interface between the two catalytic halves of the iron and the molybdenum nitrogenase, potentially influencing the intrasubunit 'communication' and thus the nitrogenase mechanism.
History
DepositionMar 22, 2023-
Header (metadata) releaseOct 4, 2023-
Map releaseOct 4, 2023-
UpdateJan 31, 2024-
Current statusJan 31, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16890.png

Downloads & links

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Map

FileDownload / File: emd_16890.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 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: 0.4
Minimum - Maximum-1.6395406 - 2.851253
Average (Standard dev.)0.001391248 (±0.07876448)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
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: #1

Fileemd_16890_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_16890_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 : Iron Nitrogenase Complex from Rhodobacter capsulatus

EntireName: Iron Nitrogenase Complex from Rhodobacter capsulatus
Components
  • Complex: Iron Nitrogenase Complex from Rhodobacter capsulatus
    • Protein or peptide: Nitrogenase protein alpha chain
    • Protein or peptide: Nitrogenase iron-iron protein delta chain
    • Protein or peptide: Nitrogenase iron-iron protein, beta subunit
    • Protein or peptide: Nitrogenase iron protein
  • Ligand: FeFe cofactor
  • Ligand: 3-HYDROXY-3-CARBOXY-ADIPIC ACID
  • Ligand: FE(8)-S(7) CLUSTER
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ALUMINUM FLUORIDE
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: water

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Supramolecule #1: Iron Nitrogenase Complex from Rhodobacter capsulatus

SupramoleculeName: Iron Nitrogenase Complex from Rhodobacter capsulatus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria)
Molecular weightTheoretical: 360 KDa

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Macromolecule #1: Nitrogenase protein alpha chain

MacromoleculeName: Nitrogenase protein alpha chain / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria)
Molecular weightTheoretical: 60.221117 KDa
Recombinant expressionOrganism: Rhodobacter capsulatus SB 1003 (bacteria)
SequenceString: MPYHEFEVSK CIPERREHAV MKAAGEDLTS CLPKGYLNTI PGTISERGCA YCGAKHVIGT PMKDVIHISH GPNGCTYDTW QTKRYISDN DNFQLKYTFA TDVKEKHVVF GAEGLLKKSM HEAFDAFPNI KRMTVYQTCT TALIGDDVDA IAKEVMEERG D VDVFVCNS ...String:
MPYHEFEVSK CIPERREHAV MKAAGEDLTS CLPKGYLNTI PGTISERGCA YCGAKHVIGT PMKDVIHISH GPNGCTYDTW QTKRYISDN DNFQLKYTFA TDVKEKHVVF GAEGLLKKSM HEAFDAFPNI KRMTVYQTCT TALIGDDVDA IAKEVMEERG D VDVFVCNS PGFAGPSQSG GHHKINIAWL NQKVGTVEPD YLGEHVINYV GEYNIQGDQE VMIDYFNRMG IQVLSTFTGN GS YDSLRMM HRAHLNVLEC ARSAEYICDE LRARYGIPRL DIDGFGFEPL ANSLRKVALF FGIEDKAEAI IAEEYAKWKP QLD WYKERL KGKKVCLWPG GSKLWHWAHA IEEEMGLKVV SVYTKFGHQG DMEKGVSRCG EGALAIDDPN ELESVEAIEM LKPD IIFTG KRPGEFVKKH GVPYLNAHAY HNGPYKGFEG WVRFARDIYN AIYSPMRQLA ALDISAPDAA ITSGFRTAKM NADLT VSDE VKFSEVLHEY TGKYDSIAEI RARNQAYAAE QKALRDAVQP AAEWSHPQFE K

UniProtKB: Nitrogenase protein alpha chain

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Macromolecule #2: Nitrogenase iron-iron protein delta chain

MacromoleculeName: Nitrogenase iron-iron protein delta chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: nitrogenase
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria)
Molecular weightTheoretical: 13.414546 KDa
Recombinant expressionOrganism: Rhodobacter capsulatus SB 1003 (bacteria)
SequenceString:
MTDISEKLDP LVDYIMKNCL WQFNSRGWDR LKQNAGILSQ TCEILCGEEP VHETAMDRCY WVDAVILSRA YKARFPWLMA MTKPEIKSL FKALHEKIDH LTVHGSLNTE LTVPHY

UniProtKB: Nitrogenase iron-iron protein delta chain

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Macromolecule #3: Nitrogenase iron-iron protein, beta subunit

MacromoleculeName: Nitrogenase iron-iron protein, beta subunit / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: nitrogenase
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria)
Molecular weightTheoretical: 50.776398 KDa
Recombinant expressionOrganism: Rhodobacter capsulatus SB 1003 (bacteria)
SequenceString: MTCQVTQKAR EGTINPIFTC QPAGAQFASI GIKDCIGIVH GGQGCVMFVR LLISQHMKES FEIASSSVHE DGAVFGALDR VETAVEVLL TRYPDVKVVP IITTCSTEII GDDVDGLLSK LEDELLPTKF PGREVHLLTV HCPSFVGSMI TGYDKAVHDF V KKFATKDE ...String:
MTCQVTQKAR EGTINPIFTC QPAGAQFASI GIKDCIGIVH GGQGCVMFVR LLISQHMKES FEIASSSVHE DGAVFGALDR VETAVEVLL TRYPDVKVVP IITTCSTEII GDDVDGLLSK LEDELLPTKF PGREVHLLTV HCPSFVGSMI TGYDKAVHDF V KKFATKDE PSDKINLITG WVNPGDVKEL KHLLEVMEVK ANVLFEVESF DSPLMPDLEH HSHGSTTIED LRDTANAKGT IA LNRYEGM KAADYLKKKF KVPAVIGPTP VGIRNTDAFL KAVSEMTGQP IPAQLVKERG LALDAIADIG HMFLADKRVA IYA NPDLAI GLTEFCLDLE MKPKLLLLGD DNSGYVKDPR VLALQENAPD LEIVTNADFW DLESRIQQGL ELDLILGHSK GRFI SIDYK VPMVRVGFPT YDRAGMYRHP VLGYGGAMFL AETMANTLFA DMEAKKNKEW ILNVW

UniProtKB: Nitrogenase iron-iron protein, beta subunit

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Macromolecule #4: Nitrogenase iron protein

MacromoleculeName: Nitrogenase iron protein / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO / EC number: nitrogenase
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria)
Molecular weightTheoretical: 30.21259 KDa
Recombinant expressionOrganism: Rhodobacter capsulatus SB 1003 (bacteria)
SequenceString: MTRKIAIYGK GGIGKSTTTQ NTAAALAFFH EKNVFIHGCD PKADSTRLIL GGLPQQTVMD TLRIEGAERV TVDKVVKTGF KDIRCVESG GPEPGVGCAG RGVITAIDLM EENEAYSEDL DFLFFDVLGD VVCGGFAMPI RDGKAEEVYI VASGEMMAIY A ANNICKGL ...String:
MTRKIAIYGK GGIGKSTTTQ NTAAALAFFH EKNVFIHGCD PKADSTRLIL GGLPQQTVMD TLRIEGAERV TVDKVVKTGF KDIRCVESG GPEPGVGCAG RGVITAIDLM EENEAYSEDL DFLFFDVLGD VVCGGFAMPI RDGKAEEVYI VASGEMMAIY A ANNICKGL AKYARQSGVR LGGIICNSRN VDGEKEFLEE FTKAIGTKMI HFVPRDNIVQ KAEFNKQTVT EFQPEANQAQ EY RELGRKI IENEDFVIPK PLAMDELEAM VVKYGLMD

UniProtKB: Nitrogenase iron protein

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Macromolecule #5: FeFe cofactor

MacromoleculeName: FeFe cofactor / type: ligand / ID: 5 / Number of copies: 2 / Formula: S5Q
Molecular weightTheoretical: 747.356 Da
Chemical component information

ChemComp-S5Q:
FeFe cofactor

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Macromolecule #6: 3-HYDROXY-3-CARBOXY-ADIPIC ACID

MacromoleculeName: 3-HYDROXY-3-CARBOXY-ADIPIC ACID / type: ligand / ID: 6 / Number of copies: 2 / Formula: HCA
Molecular weightTheoretical: 206.15 Da
Chemical component information

ChemComp-HCA:
3-HYDROXY-3-CARBOXY-ADIPIC ACID

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

MacromoleculeName: FE(8)-S(7) CLUSTER / type: ligand / ID: 7 / 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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Macromolecule #8: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 8 / Number of copies: 4 / 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 #9: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 9 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #10: ALUMINUM FLUORIDE

MacromoleculeName: ALUMINUM FLUORIDE / type: ligand / ID: 10 / Number of copies: 4 / Formula: AF3
Molecular weightTheoretical: 83.977 Da
Chemical component information

ChemComp-AF3:
ALUMINUM FLUORIDE

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Macromolecule #11: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 11 / Number of copies: 2 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #12: water

MacromoleculeName: water / type: ligand / ID: 12 / Number of copies: 465 / 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: 7.8
Details: 50 mM TRIS (pH = 7.8) 200 mM NaCl 5 mM sodium dithionite
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN 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: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3014316
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.35 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 218653
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 4.1.1)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 4.1.1)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.1.1)
FSC plot (resolution estimation)

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