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- EMDB-75858: Azotobacter vinelandii MoFeP (C1 symmetry) determined using the S... -

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Entry
Database: EMDB / ID: EMD-75858
TitleAzotobacter vinelandii MoFeP (C1 symmetry) determined using the SPT Labtech chameleon in the presence of 1x SurfACT
Map dataAzotobacter vinelandii MoFeP (C1 symmetry) determined using the SPT Labtech chameleon in the presence of 1x SurfACT
Sample
  • Complex: Azotobacter vinelandii MoFeP (C1 symmetry) determined using the SPT Labtech chameleon in the presence of 1x SurfACT
    • Protein or peptide: Nitrogenase molybdenum-iron protein alpha chain
    • Protein or peptide: Nitrogenase molybdenum-iron protein beta chain
  • Ligand: 3-HYDROXY-3-CARBOXY-ADIPIC ACID
  • Ligand: iron-sulfur-molybdenum cluster with interstitial carbon
  • Ligand: FE (III) ION
  • Ligand: FE(8)-S(7) CLUSTER
  • Ligand: water
KeywordsNitrogenase / FeMoCo / nitrogen / P-cluster / METAL BINDING PROTEIN / OXIDOREDUCTASE
Function / homology
Function and homology information


nitrogen fixation / molybdenum-iron nitrogenase complex / nitrogenase / nitrogenase activity / iron-sulfur cluster binding / ATP binding / metal ion binding
Similarity search - Function
Nitrogenase molybdenum-iron protein beta chain, N-terminal / Domain of unknown function (DUF3364) / Nitrogenase molybdenum-iron protein alpha chain / Nitrogenase molybdenum-iron protein beta chain / 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
Similarity search - Domain/homology
Nitrogenase molybdenum-iron protein alpha chain / Nitrogenase molybdenum-iron protein beta chain
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.49 Å
AuthorsEnos SE / Cook BD / Rahmani H / Narehood SM / Li Y / Kuschnerus IC / Redford HT / Dukakis P / Ji D / Bachochin MJ ...Enos SE / Cook BD / Rahmani H / Narehood SM / Li Y / Kuschnerus IC / Redford HT / Dukakis P / Ji D / Bachochin MJ / Grotjahn DA / Herzik MA
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R35GM138206 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1S10OD032471 United States
Other privateSearle Scholars United States
Other privateCottrell Scholars United States
Other privateGeorge W. and Carol A. Lattimer Faculty Research Fellowship United States
CitationJournal: bioRxiv / Year: 2026
Title: A Surfactant Cocktail Overcomes Air-Water Interface Artifacts in Single-Particle CryoEM.
Authors: Suzanne E Enos / Brian D Cook / Hamidreza Rahmani / Sarah M Narehood / Yizhou Li / Inga C Kuschnerus / Trevor H Redford / Peter Dukakis / Daniel Ji / Maxwell J Bachochin / Danielle A Grotjahn / Mark A Herzik
Abstract: Single-particle cryogenic electron microscopy (cryoEM) is a widely used technique for structure determination of biomacromolecules to near-atomic resolution. Random distributions of these molecules ...Single-particle cryogenic electron microscopy (cryoEM) is a widely used technique for structure determination of biomacromolecules to near-atomic resolution. Random distributions of these molecules in vitrified ice are necessary to accumulate enough two-dimensional views to generate a complete three-dimensional (3-D) reconstruction. However, interactions between the sample and the air-water interface (AWI) that occur during vitrification often bias the views of the sample, a phenomenon termed preferred orientation, limiting our ability to obtain 3-D reconstructions. Surfactants are often used as sample additives to prevent AWI-induced deterioration, but no general strategy exists for surfactant choice, requiring laborious screening for each sample. To circumvent these issues, we developed SurfACT, a cocktail of diverse surfactants with distinct physicochemical properties that limits AWI-dependent sample denaturation and orientation bias, while mitigating individual surfactant-specific drawbacks. Here we demonstrate SurfACT's effectiveness with four proteins plagued by AWI-induced issues, including two species of hemagglutinin (HA), molybdenum-iron protein (MoFeP) from the nitrogenase enzyme, and aldolase. All four samples show drastically improved viewing distribution and map completeness when SurfACT is applied. Cryogenic electron tomography demonstrates that SurfACT redistributes particles from the AWI into the bulk ice, driving signal recovery and inhibiting denaturation. This versatile sample additive minimizes sample-specific screening and expands the capabilities and range of suitable samples for cryoEM.
History
DepositionMar 5, 2026-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75858.png

Downloads & links

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Map

FileDownload / File: emd_75858.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAzotobacter vinelandii MoFeP (C1 symmetry) determined using the SPT Labtech chameleon in the presence of 1x SurfACT
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 384 pix.
= 282.24 Å		0.74 Å/pix.
x 384 pix.
= 282.24 Å		0.74 Å/pix.
x 384 pix.
= 282.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.735 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0487
Minimum - Maximum-0.16798821 - 0.30313718
Average (Standard dev.)0.00012782689 (±0.008672141)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 282.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_75858_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Phenix RESOLVE modified EM map of Azotobacter vinelandii...

Fileemd_75858_additional_1.map
AnnotationPhenix RESOLVE modified EM map of Azotobacter vinelandii MoFeP (C1 symmetry) determined using the SPT Labtech chameleon in the presence of 1x SurfACT
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map of Azotobacter vinelandii MoFeP (C1 symmetry)...

Fileemd_75858_additional_2.map
AnnotationUnsharpened map of Azotobacter vinelandii MoFeP (C1 symmetry) determined using the SPT Labtech chameleon in the presence of 1x SurfACT
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of Azotobacter vinelandii MoFeP determined...

Fileemd_75858_half_map_1.map
AnnotationHalf map A of Azotobacter vinelandii MoFeP determined using the SPT Labtech chameleon in the presence of 1x SurfACT; C1 symmetry
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of Azotobacter vinelandii MoFeP determined...

Fileemd_75858_half_map_2.map
AnnotationHalf map B of Azotobacter vinelandii MoFeP determined using the SPT Labtech chameleon in the presence of 1x SurfACT; C1 symmetry
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Azotobacter vinelandii MoFeP (C1 symmetry) determined using the S...

EntireName: Azotobacter vinelandii MoFeP (C1 symmetry) determined using the SPT Labtech chameleon in the presence of 1x SurfACT
Components
  • Complex: Azotobacter vinelandii MoFeP (C1 symmetry) determined using the SPT Labtech chameleon in the presence of 1x SurfACT
    • Protein or peptide: Nitrogenase molybdenum-iron protein alpha chain
    • Protein or peptide: Nitrogenase molybdenum-iron protein beta chain
  • Ligand: 3-HYDROXY-3-CARBOXY-ADIPIC ACID
  • Ligand: iron-sulfur-molybdenum cluster with interstitial carbon
  • Ligand: FE (III) ION
  • Ligand: FE(8)-S(7) CLUSTER
  • Ligand: water

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Supramolecule #1: Azotobacter vinelandii MoFeP (C1 symmetry) determined using the S...

SupramoleculeName: Azotobacter vinelandii MoFeP (C1 symmetry) determined using the SPT Labtech chameleon in the presence of 1x SurfACT
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Azotobacter vinelandii (bacteria)
Molecular weightTheoretical: 230 KDa

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Macromolecule #1: Nitrogenase molybdenum-iron protein alpha chain

MacromoleculeName: Nitrogenase molybdenum-iron protein alpha chain / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: nitrogenase
Source (natural)Organism: Azotobacter vinelandii (bacteria)
Molecular weightTheoretical: 54.000559 KDa
SequenceString: MSREEVESLI QEVLEVYPEK ARKDRNKHLA VNDPAVTQSK KCIISNKKSQ PGLMTIRGCA YAGSKGVVWG PIKDMIHISH GPVGCGQYS RAGRRNYYIG TTGVNAFVTM NFTSDFQEKD IVFGGDKKLA KLIDEVETLF PLNKGISVQS ECPIGLIGDD I ESVSKVKG ...String:
MSREEVESLI QEVLEVYPEK ARKDRNKHLA VNDPAVTQSK KCIISNKKSQ PGLMTIRGCA YAGSKGVVWG PIKDMIHISH GPVGCGQYS RAGRRNYYIG TTGVNAFVTM NFTSDFQEKD IVFGGDKKLA KLIDEVETLF PLNKGISVQS ECPIGLIGDD I ESVSKVKG AELSKTIVPV RCEGFRGVSQ SLGHHIANDA VRDWVLGKRD EDTTFASTPY DVAIIGDYNI GGDAWSSRIL LE EMGLRCV AQWSGDGSIS EIELTPKVKL NLVHCYRSMN YISRHMEEKY GIPWMEYNFF GPTKTIESLR AIAAKFDESI QKK CEEVIA KYKPEWEAVV AKYRPRLEGK RVMLYIGGLR PRHVIGAYED LGMEVVGTGY EFAHNDDYDR TMKEMGDSTL LYDD VTGYE FEEFVKRIKP DLIGSGIKEK FIFQKMGIPF REMHSWDYSG PYHGFDGFAI FARDMDMTLN NPCWKKLQAP WE

UniProtKB: Nitrogenase molybdenum-iron protein alpha chain

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Macromolecule #2: Nitrogenase molybdenum-iron protein beta chain

MacromoleculeName: Nitrogenase molybdenum-iron protein beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: nitrogenase
Source (natural)Organism: Azotobacter vinelandii (bacteria)
Molecular weightTheoretical: 59.404684 KDa
SequenceString: SQQVDKIKAS YPLFLDQDYK DMLAKKRDGF EEKYPQDKID EVFQWTTTKE YQELNFQREA LTVNPAKACQ PLGAVLCALG FEKTMPYVH GSQGCVAYFR SYFNRHFREP VSCVSDSMTE DAAVFGGQQN MKDGLQNCKA TYKPDMIAVS TTCMAEVIGD D LNAFINNS ...String:
SQQVDKIKAS YPLFLDQDYK DMLAKKRDGF EEKYPQDKID EVFQWTTTKE YQELNFQREA LTVNPAKACQ PLGAVLCALG FEKTMPYVH GSQGCVAYFR SYFNRHFREP VSCVSDSMTE DAAVFGGQQN MKDGLQNCKA TYKPDMIAVS TTCMAEVIGD D LNAFINNS KKEGFIPDEF PVPFAHTPSF VGSHVTGWDN MFEGIARYFT LKSMDDKVVG SNKKINIVPG FETYLGNFRV IK RMLSEMG VGYSLLSDPE EVLDTPADGQ FRMYAGGTTQ EEMKDAPNAL NTVLLQPWHL EKTKKFVEGT WKHEVPKLNI PMG LDWTDE FLMKVSEISG QPIPASLTKE RGRLVDMMTD SHTWLHGKRF ALWGDPDFVM GLVKFLLELG CEPVHILCHN GNKR WKKAV DAILAASPYG KNATVYIGKD LWHLRSLVFT DKPDFMIGNS YGKFIQRDTL HKGKEFEVPL IRIGFPIFDR HHLHR STTL GYEGAMQILT TLVNSILERL DEETRGMQAT DYNHDLVR

UniProtKB: Nitrogenase molybdenum-iron protein beta chain

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

MacromoleculeName: 3-HYDROXY-3-CARBOXY-ADIPIC ACID / type: ligand / ID: 3 / 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 #4: iron-sulfur-molybdenum cluster with interstitial carbon

MacromoleculeName: iron-sulfur-molybdenum cluster with interstitial carbon
type: ligand / ID: 4 / Number of copies: 2 / Formula: ICS
Molecular weightTheoretical: 787.451 Da
Chemical component information

ChemComp-ICE:
iron-sulfur-molybdenum cluster with interstitial carbon

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Macromolecule #5: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Macromolecule #6: FE(8)-S(7) CLUSTER

MacromoleculeName: FE(8)-S(7) CLUSTER / type: ligand / ID: 6 / 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 #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 1680 / 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

Concentration3.6 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMNH2C(CH2OH)3-HClTRIS HCl
25.0 mMNaClSodium Chloride
0.05 %w/vC32H58N2O8SCHAPSO
0.0048 %w/vC20H25F13O11FOM
0.25 %w/v(C6.2H10.3O1.35N0.65Na0.35)72Amphipol A8-35
0.06 %w/v(C2H4O)nC12H26OBrij-35
GridModel: Quantifoil Active R1.2/0.8 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 75 % / Chamber temperature: 298.15 K / Instrument: SPT LABTECH CHAMELEON
Details: Samples were frozen with the SPT Labtech chameleon.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 1080 / Average exposure time: 5.0 sec. / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 165000
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

CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab-Initio Reconstruction
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.49 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Number images used: 23561
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7ut7


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 49.9
Output model

PDB-11ne:
Azotobacter vinelandii MoFeP (C1 symmetry) determined using the SPT Labtech chameleon in the presence of 1x SurfACT

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