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- EMDB-40303: Cryo-EM structure of FtAlkB -

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Basic information

Entry
Database: EMDB / ID: EMD-40303
TitleCryo-EM structure of FtAlkB
Map data
Sample
  • Complex: FtAklB-Nanobody
    • Protein or peptide: Alkane 1-monooxygenase
    • Protein or peptide: Nanobody
  • Ligand: FE (III) ION
  • Ligand: DODECANE
KeywordsEnzyme / MEMBRANE PROTEIN
Function / homologyAlkane/xylene monooxygenase / Fatty acid desaturase domain / Fatty acid desaturase / monooxygenase activity / lipid metabolic process / plasma membrane / Alkane 1-monooxygenase
Function and homology information
Biological speciesFontimonas thermophila (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.59 Å
AuthorsZhang J / Feng L
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Commun / Year: 2023
Title: Structure and mechanism of the alkane-oxidizing enzyme AlkB.
Authors: Xue Guo / Jianxiu Zhang / Lei Han / Juliet Lee / Shoshana C Williams / Allison Forsberg / Yan Xu / Rachel Narehood Austin / Liang Feng /
Abstract: Alkanes are the most energy-rich form of carbon and are widely dispersed in the environment. Their transformation by microbes represents a key step in the global carbon cycle. Alkane monooxygenase ...Alkanes are the most energy-rich form of carbon and are widely dispersed in the environment. Their transformation by microbes represents a key step in the global carbon cycle. Alkane monooxygenase (AlkB), a membrane-spanning metalloenzyme, converts straight chain alkanes to alcohols in the first step of the microbially-mediated degradation of alkanes, thereby playing a critical role in the global cycling of carbon and the bioremediation of oil. AlkB biodiversity is attributed to its ability to oxidize alkanes of various chain lengths, while individual AlkBs target a relatively narrow range. Mechanisms of substrate selectivity and catalytic activity remain elusive. Here we report the cryo-EM structure of AlkB, which provides a distinct architecture for membrane enzymes. Our structure and functional studies reveal an unexpected diiron center configuration and identify molecular determinants for substrate selectivity. These findings provide insight into the catalytic mechanism of AlkB and shed light on its function in alkane-degrading microorganisms.
History
DepositionApr 3, 2023-
Header (metadata) releaseApr 26, 2023-
Map releaseApr 26, 2023-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40303.png

Downloads & links

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Map

FileDownload / File: emd_40303.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 224 pix.
= 212.8 Å		0.95 Å/pix.
x 224 pix.
= 212.8 Å		0.95 Å/pix.
x 224 pix.
= 212.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.638
Minimum - Maximum-4.0876236 - 6.7980437
Average (Standard dev.)0.012095989 (±0.1516909)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 212.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_40303_msk_1.map
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Additional map: #1

Fileemd_40303_additional_1.map
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Half map: #2

Fileemd_40303_half_map_1.map
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Half map: #1

Fileemd_40303_half_map_2.map
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Sample components

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Entire : FtAklB-Nanobody

EntireName: FtAklB-Nanobody
Components
  • Complex: FtAklB-Nanobody
    • Protein or peptide: Alkane 1-monooxygenase
    • Protein or peptide: Nanobody
  • Ligand: FE (III) ION
  • Ligand: DODECANE

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Supramolecule #1: FtAklB-Nanobody

SupramoleculeName: FtAklB-Nanobody / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Fontimonas thermophila (bacteria)

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Macromolecule #1: Alkane 1-monooxygenase

MacromoleculeName: Alkane 1-monooxygenase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Fontimonas thermophila (bacteria)
Molecular weightTheoretical: 45.56948 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MATSMGSHPG FGADSSGTIA YRDRKRPFWT LSVLWPVSPL IGIYLAHTTG VGAFFWLTLA VWYLIIPLLD WVLGDDQSNP PEAVVPALE SDRYYRILTY LTVPIHYVVL IGSAWYVSTH YGSMTWYDIL GLALSVGIVN GLAINTGHEL GHKKTELERW L AKIVLAVV ...String:
MATSMGSHPG FGADSSGTIA YRDRKRPFWT LSVLWPVSPL IGIYLAHTTG VGAFFWLTLA VWYLIIPLLD WVLGDDQSNP PEAVVPALE SDRYYRILTY LTVPIHYVVL IGSAWYVSTH YGSMTWYDIL GLALSVGIVN GLAINTGHEL GHKKTELERW L AKIVLAVV GYGHFFIEHN KGHHKDVATP EDPASAPFGQ SIYRFALREI PGAIIRAWNS EKERLGRLGH SPWSLQNEVL QP LLITIPL YVGLIAVLGV KIIPFLLIQI VFGWWQLTSA NYIEHYGLLR QKLPDGRYER CQPYHSWNSN HVMSNLILFH LQR HSDHHA HPTRRYQSLR DFPDLPTLPS GYPLMFALSY FPPLWRAVMD RRVLDVCGRD ARKINIDPNQ REKIIHKFNL LTG

UniProtKB: Alkane 1-monooxygenase

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Macromolecule #2: Nanobody

MacromoleculeName: Nanobody / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 14.502039 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MAQVQLQESG GGLVQAGGSL RLSCAASGTI SRYWTMGWYR QAPGKERELV AGISEGGSTN YADSVKGRFT ISRDNAKNTV YLQMNSLKP EDTAVYYCAV TYRGPWFNRD PHYYWGQGTQ VTVSSHHHHH H

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Macromolecule #3: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Macromolecule #4: DODECANE

MacromoleculeName: DODECANE / type: ligand / ID: 4 / Number of copies: 1 / Formula: D12
Molecular weightTheoretical: 170.335 Da
Chemical component information

ChemComp-D12:
DODECANE

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k 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: 2.2 µm / Nominal defocus min: 1.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 107776
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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