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- PDB-9leg: AMO complex -

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Basic information

Entry
Database: PDB / ID: 9leg
TitleAMO complex
Components
  • (Ammonia monooxygenase subunit ...) x 3
  • AmoD
  • Lipoprotein
KeywordsMEMBRANE PROTEIN / AMO complex
Function / homology
Function and homology information


monooxygenase activity / membrane
Similarity search - Function
Ammonia monooxygenase/particulate methane monooxygenase, subunit C / Ammonia monooxygenase/particulate methane monooxygenase, subunit C domain superfamily / Ammonia monooxygenase/methane monooxygenase, subunit C / Ammonia monooxygenase/particulate methane monooxygenase, subunit A / Ammonia/methane monooxygenase, subunit B, hairpin domain superfamily / Ammonia/methane monooxygenase, subunit B, C-terminal / Ammonia/particulate methane monooxygenase, subunit A superfamily / Ammonia monooxygenase / Ammonia monooxygenase/particulate methane monooxygenase, subunit B / Ammonia/methane monooxygenase, subunitB, N-terminal ...Ammonia monooxygenase/particulate methane monooxygenase, subunit C / Ammonia monooxygenase/particulate methane monooxygenase, subunit C domain superfamily / Ammonia monooxygenase/methane monooxygenase, subunit C / Ammonia monooxygenase/particulate methane monooxygenase, subunit A / Ammonia/methane monooxygenase, subunit B, hairpin domain superfamily / Ammonia/methane monooxygenase, subunit B, C-terminal / Ammonia/particulate methane monooxygenase, subunit A superfamily / Ammonia monooxygenase / Ammonia monooxygenase/particulate methane monooxygenase, subunit B / Ammonia/methane monooxygenase, subunitB, N-terminal / Monooxygenase subunit B protein / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
(2R)-3-HYDROXYPROPANE-1,2-DIYL DIHEXADECANOATE / : / : / COPPER (II) ION / DECANOIC ACID / PALMITIC ACID / (2S)-2,3-dihydroxypropyl hexadecanoate / Lipoprotein / Uncharacterized protein / Ammonia monooxygenase subunit C ...(2R)-3-HYDROXYPROPANE-1,2-DIYL DIHEXADECANOATE / : / : / COPPER (II) ION / DECANOIC ACID / PALMITIC ACID / (2S)-2,3-dihydroxypropyl hexadecanoate / Lipoprotein / Uncharacterized protein / Ammonia monooxygenase subunit C / Ammonia monooxygenase subunit A / Ammonia monooxygenase subunit B
Similarity search - Component
Biological speciesNitrosomonas halophila (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.36 Å
AuthorsLi, Z.Q. / Yang, X.Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32301015 China
National Natural Science Foundation of China (NSFC)42476110 China
CitationJournal: Nat Commun / Year: 2025
Title: Structural insights into the catalytic mechanism of ammonia monooxygenase.
Authors: Xiaoyun Yang / Zongqiang Li / Tie-Qiang Mao / Chaofu Ma / Guo-Hao Chen / Hong-Po Dong / Sen-Fang Sui /
Abstract: Ammonia monooxygenase (AMO) oxidizes ammonia to hydroxylamine. Limited knowledge of the structural information of AMO hinders our understanding of the molecular mechanism underlying ammonia ...Ammonia monooxygenase (AMO) oxidizes ammonia to hydroxylamine. Limited knowledge of the structural information of AMO hinders our understanding of the molecular mechanism underlying ammonia oxidation, impacting the mitigation of greenhouse gas emissions and enhancing agricultural productivity using ammonium as a nitrogen source. Herein, we report the cryo-electron microscopy structure of the AMO complex from an isolated strain of ammonia-oxidizing bacteria (AOB). AMO is a cylinder-shaped homotrimeric assembly composed of five subunits. A single-transmembrane protein and a soluble protein are potentially crucial in signal transduction during ammonia oxidation and mediating interactions with the outer membrane protein assembly machinery. Three modeled coppers, along with an adjacent water-mediated hydrogen-bond network, may facilitate an efficient proton transfer pathway from the periplasmic Cu to the active site Cu within the inner membrane, where Cu and Cu will act in concert to catalyze substrate reaction. The distinctive surface charge characteristics of AMO provide valuable insights into the structural features that govern ammonium assimilation and material transport during ammonia oxidation. These findings shed light on the molecular complexities of AMO and provides a structural foundation for elucidating the catalytic mechanism of ammonia oxidation.
History
DepositionJan 7, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ammonia monooxygenase subunit A
B: Ammonia monooxygenase subunit B
C: Ammonia monooxygenase subunit C
D: Lipoprotein
E: AmoD
L: Ammonia monooxygenase subunit A
M: Ammonia monooxygenase subunit B
N: Ammonia monooxygenase subunit C
O: Lipoprotein
P: AmoD
U: Ammonia monooxygenase subunit A
V: Ammonia monooxygenase subunit B
W: Ammonia monooxygenase subunit C
X: Lipoprotein
Y: AmoD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)393,059108
Polymers367,40615
Non-polymers25,65393
Water9,890549
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Ammonia monooxygenase subunit ... , 3 types, 9 molecules ALUBMVCNW

#1: Protein Ammonia monooxygenase subunit A


Mass: 31736.248 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosomonas halophila (bacteria) / Gene: SAMN05421881_11133 / Production host: Nitrosomonas halophila (bacteria) / References: UniProt: A0A1H3PUN8
#2: Protein Ammonia monooxygenase subunit B


Mass: 46935.816 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosomonas halophila (bacteria) / Gene: SAMN05421881_11134 / Production host: Nitrosomonas halophila (bacteria) / References: UniProt: A0A1H3PUR7
#3: Protein Ammonia monooxygenase subunit C


Mass: 31698.678 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosomonas halophila (bacteria) / Gene: SAMN05421881_11132 / Production host: Nitrosomonas halophila (bacteria) / References: UniProt: A0A1H3PUB4

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Protein / Protein/peptide , 2 types, 6 molecules DOXEPY

#4: Protein Lipoprotein


Mass: 7051.081 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosomonas halophila (bacteria) / Gene: SAMN05421881_103624 / Production host: Nitrosomonas halophila (bacteria) / References: UniProt: A0A1H3JYQ0
#5: Protein/peptide AmoD


Mass: 5046.772 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosomonas halophila (bacteria) / Gene: SAMN05421881_104318 / Production host: Nitrosomonas halophila (bacteria) / References: UniProt: A0A1H3KVX9

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Non-polymers , 8 types, 642 molecules

#6: Chemical
ChemComp-A1EZJ / (2~{R})-2-azanyl-3-[[(2~{R})-2-hexadecanoyloxy-3-pentadecanoyloxy-propoxy]-oxidanyl-phosphoryl]oxy-propanoic acid


Mass: 721.942 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C37H72NO10P / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical...
ChemComp-DKA / DECANOIC ACID


Mass: 172.265 Da / Num. of mol.: 51 / Source method: obtained synthetically / Formula: C10H20O2
#8: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C16H32O2
#9: Chemical
ChemComp-ZP7 / (2S)-2,3-dihydroxypropyl hexadecanoate


Mass: 330.503 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C19H38O4
#10: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cu
#11: Chemical
ChemComp-A1EZI / [(2~{S})-2-hexadecanoyloxy-3-[methoxy(oxidanyl)phosphoryl]oxy-propyl] hexadecanoate


Mass: 662.918 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C36H71O8P / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-4AG / (2R)-3-HYDROXYPROPANE-1,2-DIYL DIHEXADECANOATE / SN-1,2-DIPALMITOYL DIACYLGLYCEROL


Mass: 568.911 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C35H68O5 / Feature type: SUBJECT OF INVESTIGATION
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 549 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Bacterial AMO complex / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Source (natural)Organism: Nitrosomonas halophila (bacteria)
Source (recombinant)Organism: Nitrosomonas halophila (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.36 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 94482 / Symmetry type: POINT
RefinementCross valid method: NONE

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