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- EMDB-28264: Cryo-EM analysis of the human aldehyde oxidase from liver -

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Basic information

Entry
Database: EMDB / ID: EMD-28264
TitleCryo-EM analysis of the human aldehyde oxidase from liver
Map data
Sample
  • Complex: Aldehyde oxidase
    • Protein or peptide: Aldehyde oxidase
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER
  • Ligand: DIOXOTHIOMOLYBDENUM(VI) ION
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
KeywordsAldehyde oxidase / AOX1 / OXIDOREDUCTASE
Function / homology
Function and homology information


Oxidoreductases; Acting on CH or CH2 groups; With oxygen as acceptor / aldehyde oxidase / aldehyde oxidase activity / Vitamin B6 activation to pyridoxal phosphate / molybdopterin cofactor binding / xenobiotic metabolic process / FAD binding / lipid metabolic process / 2 iron, 2 sulfur cluster binding / NAD binding ...Oxidoreductases; Acting on CH or CH2 groups; With oxygen as acceptor / aldehyde oxidase / aldehyde oxidase activity / Vitamin B6 activation to pyridoxal phosphate / molybdopterin cofactor binding / xenobiotic metabolic process / FAD binding / lipid metabolic process / 2 iron, 2 sulfur cluster binding / NAD binding / flavin adenine dinucleotide binding / iron ion binding / protein homodimerization activity / extracellular exosome / identical protein binding / cytosol
Similarity search - Function
Aldehyde oxidase / Oxidoreductase, molybdopterin binding site / Eukaryotic molybdopterin oxidoreductases signature. / CO dehydrogenase flavoprotein C-terminal domain / Molybdopterin dehydrogenase, FAD-binding / CO dehydrogenase flavoprotein, C-terminal / CO dehydrogenase flavoprotein, C-terminal domain superfamily / FAD binding domain in molybdopterin dehydrogenase / CO dehydrogenase flavoprotein C-terminal domain / Aldehyde oxidase/xanthine dehydrogenase ...Aldehyde oxidase / Oxidoreductase, molybdopterin binding site / Eukaryotic molybdopterin oxidoreductases signature. / CO dehydrogenase flavoprotein C-terminal domain / Molybdopterin dehydrogenase, FAD-binding / CO dehydrogenase flavoprotein, C-terminal / CO dehydrogenase flavoprotein, C-terminal domain superfamily / FAD binding domain in molybdopterin dehydrogenase / CO dehydrogenase flavoprotein C-terminal domain / Aldehyde oxidase/xanthine dehydrogenase / Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / [2Fe-2S]-binding / Aldehyde oxidase/xanthine dehydrogenase, first molybdopterin binding domain / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead superfamily / [2Fe-2S]-binding domain superfamily / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain superfamily / Aldehyde oxidase/xanthine dehydrogenase, second molybdopterin binding domain / [2Fe-2S] binding domain / Molybdopterin cofactor-binding domain / Molybdopterin cofactor-binding domain / Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain / FAD-binding, type PCMH, subdomain 1 / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / 2Fe-2S iron-sulfur cluster binding domain / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsSu C / Lyu M / Zhang Z / Yu EW
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Cell Rep / Year: 2023
Title: High-resolution structural-omics of human liver enzymes.
Authors: Chih-Chia Su / Meinan Lyu / Zhemin Zhang / Masaru Miyagi / Wei Huang / Derek J Taylor / Edward W Yu /
Abstract: We applied raw human liver microsome lysate to a holey carbon grid and used cryo-electron microscopy (cryo-EM) to define its composition. From this sample we identified and simultaneously determined ...We applied raw human liver microsome lysate to a holey carbon grid and used cryo-electron microscopy (cryo-EM) to define its composition. From this sample we identified and simultaneously determined high-resolution structural information for ten unique human liver enzymes involved in diverse cellular processes. Notably, we determined the structure of the endoplasmic bifunctional protein H6PD, where the N- and C-terminal domains independently possess glucose-6-phosphate dehydrogenase and 6-phosphogluconolactonase enzymatic activity, respectively. We also obtained the structure of heterodimeric human GANAB, an ER glycoprotein quality-control machinery that contains a catalytic α subunit and a noncatalytic β subunit. In addition, we observed a decameric peroxidase, PRDX4, which directly contacts a disulfide isomerase-related protein, ERp46. Structural data suggest that several glycosylations, bound endogenous compounds, and ions associate with these human liver enzymes. These results highlight the importance of cryo-EM in facilitating the elucidation of human organ proteomics at the atomic level.
History
DepositionSep 28, 2022-
Header (metadata) releaseMay 10, 2023-
Map releaseMay 10, 2023-
UpdateNov 15, 2023-
Current statusNov 15, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28264.png

Downloads & links

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Map

FileDownload / File: emd_28264.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 300 pix.
= 324. Å		1.08 Å/pix.
x 300 pix.
= 324. Å		1.08 Å/pix.
x 300 pix.
= 324. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.18
Minimum - Maximum-0.5108278 - 1.4767815
Average (Standard dev.)0.011002482 (±0.036537874)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 324.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_28264_msk_1.map
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Mask #2

Fileemd_28264_msk_2.map
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Additional map: Local refinement Foused on chainA

Fileemd_28264_additional_1.map
AnnotationLocal refinement Foused on chainA
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Additional map: Local refinement Foused on chainB

Fileemd_28264_additional_2.map
AnnotationLocal refinement Foused on chainB
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Additional map: half map of Local refinement Foused on chainB

Fileemd_28264_additional_3.map
Annotationhalf map of Local refinement Foused on chainB
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Additional map: half map of Local refinement Foused on chainB

Fileemd_28264_additional_4.map
Annotationhalf map of Local refinement Foused on chainB
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Half map: half map of Local refinement Foused on chainA

Fileemd_28264_half_map_1.map
Annotationhalf map of Local refinement Foused on chainA
Projections & Slices
AxesZYX

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Half map: half map of Local refinement Foused on chainA

Fileemd_28264_half_map_2.map
Annotationhalf map of Local refinement Foused on chainA
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Sample components

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Entire : Aldehyde oxidase

EntireName: Aldehyde oxidase
Components
  • Complex: Aldehyde oxidase
    • Protein or peptide: Aldehyde oxidase
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER
  • Ligand: DIOXOTHIOMOLYBDENUM(VI) ION
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE

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Supramolecule #1: Aldehyde oxidase

SupramoleculeName: Aldehyde oxidase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Aldehyde oxidase

MacromoleculeName: Aldehyde oxidase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: aldehyde oxidase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 148.0965 KDa
SequenceString: MDRASELLFY VNGRKVIEKN VDPETMLLPY LRKKLRLTGT KYGCGGGGCG ACTVMISRYN PITKRIRHHP ANACLIPICS LYGAAVTTV EGIGSTHTRI HPVQERIAKC HGTQCGFCTP GMVMSIYTLL RNHPEPTLDQ LTDALGGNLC RCTGYRPIID A CKTFCKTS ...String:
MDRASELLFY VNGRKVIEKN VDPETMLLPY LRKKLRLTGT KYGCGGGGCG ACTVMISRYN PITKRIRHHP ANACLIPICS LYGAAVTTV EGIGSTHTRI HPVQERIAKC HGTQCGFCTP GMVMSIYTLL RNHPEPTLDQ LTDALGGNLC RCTGYRPIID A CKTFCKTS GCCQSKENGV CCLDQGINGL PEFEEGSKTS PKLFAEEEFL PLDPTQELIF PPELMIMAEK QSQRTRVFGS ER MMWFSPV TLKELLEFKF KYPQAPVIMG NTSVGPEVKF KGVFHPVIIS PDRIEELSVV NHAYNGLTLG AGLSLAQVKD ILA DVVQKL PEEKTQMYHA LLKHLGTLAG SQIRNMASLG GHIISRHPDS DLNPILAVGN CTLNLLSKEG KRQIPLNEQF LSKC PNADL KPQEILVSVN IPYSRKWEFV SAFRQAQRQE NALAIVNSGM RVFFGEGDGI IRELCISYGG VGPATICAKN SCQKL IGRH WNEQMLDIAC RLILNEVSLL GSAPGGKVEF KRTLIISFLF KFYLEVSQIL KKMDPVHYPS LADKYESALE DLHSKH HCS TLKYQNIGPK QHPEDPIGHP IMHLSGVKHA TGEAIYCDDM PLVDQELFLT FVTSSRAHAK IVSIDLSEAL SMPGVVD IM TAEHLSDVNS FCFFTEAEKF LATDKVFCVG QLVCAVLADS EVQAKRAAKR VKIVYQDLEP LILTIEESIQ HNSSFKPE R KLEYGNVDEA FKVVDQILEG EIHMGGQEHF YMETQSMLVV PKGEDQEMDV YVSTQFPKYI QDIVASTLKL PANKVMCHV RRVGGAFGGK VLKTGIIAAV TAFAANKHGR AVRCVLERGE DMLITGGRHP YLGKYKAGFM NDGRILALDM EHYSNAGASL DESLFVIEM GLLKMDNAYK FPNLRCRGWA CRTNLPSNTA FRGFGFPQAA LITESCITEV AAKCGLSPEK VRIINMYKEI D QTPYKQEI NAKNLIQCWR ECMAMSSYSL RKVAVEKFNA ENYWKKKGLA MVPLKFPVGL GSRAAGQAAA LVHIYLDGSV LV THGGIEM GQGVHTKMIQ VVSRELRMPM SNVHLRGTST ETVPNANISG GSVVADLNGL AVKDACQTLL KRLEPIISKN PKG TWKDWA QTAFDESINL SAVGYFRGYE SDMNWEKGEG QPFEYFVYGA ACSEVEIDCL TGDHKNIRTD IVMDVGCSIN PAID IGQIE GAFIQGMGLY TIEELNYSPQ GILHTRGPDQ YKIPAICDMP TELHIALLPP SQNSNTLYSS KGLGESGVFL GCSVF FAIH DAVSAARQER GLHGPLTLNS PLTPEKIRMA CEDKFTKMIP RDEPGSYVPW NVPI

UniProtKB: Aldehyde oxidase

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Macromolecule #2: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 2 / Number of copies: 4 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

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Macromolecule #3: PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A...

MacromoleculeName: PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER
type: ligand / ID: 3 / Number of copies: 2 / Formula: MTE
Molecular weightTheoretical: 395.352 Da
Chemical component information

ChemComp-MTE:
PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER

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Macromolecule #4: DIOXOTHIOMOLYBDENUM(VI) ION

MacromoleculeName: DIOXOTHIOMOLYBDENUM(VI) ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MOS
Molecular weightTheoretical: 161.012 Da
Chemical component information

ChemComp-MOS:
DIOXOTHIOMOLYBDENUM(VI) ION

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Macromolecule #5: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 5 / Number of copies: 2 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 41.25 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

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 185973
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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