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- EMDB-48545: electron-bifurcating tungstopyranopterin-containing aldehyde oxid... -

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Basic information

Entry
Database: EMDB / ID: EMD-48545
Titleelectron-bifurcating tungstopyranopterin-containing aldehyde oxidoreductase WorABCSL
Map data
Sample
  • Complex: electron-bifurcating tungstopyranopterin-containing aldehyde oxidoreductase complex
    • Protein or peptide: tungstopyranopterin-containing aldehyde oxidoreductase electron-bifurcating subunit A
    • Protein or peptide: tungstopyranopterin-containing aldehyde oxidoreductase electron-bifurcating subunit B
    • Protein or peptide: tungstopyranopterin-containing aldehyde oxidoreductase electron-bifurcating subunit C
    • Protein or peptide: tungstopyranopterin-containing aldehyde oxidoreductase subunit L
    • Protein or peptide: tungstopyranopterin-containing aldehyde oxidoreductase subunit S
Keywordselectron bifurcation / OXIDOREDUCTASE
Function / homology
Function and homology information


oxidoreductase activity, acting on the aldehyde or oxo group of donors, iron-sulfur protein as acceptor / NADH dehydrogenase (ubiquinone) activity / 2 iron, 2 sulfur cluster binding / FMN binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / metal ion binding
Similarity search - Function
: / Aldehyde ferredoxin oxidoreductase, C-terminal / Aldehyde ferredoxin oxidoreductase, N-terminal / Aldehyde ferredoxin oxidoreductase, domain 2 / Aldehyde ferredoxin oxidoreductase, domain 3 / Aldehyde ferredoxin oxidoreductase-like, C-terminal / Aldehyde ferredoxin oxidoreductase, N-terminal domain superfamily / : / Aldehyde ferredoxin oxidoreductase, domains 2 & 3 / Aldehyde ferredoxin oxidoreductase, N-terminal domain ...: / Aldehyde ferredoxin oxidoreductase, C-terminal / Aldehyde ferredoxin oxidoreductase, N-terminal / Aldehyde ferredoxin oxidoreductase, domain 2 / Aldehyde ferredoxin oxidoreductase, domain 3 / Aldehyde ferredoxin oxidoreductase-like, C-terminal / Aldehyde ferredoxin oxidoreductase, N-terminal domain superfamily / : / Aldehyde ferredoxin oxidoreductase, domains 2 & 3 / Aldehyde ferredoxin oxidoreductase, N-terminal domain / Aldehyde ferredoxin oxidoreductase, N-terminal domain / NADP-reducing hydrogenase subunit HndA / 4Fe-4S dicluster domain / 4Fe-4S dicluster domain / Soluble ligand binding domain / SLBB domain / 4Fe-4S binding domain / : / 2Fe-2S iron-sulfur cluster binding domain / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NuoE domain / NADH-quinone oxidoreductase subunit E-like / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-quinone oxidoreductase subunit E, N-terminal / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / Thioredoxin-like [2Fe-2S] ferredoxin / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Nuo51 FMN-binding domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
NADH:ubiquinone oxidoreductase 24 kD subunit / NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit / NADH:ubiquinone oxidoreductase chain G-like protein / Fe-S-cluster-containing hydrogenase subunit / Aldehyde:ferredoxin oxidoreductase
Similarity search - Component
Biological speciesAcetomicrobium mobile (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsFeng X / Li H
Funding support United States, 3 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0020085 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM136885 United States
Department of Energy (DOE, United States)DE-FG02-95ER20175 United States
CitationJournal: To Be Published
Title: An electron bifurcating "plug" to a protein nanowire in tungsten-dependent aldehyde detoxification
Authors: Feng X / Schut GJ / Putumbaka S / Li H / Adams MWW
History
DepositionJan 6, 2025-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48545.png

Downloads & links

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Map

FileDownload / File: emd_48545.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 317.952 Å		0.83 Å/pix.
x 384 pix.
= 317.952 Å		0.83 Å/pix.
x 384 pix.
= 317.952 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.6786116 - 1.5975612
Average (Standard dev.)0.00024460573 (±0.022198725)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 317.952 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_48545_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_48545_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 : electron-bifurcating tungstopyranopterin-containing aldehyde oxid...

EntireName: electron-bifurcating tungstopyranopterin-containing aldehyde oxidoreductase complex
Components
  • Complex: electron-bifurcating tungstopyranopterin-containing aldehyde oxidoreductase complex
    • Protein or peptide: tungstopyranopterin-containing aldehyde oxidoreductase electron-bifurcating subunit A
    • Protein or peptide: tungstopyranopterin-containing aldehyde oxidoreductase electron-bifurcating subunit B
    • Protein or peptide: tungstopyranopterin-containing aldehyde oxidoreductase electron-bifurcating subunit C
    • Protein or peptide: tungstopyranopterin-containing aldehyde oxidoreductase subunit L
    • Protein or peptide: tungstopyranopterin-containing aldehyde oxidoreductase subunit S

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Supramolecule #1: electron-bifurcating tungstopyranopterin-containing aldehyde oxid...

SupramoleculeName: electron-bifurcating tungstopyranopterin-containing aldehyde oxidoreductase complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Acetomicrobium mobile (bacteria)
Molecular weightTheoretical: 400 KDa

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Macromolecule #1: tungstopyranopterin-containing aldehyde oxidoreductase electron-b...

MacromoleculeName: tungstopyranopterin-containing aldehyde oxidoreductase electron-bifurcating subunit A
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Acetomicrobium mobile (bacteria)
SequenceString: MRDPIDIVID GVSLSVPMET TVLEAAQMAG VEIPTLCHHP ALPPDGNCRL CMVEILRPGR RGELAISCMY PIRAQIEVNT KSDEVIRARK FVLKLLLNRA PKSARLNALA NEYGVSVESR FSFDPDECVR CDRCVRACET LGPSAIGPAW RGFNKRIVPP FMEPPRQCIG ...String:
MRDPIDIVID GVSLSVPMET TVLEAAQMAG VEIPTLCHHP ALPPDGNCRL CMVEILRPGR RGELAISCMY PIRAQIEVNT KSDEVIRARK FVLKLLLNRA PKSARLNALA NEYGVSVESR FSFDPDECVR CDRCVRACET LGPSAIGPAW RGFNKRIVPP FMEPPRQCIG CGACADVCPT GYIECVDEGD ERTIWDRKFT LIRCPICGQT YTTEEALKFT GIEDPDARLC PTCRKREYAS KFRIFVH

UniProtKB: NADH:ubiquinone oxidoreductase chain G-like protein

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Macromolecule #2: tungstopyranopterin-containing aldehyde oxidoreductase electron-b...

MacromoleculeName: tungstopyranopterin-containing aldehyde oxidoreductase electron-bifurcating subunit B
type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Acetomicrobium mobile (bacteria)
SequenceString: MPLFLKPDDL RNYRLKLKDD LKRASLLPVV RVCCGTGCVS NGSMEVLSAL EEALKGIGKV EPVVKFTGCH GFCERGPIVI VSPGEIFYQN VKTKDVPEIV QKTILDGEVI ERLLYRDPVT KKTYRSDHEI PFYANQQRLV LRRSGHIDPT SIEDYIATDG YEALCLAFKL ...String:
MPLFLKPDDL RNYRLKLKDD LKRASLLPVV RVCCGTGCVS NGSMEVLSAL EEALKGIGKV EPVVKFTGCH GFCERGPIVI VSPGEIFYQN VKTKDVPEIV QKTILDGEVI ERLLYRDPVT KKTYRSDHEI PFYANQQRLV LRRSGHIDPT SIEDYIATDG YEALCLAFKL GPDEIIKQIT DSYLRGRGGG GFRTGYKWKS CREVDDFPKY VIANGDEGDP GAFMDRSLME GDPHSVIEGM IIGAYAIGAN EGYIYVRNEY PLAVRRLQIA IERAREYGLL GKNILGSGFD FDIQICKGGG AFVCGESSAL MRSIEGYPGV PRVKYIHATE QGLWDKPTVL NNVETWANVP IILMNGVEWY KSLGTERNSG TKIFALVGKV KNTGLVEVPM GVTLRKIIYE IGGGTLKDKA FKAVQTGGPS GGCIPASLLD LSVDFDTLVK AGSMMGSGGM IVMDERSCMV DVAKYFIDFL VEESCGKCTP CREGLKVLQK LLHDLTEGKG SLQDVGLLED TAHELGKTAL CGLGKTAANP VLSTLKYFHE EYEEHVEGYC RAGVCTGLFA AKIDKDSCIG CGQCARTCPV KAISGEVRGP HVVDALKCIG CGQCMDVCPT NSIASSRRVK NA

UniProtKB: NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit

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Macromolecule #3: tungstopyranopterin-containing aldehyde oxidoreductase electron-b...

MacromoleculeName: tungstopyranopterin-containing aldehyde oxidoreductase electron-bifurcating subunit C
type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Acetomicrobium mobile (bacteria)
SequenceString:
MLSATSDVAI SDILCRYEKN PRFLLQVLLD VQEKFRYLPT DAMRSVAEYF EIPESRVFAV ATFYKVLSLV PKGEKTIKVC QGTACHLRGG SQILNAISER LKIRAGETTK DGIFTLETVN CLGCCAMAPV MMVGDKVYGK LSVADVARIL EAEKEDAIIS KAR

UniProtKB: NADH:ubiquinone oxidoreductase 24 kD subunit

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Macromolecule #4: tungstopyranopterin-containing aldehyde oxidoreductase subunit L

MacromoleculeName: tungstopyranopterin-containing aldehyde oxidoreductase subunit L
type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Acetomicrobium mobile (bacteria)
SequenceString: MFGYMGKVLR VNLSTKNITL EPLRMDWAKD FLGARGLGSR YLVEEVDPNV DPFSPDNKLI FATGPVTGTL ATSAGRFNVV TKGPLTGTIA ASNSGGYFGP ELKYAGYDMI IFEGKSANPV YLWIYNDHVE LRDASHVWGK DSYETTDALL SETDPEAKVA CIGPAGERLV ...String:
MFGYMGKVLR VNLSTKNITL EPLRMDWAKD FLGARGLGSR YLVEEVDPNV DPFSPDNKLI FATGPVTGTL ATSAGRFNVV TKGPLTGTIA ASNSGGYFGP ELKYAGYDMI IFEGKSANPV YLWIYNDHVE LRDASHVWGK DSYETTDALL SETDPEAKVA CIGPAGERLV LFACVMNDKH RAAGRTGVGA VMGSKNLKAV VVRGTGGIKL ADKEAFLEAL RKARKKIAEH PVTGGGLPAY GTNVLVNVIN AAGALPTRNF KEAWFEGADK ISGETMAETI LLKNKACASC ASACGRVTKA MGEIGEGPEY EAVWAYGAQC GVDNLEAICK ANFICNKLGM DPITMGSTIG CAMELAELGL IDEKKAGVSL HWGNAEAIVK LTEDTGYRRG FGEELALGSY RLGEKYGHPE LSMSAKKQEM PAYDPRALQG MGLEYATSNR GGCHVRGYLT SPEVLGIPEK LDPTDIASKP QWTKTFQDLT AAVDSLGFCL FLTFALDAGD LAAQVAPIIG REVTAEELLL AGERIWNLER LFNLKAGISP KEDTLPPRLL NEPIPAGPSK GRVNKLHEML PKYYELRGWG KNGIPTKERL ESLGLLDIAA KYSL

UniProtKB: Aldehyde:ferredoxin oxidoreductase

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Macromolecule #5: tungstopyranopterin-containing aldehyde oxidoreductase subunit S

MacromoleculeName: tungstopyranopterin-containing aldehyde oxidoreductase subunit S
type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Acetomicrobium mobile (bacteria)
SequenceString:
MEKVLVISPE KCVGCGSCEL ACSLEKEGEC RPSLARVTVY RFEAGANVPM TCQQCDDAPC ISVCKAGALA RDEKNVVQVD SSKCIGCRMC VMACPFGNMS YHWEQSTAIK CDQCNGSPYC VEFCPTKALD YVPADAISLQ KKKEFSARFA KIAQEVSE

UniProtKB: Fe-S-cluster-containing hydrogenase subunit

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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
Component:
ConcentrationNameFormula
25.0 mMHEPES
300.0 mMSodium chlorideNaCl
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 59.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 600000
CTF correctionSoftware - Name: cryoSPARC (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1) / Number images used: 414906
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.1)
FSC plot (resolution estimation)

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