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- EMDB-69162: C-His tagged YghJ protein substrate-accessible state -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-69162
TitleC-His tagged YghJ protein substrate-accessible state
Map data
Sample
  • Cell: C-His tagged YghJ substrate-accessible state
    • Protein or peptide: Putative lipoprotein AcfD homolog
  • Ligand: ZINC ION
Keywordsactive enzyme / mucinase / O-glycoprotease / HYDROLASE
Function / homology
Function and homology information


transmembrane transporter binding / plasma membrane
Similarity search - Function
Domain of unknown function DUF4092 / Domain of unknown function (DUF4092) / AcfD helical domain / M60-like domain, N-terminal / N-terminal domain of M60-like peptidases / : / Peptidase family M60 domain / Peptidase M60, enhancin-like domain 3 / Peptidase M60, enhancin and enhancin-like / Peptidase family M60 domain profile. ...Domain of unknown function DUF4092 / Domain of unknown function (DUF4092) / AcfD helical domain / M60-like domain, N-terminal / N-terminal domain of M60-like peptidases / : / Peptidase family M60 domain / Peptidase M60, enhancin-like domain 3 / Peptidase M60, enhancin and enhancin-like / Peptidase family M60 domain profile. / Peptidase M60-like family / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Putative lipoprotein AcfD homolog
Similarity search - Component
Biological speciesEscherichia coli (strain K12) (bacteria) / Escherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsGu JK / Zhang MH
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32270832 China
CitationJournal: Protein Cell / Year: 2026
Title: Molecular basis for zymogen-like autoinhibition of the M60-like metallopeptidase YghJ.
Authors: Minghui Zhang / Bowen Wu / Zhouzhu Liang / Yintao Su / Huacai Peng / Jinke Gu /
History
DepositionFeb 13, 2026-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_69162.png

Downloads & links

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Map

FileDownload / File: emd_69162.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 220 pix.
= 233.2 Å		1.06 Å/pix.
x 220 pix.
= 233.2 Å		1.06 Å/pix.
x 220 pix.
= 233.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.0017247436 - 1.8568661
Average (Standard dev.)0.0017784212 (±0.031688154)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 233.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_69162_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_69162_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 : C-His tagged YghJ substrate-accessible state

EntireName: C-His tagged YghJ substrate-accessible state
Components
  • Cell: C-His tagged YghJ substrate-accessible state
    • Protein or peptide: Putative lipoprotein AcfD homolog
  • Ligand: ZINC ION

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Supramolecule #1: C-His tagged YghJ substrate-accessible state

SupramoleculeName: C-His tagged YghJ substrate-accessible state / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)

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Macromolecule #1: Putative lipoprotein AcfD homolog

MacromoleculeName: Putative lipoprotein AcfD homolog / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 167.405047 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNKKFKYKKS LLAAILSATL LAGCDGGGSG SSSDTPPVDS GTGSLPEVKP DPTPNPEPTP EPTPDPEPTP EPIPDPEPTP EPEPEPVPT KTGYLTLGGS QRVTGATCNG ESSDGFTFKP GEDVTCVAGN TTIATFNTQS EAARSLRAVE KVSFSLEDAQ E LAGSDDKK ...String:
MNKKFKYKKS LLAAILSATL LAGCDGGGSG SSSDTPPVDS GTGSLPEVKP DPTPNPEPTP EPTPDPEPTP EPIPDPEPTP EPEPEPVPT KTGYLTLGGS QRVTGATCNG ESSDGFTFKP GEDVTCVAGN TTIATFNTQS EAARSLRAVE KVSFSLEDAQ E LAGSDDKK SNAVSLVTSS NSCPANTEQV CLTFSSVIES KRFDSLYKQI DLAPEEFKKL VNEEVENNAA TDKAPSTHTS PV VPVTTPG TKPDLNASFV SANAEQFYQY QPTEIILSEG RLVDSQGYGV AGVNYYTNSG RGVTGENGEF SFSWGETISF GID TFELGS VRGNKSTIAL TELGDEVRGA NIDQLIHRYS TTGQNNTRVV PDDVRKVFAE YPNVINEIIN LSLSNGATLG EGEQ VVNLP NEFIEQFNTG QAKEIDTAIC AKTDGCNEAR WFSLTTRNVN DGQIQGVINK LWGVDTNYKS VSKFHVFHDS TNFYG STGN ARGQAVVNIS NAAFPILMAR NDKNYWLAFG EKRAWDKNEL AYITEAPSLV EPENVTRDTA TFNLPFISLG QVGEGK LMV IGNPHYNSIL RCPNGYSWNG GVNKDGQCTL NSDPDDMKNF MENVLRYLSD DKWKPDAKAS MTVGTNLDTV YFKRHGQ VT GNSAAFDFHP DFAGISVEHL SSYGDLDPQE MPLLILNGFE YVTQVGNDPY AIPLRADTSK PKLTQQDVTD LIAYLNKG G SVLIMENVMS NLKEESASGF VRLLDAAGLS MALNKSVVNN DPQGYPNRVR QQRATGIWVY ERYPAVDGAL PYTIDSKTG EVKWKYQVEN KPDDKPKLEV ASWLEDVDGK QETRYAFIDE ADHKTEDSLK AAKEKIFAAF PGLKECTNPA YHYEVNCLEY RPGTGVPVT GGMYVPQYTQ LSLNADTAKA MVQAADLGTN IQRLYQHELY FRTNGRKGER LSSVDLERLY QNMSVWLWND T SYRYEEGK NDELGFKTFT EFLNCYANDA YAGGTKCSAD LKKSLVDNNM IYGDGSSKAG MMNPSYPLNY MEKPLTRLML GR SWWDLNI KVDVEKYPGA VSEEGQNVTE TISLYSNPTK WFAGNMQSTG LWAPAQKEVT IKSNANVPVT VTVALADDLT GRE KHEVAL NRPPRVTKTY SLDASGTVKF KVPYGGLIYI KGNSSTNESA SFTFTGVVKA PFYKDGAWKN DLNSPAPLGE LESD AFVYT TPKKNLNASN YTGGLEQFAN DLDTFASSMN DFYGRDSEDG KHRMFTYKNL PGHKHRFTND VQISIGDAHS GYPVM NSSF SPNSTTLPTT PLNDWLIWHE VGHNAAETPL TVPGATEVAN NVLALYMQDR YLGKMNRVAD DITVAPEYLE ESNNQA WAR GGAGDRLLMY AQLKEWAEKN FDIKKWYPDG TPLPEFYSER EGMKGWNLFQ LMHRKARGDE VSNDKFGGKN YCAESNG NA ADTLMLCASW VAQTDLSEFF KKWNPGANAY QLPGASEMSF EGGVSQSAYN TLASLDLPKP EQGPETINQV TEHKMSAE

UniProtKB: Putative lipoprotein AcfD homolog

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number images used: 156958
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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