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- EMDB-82559: Undecameric complex of serine proteinase (SDH) with hypothetical ... -

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Basic information

Entry
Database: EMDB / ID: EMD-82559
TitleUndecameric complex of serine proteinase (SDH) with hypothetical protein (HP)
Map data
Sample
  • Complex: Undecameric complex of serine proteinase (SDH) with hypothetical protein (HP)
    • Protein or peptide: serine proteinase(SDH)
    • Protein or peptide: hypothetical protein
    • Protein or peptide: hypothetical protein
    • Protein or peptide: hypothetical protein
    • Protein or peptide: hypothetical protein
    • Protein or peptide: hypothetical protein
Keywordsundecamer / IMMUNE SYSTEM
Biological speciesKlebsiella pneumoniae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.51 Å
AuthorsYu Y / Chen Q
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Passive abortive infection mechanisms targeting phage long tail fiber proteins
Authors: Yu Y / Chen Q
History
DepositionJul 27, 2026-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_82559.png

Downloads & links

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Map

FileDownload / File: emd_82559.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0536
Minimum - Maximum-0.0019269501 - 2.2850263
Average (Standard dev.)0.0030984296 (±0.03961251)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 272.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_82559_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_82559_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 : Undecameric complex of serine proteinase (SDH) with hypothetical ...

EntireName: Undecameric complex of serine proteinase (SDH) with hypothetical protein (HP)
Components
  • Complex: Undecameric complex of serine proteinase (SDH) with hypothetical protein (HP)
    • Protein or peptide: serine proteinase(SDH)
    • Protein or peptide: hypothetical protein
    • Protein or peptide: hypothetical protein
    • Protein or peptide: hypothetical protein
    • Protein or peptide: hypothetical protein
    • Protein or peptide: hypothetical protein

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Supramolecule #1: Undecameric complex of serine proteinase (SDH) with hypothetical ...

SupramoleculeName: Undecameric complex of serine proteinase (SDH) with hypothetical protein (HP)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Klebsiella pneumoniae (bacteria)

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Macromolecule #1: serine proteinase(SDH)

MacromoleculeName: serine proteinase(SDH) / type: protein_or_peptide / ID: 1 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 33.864375 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GASGSAMPNL AQVLEEIQSL QDDSRFDIVR RKYIKALSES TDRNVICYYT DFLHNGNHQH VSINDDDKNG FMAVVNGMDR TKGLDLFLH TPGGSITAAE SLVYYLKKLF NGDIRAIVPQ MSMSAGTMIA CACKEIVMGH HSSIGPFDPH IFGGLSAYGI L EELKNAID ...String:
GASGSAMPNL AQVLEEIQSL QDDSRFDIVR RKYIKALSES TDRNVICYYT DFLHNGNHQH VSINDDDKNG FMAVVNGMDR TKGLDLFLH TPGGSITAAE SLVYYLKKLF NGDIRAIVPQ MSMSAGTMIA CACKEIVMGH HSSIGPFDPH IFGGLSAYGI L EELKNAID SIQKDPSSLP IWQTIISRYP PTIFDTASKA IQLADDLVTE WLKNGMLKDL PEPERSELST AIVKSLNNRT DT KDHSRHI HAERAVELGL RITQLEEHPQ LQDAVLTVHH CCTQTLFNTP TVKLIEGSNN QSFIRHI

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Macromolecule #2: hypothetical protein

MacromoleculeName: hypothetical protein / type: protein_or_peptide / ID: 2
Details: The full sequence of hypothetical protein is GASGSAMAEINYEKILLETGLVASNASGIQFPQQFGAMSHEFGGLSGVANFSHQHETTKLKCSTRTTSYSTLHVSTTTKA. Due to the poor quality of the electron density map for the ...Details: The full sequence of hypothetical protein is GASGSAMAEINYEKILLETGLVASNASGIQFPQQFGAMSHEFGGLSGVANFSHQHETTKLKCSTRTTSYSTLHVSTTTKA. Due to the poor quality of the electron density map for the portion of hypothetical protein (HP) in a stable functional complex with SDH, it is unclear which segment of hypothetical protein is visualized in the structure. Therefore, this region (chain O and chain P) was modeled as poly-UNK.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 613.749 Da
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #3: hypothetical protein

MacromoleculeName: hypothetical protein / type: protein_or_peptide / ID: 3
Details: The full sequence of hypothetical protein is GASGSAMAEINYEKILLETGLVASNASGIQFPQQFGAMSHEFGGLSGVANFSHQHETTKLKCSTRTTSYSTLHVSTTTKA. Due to the poor quality of the electron density map for the ...Details: The full sequence of hypothetical protein is GASGSAMAEINYEKILLETGLVASNASGIQFPQQFGAMSHEFGGLSGVANFSHQHETTKLKCSTRTTSYSTLHVSTTTKA. Due to the poor quality of the electron density map for the portion of hypothetical protein (HP) in a stable functional complex with SDH, it is unclear which segment of hypothetical protein is visualized in the structure. Therefore, this region (chain M) was modeled as poly-UNK.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 869.063 Da
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #4: hypothetical protein

MacromoleculeName: hypothetical protein / type: protein_or_peptide / ID: 4
Details: The full sequence of hypothetical protein is GASGSAMAEINYEKILLETGLVASNASGIQFPQQFGAMSHEFGGLSGVANFSHQHETTKLKCSTRTTSYSTLHVSTTTKA. Due to the poor quality of the electron density map for the ...Details: The full sequence of hypothetical protein is GASGSAMAEINYEKILLETGLVASNASGIQFPQQFGAMSHEFGGLSGVANFSHQHETTKLKCSTRTTSYSTLHVSTTTKA. Due to the poor quality of the electron density map for the portion of hypothetical protein (HP) in a stable functional complex with SDH, it is unclear which segment of hypothetical protein is visualized in the structure. Therefore, this region (chain L) was modeled as poly-UNK.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 1.635006 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)

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Macromolecule #5: hypothetical protein

MacromoleculeName: hypothetical protein / type: protein_or_peptide / ID: 5
Details: The full sequence of hypothetical protein is GASGSAMAEINYEKILLETGLVASNASGIQFPQQFGAMSHEFGGLSGVANFSHQHETTKLKCSTRTTSYSTLHVSTTTKA. Due to the poor quality of the electron density map for the ...Details: The full sequence of hypothetical protein is GASGSAMAEINYEKILLETGLVASNASGIQFPQQFGAMSHEFGGLSGVANFSHQHETTKLKCSTRTTSYSTLHVSTTTKA. Due to the poor quality of the electron density map for the portion of hypothetical protein (HP) in a stable functional complex with SDH, it is unclear which segment of hypothetical protein is visualized in the structure.Therefore, this region (chain N) was modeled as poly-UNK.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 783.958 Da
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #6: hypothetical protein

MacromoleculeName: hypothetical protein / type: protein_or_peptide / ID: 6
Details: The full sequence of hypothetical protein is GASGSAMAEINYEKILLETGLVASNASGIQFPQQFGAMSHEFGGLSGVANFSHQHETTKLKCSTRTTSYSTLHVSTTTKA. Due to the poor quality of the electron density map for the ...Details: The full sequence of hypothetical protein is GASGSAMAEINYEKILLETGLVASNASGIQFPQQFGAMSHEFGGLSGVANFSHQHETTKLKCSTRTTSYSTLHVSTTTKA. Due to the poor quality of the electron density map for the portion of hypothetical protein (HP) in a stable functional complex with SDH, it is unclear which segment of hypothetical protein is visualized in the structure. Therefore, this region (chain Q) was modeled as poly-UNK.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 954.168 Da
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 56.12 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.551 µm / Nominal defocus min: 2.888 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: 3.51 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 150976
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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