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- PDB-44fi: Undecameric complex of serine proteinase (SDH) with hypothetical ... -

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Basic information

Entry
Database: PDB / ID: 44fi
TitleUndecameric complex of serine proteinase (SDH) with hypothetical protein (HP)
Components
  • (hypothetical ...) x 5
  • serine proteinase(SDH)
KeywordsIMMUNE SYSTEM / undecamer
Biological speciesKlebsiella pneumoniae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.51 Å
AuthorsYu, Y. / Chen, Q.
Funding support China, 1items
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, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 16, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 16, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: serine proteinase(SDH)
A: serine proteinase(SDH)
B: serine proteinase(SDH)
C: serine proteinase(SDH)
D: serine proteinase(SDH)
F: serine proteinase(SDH)
G: serine proteinase(SDH)
H: serine proteinase(SDH)
I: serine proteinase(SDH)
J: serine proteinase(SDH)
K: serine proteinase(SDH)
O: hypothetical protein
M: hypothetical protein
L: hypothetical protein
P: hypothetical protein
N: hypothetical protein
Q: hypothetical protein


Theoretical massNumber of molelcules
Total (without water)377,97817
Polymers377,97817
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 1 types, 11 molecules EABCDFGHIJK

#1: Protein
serine proteinase(SDH)


Mass: 33864.375 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Hypothetical ... , 5 types, 6 molecules OPMLNQ

#2: Protein/peptide hypothetical protein


Mass: 613.749 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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.
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Protein/peptide hypothetical protein


Mass: 869.063 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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.
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#4: Protein/peptide hypothetical protein


Mass: 1635.006 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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.
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#5: Protein/peptide hypothetical protein


Mass: 783.958 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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.
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#6: Protein/peptide hypothetical protein


Mass: 954.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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.
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Details

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: Undecameric complex of serine proteinase (SDH) with hypothetical protein (HP)
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 5551 nm / Nominal defocus min: 2888 nm
Image recordingElectron dose: 56.12 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.15.2_3472model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.51 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 150976 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01349435
ELECTRON MICROSCOPYf_angle_d1.20488511
ELECTRON MICROSCOPYf_dihedral_angle_d12.23520291
ELECTRON MICROSCOPYf_chiral_restr0.084056
ELECTRON MICROSCOPYf_plane_restr0.0087438

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