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- PDB-9whk: Structure of Klebsiella pneumoniae trypsin-HamAB bound with DNA, dimer -

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Basic information

Entry
Database: PDB / ID: 9whk
TitleStructure of Klebsiella pneumoniae trypsin-HamAB bound with DNA, dimer
Components
  • Anti-bacteriophage protein A/HamA C-terminal domain-containing protein
  • DNA (5'-D(P*AP*AP*AP*AP*AP*AP*A)-3')
  • DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
  • DNA polymerase theta (Helicase domain only)
KeywordsDNA BINDING PROTEIN/DNA / ATPase / Helicase / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


helicase activity / nucleic acid binding / hydrolase activity / ATP binding
Similarity search - Function
Anti-bacteriophage protein A/HamA, C-terminal domain / HamA / : / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily ...Anti-bacteriophage protein A/HamA, C-terminal domain / HamA / : / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Peptidase S1, PA clan / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA / DNA polymerase theta (Helicase domain only) / Anti-bacteriophage protein A/HamA C-terminal domain-containing protein
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsHuang, P.P. / Liu, J.X. / Shen, L.B. / Chen, M.R. / Xiao, Y.B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of Klebsiella pneumoniae HamAB dimer bound with DNA
Authors: Huang, P.P. / Chen, M.R.
History
DepositionAug 27, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anti-bacteriophage protein A/HamA C-terminal domain-containing protein
B: DNA polymerase theta (Helicase domain only)
C: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
D: Anti-bacteriophage protein A/HamA C-terminal domain-containing protein
E: DNA polymerase theta (Helicase domain only)
F: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)322,2236
Polymers322,2236
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

#1: Protein Anti-bacteriophage protein A/HamA C-terminal domain-containing protein


Mass: 59614.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: SAMEA4873653_00088 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A486PDC8
#2: Protein DNA polymerase theta (Helicase domain only)


Mass: 99035.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: B6I68_29715, SAMEA4873653_00087 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A486PCQ5
#3: DNA chain DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')


Mass: 2773.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Klebsiella pneumoniae (bacteria)
#4: DNA chain DNA (5'-D(P*AP*AP*AP*AP*AP*AP*A)-3')


Mass: 2147.490 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Klebsiella pneumoniae (bacteria)
Has protein modificationY

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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: Klebsiella pneumoniae HamAB dimer bound with DNA / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
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: 2400 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 88815 / Symmetry type: POINT
RefinementCross valid method: NONE

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