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- EMDB-65977: Structure of Klebsiella pneumoniae trypsin-HamAB bound with DNA, ... -

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Basic information

Entry
Database: EMDB / ID: EMD-65977
TitleStructure of Klebsiella pneumoniae trypsin-HamAB bound with DNA, trimer
Map data
Sample
  • Complex: Klebsiella pneumoniae HamAB trimer bound with DNA
    • Protein or peptide: Anti-bacteriophage protein A/HamA C-terminal domain-containing protein
    • Protein or peptide: DNA polymerase theta (Helicase domain only)
    • DNA: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*A)-3')
    • DNA: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*A)-3')
KeywordsATPase / Helicase / DNA BINDING PROTEIN/DNA / 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 polymerase theta (Helicase domain only) / Anti-bacteriophage protein A/HamA C-terminal domain-containing protein
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsHuang PP / Liu JX / Shen LB / Chen MR / Xiao YB
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Chem Biol / Year: 2026
Title: The antiphage mechanism of a widespread trypsin-MBL defense module.
Authors: Pingping Huang / Jingxian Liu / Lijie Guo / Dongyang Xu / Lingbo Shen / Purui Yan / Chen Tong / Wenying Fei / Mengjun Cheng / Zhaoxing Li / Meiling Lu / Lei Zhang / Nannan Wu / Lian-Wen Qi / ...Authors: Pingping Huang / Jingxian Liu / Lijie Guo / Dongyang Xu / Lingbo Shen / Purui Yan / Chen Tong / Wenying Fei / Mengjun Cheng / Zhaoxing Li / Meiling Lu / Lei Zhang / Nannan Wu / Lian-Wen Qi / Yibei Xiao / Meirong Chen /
Abstract: Protease-mediated activation of immune effectors is an evolutionarily conserved mechanism. This study identifies a widespread trypsin-MBL (metallo-β-lactamase) module as a core effector in diverse ...Protease-mediated activation of immune effectors is an evolutionarily conserved mechanism. This study identifies a widespread trypsin-MBL (metallo-β-lactamase) module as a core effector in diverse antiviral bacterial immune systems, such as Hachiman, AVAST and Argonaute. Focusing on the Hachiman-associated trypsin-MBL system, we show that trypsin•HamAB protease activity is inhibited by ATP, while MBL is an autoinhibited DNase with two insertion loops obstructing its catalytic site. Upon infection, trypsin•HamAB senses foreign DNA and hydrolyzes ATP, activating trypsin-like activity, which specifically cleaves MBL at the insertion loops to release repression. The activated MBL depletes DNA and arrests host cell growth. Cryo-electron microscopy structures of trypsin•HamAB-DNA reveal that DNA binding and ATP hydrolysis trigger HamAB oligomerization and trypsin-like domain release, enabling its activation. Our work elucidates a conserved immune mechanism wherein proteolytic activation of a nuclease enables robust immunity against phage while multilayered controls prevent self-toxicity, expanding the repertoire of immune processes governed by regulatory proteolysis.
History
DepositionAug 27, 2025-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65977.png

Downloads & links

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Map

FileDownload / File: emd_65977.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 512 pix.
= 477.184 Å		0.93 Å/pix.
x 512 pix.
= 477.184 Å		0.93 Å/pix.
x 512 pix.
= 477.184 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.23619436 - 0.5168719
Average (Standard dev.)0.00017051098 (±0.011459464)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 477.184 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65977_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65977_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Klebsiella pneumoniae HamAB trimer bound with DNA

EntireName: Klebsiella pneumoniae HamAB trimer bound with DNA
Components
  • Complex: Klebsiella pneumoniae HamAB trimer bound with DNA
    • Protein or peptide: Anti-bacteriophage protein A/HamA C-terminal domain-containing protein
    • Protein or peptide: DNA polymerase theta (Helicase domain only)
    • DNA: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*A)-3')
    • DNA: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*A)-3')

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Supramolecule #1: Klebsiella pneumoniae HamAB trimer bound with DNA

SupramoleculeName: Klebsiella pneumoniae HamAB trimer bound with DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Klebsiella pneumoniae (bacteria)

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

MacromoleculeName: Anti-bacteriophage protein A/HamA C-terminal domain-containing protein
type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 59.614848 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSIDIADKLG VKISYNNKNS SGFICHGDDY SYVLTAKHSI CKSSPNDCKF KHKKCDTCVF SGVAKNKVSI CKPDTDTFPL CKVKDVLLS PKKDVAILVL NKKSHIDLKT KELPSTKIIN TANYNSSHKF VSCGYPAINE HQSVQPLHYN NFSLFRNEKI C LQIINDTL ...String:
MSIDIADKLG VKISYNNKNS SGFICHGDDY SYVLTAKHSI CKSSPNDCKF KHKKCDTCVF SGVAKNKVSI CKPDTDTFPL CKVKDVLLS PKKDVAILVL NKKSHIDLKT KELPSTKIIN TANYNSSHKF VSCGYPAINE HQSVQPLHYN NFSLFRNEKI C LQIINDTL TALEDPKNGL SGNSGAGIIL NSSSCVGLLG LYTDTGDYGI CYGDIVDFSI NELLTSSGYV PLEMEEDLSN NF KALIQSD FMECFVRMEC DLNLDKNRIV NLYRLCLDGK KYNYVKIGER LIDCIPSFSL SRKQLMRCRE RNAFGKATLS AIR NFLKIE RKTKISEMLL QGFLESYLHA PKLYSFDEIN NAGFHGAHVK FNKNRNVELI HSAAFISNSL SDGVSYAIDV ILKA FPELR SLDGLLGNTF LETNFTEDEC QILASLLIPG ESSYSQGYED RLAIFIGYNH KIEESLIYEN ASRFPSLLEQ KIILN VQQA LEYRKEEINK LSIVNATIDC FFVPFDDVNK FNDEFIESLK NEED

UniProtKB: Anti-bacteriophage protein A/HamA C-terminal domain-containing protein

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Macromolecule #2: DNA polymerase theta (Helicase domain only)

MacromoleculeName: DNA polymerase theta (Helicase domain only) / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 99.035922 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKKIDSFIIE KIFNSAYFKK LYKKIIKAYS ALTIESENHF NISNTELRDI FRFIDLLANS SNQNARMCAY HWISLLEPFS DKWGKFSLI SSLVYSKLGL YALDFNDHAL PFSQRLENEA KKSAQTFSNT YIFTDAQFDI YTDMLKSPYY SFSGPTSLGK S FILKRYIE ...String:
MKKIDSFIIE KIFNSAYFKK LYKKIIKAYS ALTIESENHF NISNTELRDI FRFIDLLANS SNQNARMCAY HWISLLEPFS DKWGKFSLI SSLVYSKLGL YALDFNDHAL PFSQRLENEA KKSAQTFSNT YIFTDAQFDI YTDMLKSPYY SFSGPTSLGK S FILKRYIE EIIQNSTSNI VILVPTRALI SQFSLEIKNE LHELIENFNY KIVTHGSLAS KSDAVIIKHI FILTPERLLN LF SQGKVVS IDYLFVDEAH KLSNNDDSDV RSLTEYNAID SALFNNPNMK IVFSSPNIEN PEVFLNLFGR EKIYASRIIE SPV SQNLYL IDFHKKEIKY FSNSECIDIE SGSLYTLNKK SDFIYNIGSR HGSNMIYCSS RAKAVDSALE FYQIRLSENI VLSP LLIDS IKKISNYIHP EYYLAMFLMK RIAYHHGQLP QAIRNIVEEL FRKGDIDFIF CTPTLVEGVN MPTRNIFINC DDKIR LIAD AKKNPNKTLA FWNLAGRAGR YCKELSGNIF CLQDESNRWD NTDIFLEKTA HLTTTIDARI ESKSGLREIE RYLSDT ETD IYKRNQAIEY LANIMAVDTI RFKNNLKDSF VLRKFYDIHR EELLSLAKLK ANDILDIPID IINSYKSLNF KIQRKVF DY VSVSPVNKKL PSLDYANILS VLELFYDLYR WGETETKYVK SKGQLTYFAT LMNQWTNDYS INRIINENID IKRTIVIE R GQQPIPFDKN DINHVNKVID DILYNIERIL SFFFEKYFNH YYKCLAAILG EDNAGHNWAT FLEYGSKNPL CISLQTLGI SRHAANIIAS SKELRKYLKF NEDSYEIISV NKQGLLNSLQ KDSVEYGEVK IFL

UniProtKB: DNA polymerase theta (Helicase domain only)

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Macromolecule #3: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*A)-3')

MacromoleculeName: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*A)-3') / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 2.14749 KDa
SequenceString:
(DA)(DA)(DA)(DA)(DA)(DA)(DA)

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Macromolecule #4: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*A)-3')

MacromoleculeName: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*A)-3') / type: dna / ID: 4 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 2.460697 KDa
SequenceString:
(DA)(DA)(DA)(DA)(DA)(DA)(DA)(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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 50060
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
FSC plot (resolution estimation)

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