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- PDB-9tgn: Cryo-EM structure of Z-DNA binding antibody Z-D11 in complex with... -

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Basic information

Entry
Database: PDB / ID: 9tgn
TitleCryo-EM structure of Z-DNA binding antibody Z-D11 in complex with left-handed Z-DNA
Components
  • DNA (5'-D(*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*G)-3')
  • ZD11-VH
  • ZD11-VL
KeywordsDNA BINDING PROTEIN / Z-DNA / monoclonal antibody / left-handed geometry / antibody avidity
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.55 Å
AuthorsChin, D.H.R. / Luo, Y.B. / Luo, D.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore) Singapore
CitationJournal: bioRxiv / Year: 2025
Title: Cryo-EM structures of anti Z-DNA antibodies in complex with antigen reveal distinct recognition modes of a left-handed geometry.
Authors: Danielle Chin / Yongbo Luo / Yiteng Lau / Nivedita Dutta / Zengyting He / Chaoran Yin / Riley M Williams / Siddharth Balachandran / Quentin Vicens / Peter Dröge / Dahai Luo
Abstract: Double-stranded nucleic acids can undergo transitions from canonical B/A-forms to alternate left-handed Z-DNA/Z-RNA (Z-NAs). Z-NAs are implicated in processes such as neuroinflammation in Alzheimer's ...Double-stranded nucleic acids can undergo transitions from canonical B/A-forms to alternate left-handed Z-DNA/Z-RNA (Z-NAs). Z-NAs are implicated in processes such as neuroinflammation in Alzheimer's disease, Lupus Erythematosus, microbial biofilms, and type I interferon-mediated human pathologies. Since endogenous Z-NA sensors like the Zα domain can induce B-to-Z transitions, monoclonal antibodies (mAbs) Z-D11 and Z22 have been regarded as conformation-specific tools to confirm Z-NA , although high-resolution structural information is missing. Here, we employed single-particle cryo-electron microscopy to solve structures of Z-D11 and Z22 bound to synthetic d(CG) 12mer Z-DNA duplex. Both mAbs form filamentous trimers around the Z-DNA axis, further stabilized by Fab-Fab interactions. The mAbs achieve specificity through extensive contacts to both Z-form backbone strands and the exposed guanine/cytosine bases in the major groove. This mode of recognition is dictated by shape complementarity rather than sequence specificity, sensing the alternating syn/anti backbone torsions and the phosphate zig-zag geometry unique to Z-DNA. Our data also suggest that these mAbs are not inducing B-to-Z transitions under normal physiological conditions. Finally, comparison to other double-stranded NA-binding mAbs defines a similar structural logic adapted to different helical geometry recognition patterns, thus providing a framework for engineering highly specific nucleic acid probes.
History
DepositionDec 2, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 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

Downloads & links

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Assembly

Deposited unit
A: ZD11-VL
B: ZD11-VH
C: ZD11-VL
D: ZD11-VH
E: ZD11-VL
F: ZD11-VH
G: ZD11-VL
H: ZD11-VH
I: ZD11-VL
J: ZD11-VH
K: ZD11-VL
L: ZD11-VH
M: DNA (5'-D(*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*G)-3')
N: DNA (5'-D(*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*G)-3')
O: DNA (5'-D(*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*G)-3')
P: DNA (5'-D(*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,55024
Polymers170,35516
Non-polymers1948
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Antibody
ZD11-VL


Mass: 12085.450 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Light chain of antibody Z-D11 / Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#2: Antibody
ZD11-VH


Mass: 13863.495 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Heavy chain of antibody Z-D11 / Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#3: DNA chain
DNA (5'-D(*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*G)-3')


Mass: 3665.368 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: DNA synthesised from IDT / Source: (synth.) Homo sapiens (human)
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: Z-DNA binding antibody Z-D11 in complex with left-handed Z-DNA
Type: COMPLEX
Details: Full length antibody used for complex preparation with 12-mer DNA: complex forms a dimer of trimer along the Z-DNA axis
Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.9 MDa / Experimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.2
Details: High salt annealing buffer (for complex preparation): 20mM HEPES pH 7.2, 2.5M NaCl, 0.7M Mg Cl2 Buffer listed above is after analytical SEC.
Buffer component
IDConc.NameBuffer-ID
120 mMHEPES1
2150 mMNaCl1
31 %sucrose1
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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 magnification: 165000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 4000

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5particle selection
2PHENIX1.20.1_4487model refinement
3SerialEM4image acquisition
5cryoSPARC4.5CTF correction
13cryoSPARC4.53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 146988 / Symmetry type: POINT
RefinementHighest resolution: 2.55 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00512251
ELECTRON MICROSCOPYf_angle_d0.68616792
ELECTRON MICROSCOPYf_dihedral_angle_d16.512027
ELECTRON MICROSCOPYf_chiral_restr0.0451844
ELECTRON MICROSCOPYf_plane_restr0.0041968

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