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- EMDB-55905: Cryo-EM structure of Z-DNA binding antibody Z-D11 in complex with... -

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Entry
Database: EMDB / ID: EMD-55905
TitleCryo-EM structure of Z-DNA binding antibody Z-D11 in complex with left-handed Z-DNA
Map data
Sample
  • Complex: Z-DNA binding antibody Z-D11 in complex with left-handed Z-DNA
    • Protein or peptide: ZD11-VL
    • Protein or peptide: ZD11-VH
    • DNA: DNA (5'-D(*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*G)-3')
  • Ligand: MAGNESIUM ION
  • Ligand: water
KeywordsZ-DNA / monoclonal antibody / left-handed geometry / antibody avidity / DNA BINDING PROTEIN
Biological speciesMus musculus (house mouse) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.55 Å
AuthorsChin DHR / Luo YB / Luo D
Funding support Singapore, 1 items
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, 2025-
Header (metadata) releaseJan 14, 2026-
Map releaseJan 14, 2026-
UpdateJan 14, 2026-
Current statusJan 14, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55905.png

Downloads & links

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Map

FileDownload / File: emd_55905.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.76 Å/pix.
x 512 pix.
= 387.584 Å		0.76 Å/pix.
x 512 pix.
= 387.584 Å		0.76 Å/pix.
x 512 pix.
= 387.584 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.757 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.29434222 - 0.50158113
Average (Standard dev.)-0.000054853408 (±0.0080539305)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 387.584 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_55905_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_55905_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Z-DNA binding antibody Z-D11 in complex with left-handed Z-DNA

EntireName: Z-DNA binding antibody Z-D11 in complex with left-handed Z-DNA
Components
  • Complex: Z-DNA binding antibody Z-D11 in complex with left-handed Z-DNA
    • Protein or peptide: ZD11-VL
    • Protein or peptide: ZD11-VH
    • DNA: DNA (5'-D(*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*G)-3')
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: Z-DNA binding antibody Z-D11 in complex with left-handed Z-DNA

SupramoleculeName: Z-DNA binding antibody Z-D11 in complex with left-handed Z-DNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: Full length antibody used for complex preparation with 12-mer DNA: complex forms a dimer of trimer along the Z-DNA axis
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 900 KDa

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Macromolecule #1: ZD11-VL

MacromoleculeName: ZD11-VL / type: protein_or_peptide / ID: 1 / Details: Light chain of antibody Z-D11 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 12.08545 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQMTQTTSS LSASLGDRVT INCRASQDIS NYLNWYQQKP DGTVKLLIYY TSRLHSGVPS RFSGSGSGTD FSLTISYLEQ EDIATYFCQ QGKTLPFTFG AGTKLELKRA

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Macromolecule #2: ZD11-VH

MacromoleculeName: ZD11-VH / type: protein_or_peptide / ID: 2 / Details: Heavy chain of antibody Z-D11 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.863495 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVETGGG LVQPKGSLKL SCAASGFTFN TNAMNWVRQA PGKGLEWVAR IRSKSNNYAT YYADSVKDRF TISRDDSQSM LYLQMNNLK TEDTAMYYCV RGYVNYYYVM DYWGQGTSVT VSSA

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Macromolecule #3: DNA (5'-D(*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*G)-3')

MacromoleculeName: DNA (5'-D(*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*G)-3') / type: dna / ID: 3 / Details: DNA synthesised from IDT / Number of copies: 4 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 3.665368 KDa
SequenceString:
(DC)(DG)(DC)(DG)(DC)(DG)(DC)(DG)(DC)(DG) (DC)(DG)

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 8 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 22 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration0.3 mg/mL
BufferpH: 7.2
Component:
ConcentrationName
20.0 mMHEPES
150.0 mMNaCl
1.0 %sucrose

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.
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 4000 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.5) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5) / Number images used: 146988
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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