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- EMDB-55912: Cryo-EM structure of Z22 antibody in complex with left-handed Z-D... -

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Basic information

Entry
Database: EMDB / ID: EMD-55912
TitleCryo-EM structure of Z22 antibody in complex with left-handed Z-DNA (trimer)
Map data
Sample
  • Complex: Trimer of Z22 antibody in complex with left-handed Z-DNA
    • Protein or peptide: Z22-VH
    • Protein or peptide: Z22-VL
    • DNA: DNA (5'-D(P*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*G)-3')
  • Ligand: water
KeywordsZ-DNA / left-handed geometry / monoclonal antibody / antibody avidity / DNA BINDING PROTEIN
Biological speciesMus musculus (house mouse) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.67 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_55912.png

Downloads & links

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Map

FileDownload / File: emd_55912.map.gz / Format: CCP4 / Size: 178 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 360 pix.
= 273.6 Å		0.76 Å/pix.
x 360 pix.
= 273.6 Å		0.76 Å/pix.
x 360 pix.
= 273.6 Å

Surface

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Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.76 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.033
Minimum - Maximum-0.30597892 - 0.5139849
Average (Standard dev.)0.00016417351 (±0.01117362)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 273.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_55912_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_55912_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : Trimer of Z22 antibody in complex with left-handed Z-DNA

EntireName: Trimer of Z22 antibody in complex with left-handed Z-DNA
Components
  • Complex: Trimer of Z22 antibody in complex with left-handed Z-DNA
    • Protein or peptide: Z22-VH
    • Protein or peptide: Z22-VL
    • DNA: DNA (5'-D(P*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*G)-3')
  • Ligand: water

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Supramolecule #1: Trimer of Z22 antibody in complex with left-handed Z-DNA

SupramoleculeName: Trimer of Z22 antibody in complex with left-handed Z-DNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: Fab domains of Z22 arranged in a trimeric formation surrounding the Z-DNA
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 450 KDa

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Macromolecule #1: Z22-VH

MacromoleculeName: Z22-VH / type: protein_or_peptide / ID: 1 / Details: Heavy chain fab domain of Z22 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.627357 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
KVQLVESGGG LVQPKGSLKL SCAASGFNFN TYAMNWVRQA PGKGLEWVAR IRSKSNNYAT YYADSMKDRF TISRDDSENM LYLQMINLK AEDTAMYYCV RQAYSNYGAM DYWGQGISVT VS

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Macromolecule #2: Z22-VL

MacromoleculeName: Z22-VL / type: protein_or_peptide / ID: 2 / Details: Light chain fab of Z22 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.662902 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQMTQTISS LSASLGDRVT ISCSASQGIS NYLNWYQQKP DGTVKLLIYY TSRLHSGVPS RFSGSGSGTD YSLTISNLEP EDIATYFCQ QYSKFPFTFG SGTKLEI

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

MacromoleculeName: DNA (5'-D(P*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*G)-3') / type: dna / ID: 3 / Details: DNA chemically synthesised from IDT / Number of copies: 2 / 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: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 15 / 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

Concentration1.1 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 MgCl2 Buffer above is for 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: 4660 / 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 / Nominal defocus max: 2.23 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 165000
Sample stageCooling 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: 2.67 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5) / Number images used: 59879
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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