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- EMDB-64496: Cryo-EM structure of the oxytocin receptor bound to nanobody Nb2B11 -

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Basic information

Entry
Database: EMDB / ID: EMD-64496
TitleCryo-EM structure of the oxytocin receptor bound to nanobody Nb2B11
Map data
Sample
  • Complex: Cryo-EM structure of the oxytocin receptor bound to nanobody Nb2B11
    • Protein or peptide: Oxytocin receptor
    • Protein or peptide: Nb2B11
KeywordsGPCR / inactive-state / de novo protein / nanobody / MEMBRANE PROTEIN/IMMUNE SYSTEM / MEMBRANE PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


oxytocin receptor activity / fetal process involved in parturition / milk ejection reflex / female mating behavior / maternal process involved in parturition / positive regulation of uterine smooth muscle contraction / regulation of systemic arterial blood pressure by vasopressin / Vasopressin-like receptors / vasopressin receptor activity / maternal behavior ...oxytocin receptor activity / fetal process involved in parturition / milk ejection reflex / female mating behavior / maternal process involved in parturition / positive regulation of uterine smooth muscle contraction / regulation of systemic arterial blood pressure by vasopressin / Vasopressin-like receptors / vasopressin receptor activity / maternal behavior / positive regulation of osteoblast differentiation / social behavior / lactation / positive regulation of vasoconstriction / cellular response to hormone stimulus / muscle contraction / female pregnancy / regulation of synaptic plasticity / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cold-induced thermogenesis / G alpha (q) signalling events / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / plasma membrane
Similarity search - Function
Oxytocin receptor / Vasopressin receptor / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human) / Vicugna pacos (alpaca)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsGao K / Nie J / Zhang X / Liu X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32122041 China
CitationJournal: Nat Commun / Year: 2026
Title: Discovery of an antagonist nanobody targeting the oxytocin receptor with tocolytic effect in mice.
Authors: Jia Nie / Kaixuan Gao / Xin Zhang / Hengyu Meng / Qi Li / Xiaowen Zhang / Yanying Wu / Hongtao Zeng / Waner Liu / Lijuan Liu / Lunbo Tan / Xiaoou Sun / Xiangyu Liu / Weishe Zhang /
Abstract: Preterm birth, defined as delivery before 37 completed weeks of gestation, poses significant risks to maternal and neonatal health. These risks include neonatal respiratory distress syndrome, ...Preterm birth, defined as delivery before 37 completed weeks of gestation, poses significant risks to maternal and neonatal health. These risks include neonatal respiratory distress syndrome, intraventricular hemorrhage, long-term developmental challenges, and in severe cases, mortality. Addressing these issues, G protein-coupled receptor (GPCR)-mediated tocolysis has become a focal strategy in pharmaceutical research to mitigate preterm labor risks. Most GPCR drugs are small molecules, yet their tendency to cross the placental barrier and induce fetal toxicity presents a significant challenge. Antibody drugs, with minimal cell membrane permeability, offer a promising alternative. In this study, we leverage AI-driven protein design to enable nanobody screening and identify several nanobodies with antagonist activity against the oxytocin receptor, a key target for preterm birth therapeutics. One of these nanobodies demonstrates antagonist activity comparable to Atosiban, a commonly used clinical drug, while exhibiting higher subtype selectivity. Pharmacological and structural analyses reveal mechanisms distinct from small molecule antagonists. These findings expand the pharmacological potential of antibody drugs and introduce useful tools and perspectives for developing effective tocolytic agents.
History
DepositionMay 5, 2025-
Header (metadata) releaseOct 28, 2026-
Map releaseOct 28, 2026-
UpdateOct 28, 2026-
Current statusOct 28, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64496.png

Downloads & links

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Map

FileDownload / File: emd_64496.map.gz / Format: CCP4 / Size: 30.5 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.)
1.08 Å/pix.
x 200 pix.
= 216.5 Å		1.08 Å/pix.
x 200 pix.
= 216.5 Å		1.08 Å/pix.
x 200 pix.
= 216.5 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0825 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-3.607351 - 4.911954
Average (Standard dev.)-0.0031153362 (±0.09116593)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 216.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64496_msk_1.map
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Half map: #2

Fileemd_64496_half_map_1.map
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Half map: #1

Fileemd_64496_half_map_2.map
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Sample components

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Entire : Cryo-EM structure of the oxytocin receptor bound to nanobody Nb2B11

EntireName: Cryo-EM structure of the oxytocin receptor bound to nanobody Nb2B11
Components
  • Complex: Cryo-EM structure of the oxytocin receptor bound to nanobody Nb2B11
    • Protein or peptide: Oxytocin receptor
    • Protein or peptide: Nb2B11

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Supramolecule #1: Cryo-EM structure of the oxytocin receptor bound to nanobody Nb2B11

SupramoleculeName: Cryo-EM structure of the oxytocin receptor bound to nanobody Nb2B11
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Oxytocin receptor

MacromoleculeName: Oxytocin receptor / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.240785 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DYKDDDDAME GALAANWSAE AANASAAPPG AEGNRTAGPP RRNEALARVE VAVLCLILLL ALSGNACVLL ALHTTRQKHS RLFFFMKHL SIADLVVAVF QVLPQLLWDI TFRFYGPDLL CRLVKYLQLV GMFASTYLLL LMSLDRCLAI CQPLRSLRRR T ARLAVLAT ...String:
DYKDDDDAME GALAANWSAE AANASAAPPG AEGNRTAGPP RRNEALARVE VAVLCLILLL ALSGNACVLL ALHTTRQKHS RLFFFMKHL SIADLVVAVF QVLPQLLWDI TFRFYGPDLL CRLVKYLQLV GMFASTYLLL LMSLDRCLAI CQPLRSLRRR T ARLAVLAT WLGCLVVSAP QVHIFSLREV ADGVFDCWAV FIRPWGPKAY ITWITLAVYI VPVIVLATCY GLISFKIWQN LR LKTAAAA AAEAPEGAAA GDGGRVALAR VSSVKLISKA KIRTVKMTFI IVLAFIVCWT PFFFVQMWSV WDANAPKEAS AFI IVMLLA SLNCCCKPWI YMLFMGHLFH ELVQRFLCCS ASYLKGRRLG ETSASKKSNS SSFVLSHRSS SQRSCSQPST AHHH HHHAF KIWQNSALGK ELAAEPVAIL TLSFKAYKGL EEGSKAGEAT M

UniProtKB: Oxytocin receptor

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Macromolecule #2: Nb2B11

MacromoleculeName: Nb2B11 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vicugna pacos (alpaca)
Molecular weightTheoretical: 13.422813 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQESGGG LVQAGGSLRL SCAASGSISG ITDMGWYRQA PGKEREFVAS ITYGGNTNYA DSVKGRFTIS RDNAKNTVYL QMNSLKPED TAVYYCAVAS SRGNSYSLLG GYILTYWGQG TQVTVSS

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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: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 274430
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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