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- PDB-9p4f: Cryo-EM structure of Nectin-2 complex with Fab F1 -

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Basic information

Entry
Database: PDB / ID: 9p4f
TitleCryo-EM structure of Nectin-2 complex with Fab F1
Components
  • F1 heavy chain
  • F1 light chain
  • Nectin-2
KeywordsPROTEIN BINDING / antibody and target complex
Function / homology
Function and homology information


coreceptor-mediated virion attachment to host cell / positive regulation of immunoglobulin mediated immune response / susceptibility to T cell mediated cytotoxicity / susceptibility to natural killer cell mediated cytotoxicity / regulation of viral entry into host cell / positive regulation of mast cell activation / Nectin/Necl trans heterodimerization / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / adhesion of symbiont to host / zonula adherens ...coreceptor-mediated virion attachment to host cell / positive regulation of immunoglobulin mediated immune response / susceptibility to T cell mediated cytotoxicity / susceptibility to natural killer cell mediated cytotoxicity / regulation of viral entry into host cell / positive regulation of mast cell activation / Nectin/Necl trans heterodimerization / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / adhesion of symbiont to host / zonula adherens / cell-cell contact zone / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of T cell receptor signaling pathway / negative regulation of natural killer cell mediated cytotoxicity / Adherens junctions interactions / natural killer cell mediated cytotoxicity / spermatid development / apical junction complex / homophilic cell-cell adhesion / coreceptor activity / cell adhesion molecule binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell-cell junction / virus receptor activity / receptor ligand activity / fusion of virus membrane with host plasma membrane / focal adhesion / cell surface / protein homodimerization activity / extracellular exosome / membrane / identical protein binding / plasma membrane
Similarity search - Function
: / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain ...: / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.01 Å
AuthorsYueyue, Y.W.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: Cryo-EM structure of Nectin-2_F1 complex
Authors: Yueyue, Y.W.
History
DepositionJun 16, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 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

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Assembly

Deposited unit
A: Nectin-2
B: F1 light chain
C: F1 heavy chain
D: Nectin-2
E: F1 light chain
F: F1 heavy chain


Theoretical massNumber of molelcules
Total (without water)173,1546
Polymers173,1546
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Nectin-2 / Herpes virus entry mediator B / Herpesvirus entry mediator B / HveB / Nectin cell adhesion molecule ...Herpes virus entry mediator B / Herpesvirus entry mediator B / HveB / Nectin cell adhesion molecule 2 / Poliovirus receptor-related protein 2


Mass: 38683.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NECTIN2, HVEB, PRR2, PVRL2 / Production host: Insect associated flavi-like virus / References: UniProt: Q92692
#2: Antibody F1 light chain


Mass: 23602.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody F1 heavy chain


Mass: 24291.041 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
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: Nectin-2_F1 / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Insect associated flavi-like virus
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
7UCSF ChimeraX1.5model fitting
9PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 103161 / Symmetry type: POINT

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