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- EMDB-71265: Cryo-EM structure of Nectin-2 complex with Fab F1 -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-71265
TitleCryo-EM structure of Nectin-2 complex with Fab F1
Map datasharped 3D reconstruction Map of Nectin_2-F1
Sample
  • Complex: Nectin-2_F1
    • Protein or peptide: Nectin-2
    • Protein or peptide: F1 light chain
    • Protein or peptide: F1 heavy chain
Keywordsantibody and target complex / PROTEIN BINDING
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.01 Å
AuthorsYueyue YW
Funding support1 items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: Cryo-EM structure of Nectin-2_F1 complex
Authors: Yueyue YW
History
DepositionJun 16, 2025-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71265.png

Downloads & links

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Map

FileDownload / File: emd_71265.map.gz / Format: CCP4 / Size: 115.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharped 3D reconstruction Map of Nectin_2-F1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 312 pix.
= 271.44 Å		0.87 Å/pix.
x 312 pix.
= 271.44 Å		0.87 Å/pix.
x 312 pix.
= 271.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.87 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0137
Minimum - Maximum-0.0017986193 - 1.875951
Average (Standard dev.)0.0008262216 (±0.02183664)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions312312312
Spacing312312312
CellA=B=C: 271.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half Cryo-EM Map of Nectin 2-F1 A

Fileemd_71265_half_map_1.map
Annotationhalf Cryo-EM Map of Nectin_2-F1 A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half Cryo-EM Map of Nectin 2-F1 B

Fileemd_71265_half_map_2.map
Annotationhalf Cryo-EM Map of Nectin_2-F1 B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Nectin-2_F1

EntireName: Nectin-2_F1
Components
  • Complex: Nectin-2_F1
    • Protein or peptide: Nectin-2
    • Protein or peptide: F1 light chain
    • Protein or peptide: F1 heavy chain

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Supramolecule #1: Nectin-2_F1

SupramoleculeName: Nectin-2_F1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Nectin-2

MacromoleculeName: Nectin-2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.683949 KDa
Recombinant expressionOrganism: Insect associated flavi-like virus
SequenceString: AQDVRVQVLP EVRGQLGGTV ELPCHLLPPV PGLYISLVTW QRPDAPANHQ NVAAFHPKMG PSFPSPKPGS ERLSFVSAKQ STGQDTEAE LQDATLALHG LTVEDEGNYT CEFATFPKGS VRGMTWLRVI AKPKNQAEAQ KVTFSQDPTT VALCISKEGR P PARISWLS ...String:
AQDVRVQVLP EVRGQLGGTV ELPCHLLPPV PGLYISLVTW QRPDAPANHQ NVAAFHPKMG PSFPSPKPGS ERLSFVSAKQ STGQDTEAE LQDATLALHG LTVEDEGNYT CEFATFPKGS VRGMTWLRVI AKPKNQAEAQ KVTFSQDPTT VALCISKEGR P PARISWLS SLDWEAKETQ VSGTLAGTVT VTSRFTLVPS GRADGVTVTC KVEHESFEEP ALIPVTLSVR YPPEVSISGY DD NWYLGRT DATLSCDVRS NPEPTGYDWS TTSGTFPTSA VAQGSQLVIH AVDSLFNTTF VCTVTNAVGM GRAEQVIFVR ETP NTAGAG ATGGSRGSAW SHPQFEKGGG SGGGSGGSAW SHPQFEK

UniProtKB: Nectin-2

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Macromolecule #2: F1 light chain

MacromoleculeName: F1 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.602145 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: DIQMTQSPSS LSASVGDRVT ITCRASQSVS SAVAWYQQKP GKAPKLLIYS ASSLYSGVPS RFSGSRSGTD FTLTISSLQP EDFATYYCQ QSHYSYGGPI TFGQGTKVEI KRTVAAPSVF IFPPSDEQLK SGTASVVCLL NNFYPREAKV QWKVDNALQS G NSQESVTE ...String:
DIQMTQSPSS LSASVGDRVT ITCRASQSVS SAVAWYQQKP GKAPKLLIYS ASSLYSGVPS RFSGSRSGTD FTLTISSLQP EDFATYYCQ QSHYSYGGPI TFGQGTKVEI KRTVAAPSVF IFPPSDEQLK SGTASVVCLL NNFYPREAKV QWKVDNALQS G NSQESVTE QDSKDSTYSL SSTLTLSKAD YEKHKVYACE VTHQGLSSPV TKSFNRGEC

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Macromolecule #3: F1 heavy chain

MacromoleculeName: F1 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.291041 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EVQLVESGGG LVQPGGSLRL SCAASGFNIY SSSIHWVRQA PGKGLEWVAS ISPYSSYTYY ADSVKGRFTI SADTSKNTAY LQMNSLRAE DTAVYYCARS YGWSYAGHYG MDYWGQGTLV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA ...String:
EVQLVESGGG LVQPGGSLRL SCAASGFNIY SSSIHWVRQA PGKGLEWVAS ISPYSSYTYY ADSVKGRFTI SADTSKNTAY LQMNSLRAE DTAVYYCARS YGWSYAGHYG MDYWGQGTLV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKSCDK T

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 103161
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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