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- EMDB-64047: CryoEM structure of IgV domain of human Nectin-4 with Trimbody -

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Basic information

Entry
Database: EMDB / ID: EMD-64047
TitleCryoEM structure of IgV domain of human Nectin-4 with Trimbody
Map data
Sample
  • Complex: CryoEM structure of IgV domain of human Nectin-4 with Trimbody
    • Complex: H3-PrAC-5350A
      • Protein or peptide: H3-PrAC-5350A,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
    • Complex: N4-nanobody-TAIL
      • Protein or peptide: N4-nanobody-TAIL
    • Complex: IgV domain of human Nectin-4
      • Protein or peptide: Nectin-4
KeywordsSTRUCTURAL PROTEIN
Function / homology
Function and homology information


Nectin/Necl trans heterodimerization / D-galactonate catabolic process / 2-dehydro-3-deoxy-6-phosphogalactonate aldolase activity / cell adhesion mediator activity / negative regulation of natural killer cell mediated cytotoxicity / Adherens junctions interactions / heterophilic cell-cell adhesion / homophilic cell-cell adhesion / adherens junction / virus receptor activity ...Nectin/Necl trans heterodimerization / D-galactonate catabolic process / 2-dehydro-3-deoxy-6-phosphogalactonate aldolase activity / cell adhesion mediator activity / negative regulation of natural killer cell mediated cytotoxicity / Adherens junctions interactions / heterophilic cell-cell adhesion / homophilic cell-cell adhesion / adherens junction / virus receptor activity / receptor ligand activity / extracellular exosome / identical protein binding / plasma membrane
Similarity search - Function
Nectin-4 / : / KDPG/KHG aldolase / KDPG and KHG aldolase / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain ...Nectin-4 / : / KDPG/KHG aldolase / KDPG and KHG aldolase / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Aldolase-type TIM barrel / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Nectin-4 / 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
Similarity search - Component
Biological speciesThermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8) (bacteria) / Thermotoga maritima MSB8 (bacteria) / synthetic construct (others) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.43 Å
AuthorsSong JY / Wang W
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: CryoEM structure of IgV domain of human Nectin-4 with Trimbody
Authors: Song JY / Wang W
History
DepositionApr 4, 2025-
Header (metadata) releaseFeb 11, 2026-
Map releaseFeb 11, 2026-
UpdateFeb 11, 2026-
Current statusFeb 11, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64047.png

Downloads & links

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Map

FileDownload / File: emd_64047.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 288 pix.
= 264.96 Å		0.92 Å/pix.
x 288 pix.
= 264.96 Å		0.92 Å/pix.
x 288 pix.
= 264.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.0017194835 - 2.043929
Average (Standard dev.)0.0000025831532 (±0.031556834)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 264.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : CryoEM structure of IgV domain of human Nectin-4 with Trimbody

EntireName: CryoEM structure of IgV domain of human Nectin-4 with Trimbody
Components
  • Complex: CryoEM structure of IgV domain of human Nectin-4 with Trimbody
    • Complex: H3-PrAC-5350A
      • Protein or peptide: H3-PrAC-5350A,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
    • Complex: N4-nanobody-TAIL
      • Protein or peptide: N4-nanobody-TAIL
    • Complex: IgV domain of human Nectin-4
      • Protein or peptide: Nectin-4

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Supramolecule #1: CryoEM structure of IgV domain of human Nectin-4 with Trimbody

SupramoleculeName: CryoEM structure of IgV domain of human Nectin-4 with Trimbody
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8) (bacteria)

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Supramolecule #2: H3-PrAC-5350A

SupramoleculeName: H3-PrAC-5350A / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1

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Supramolecule #3: N4-nanobody-TAIL

SupramoleculeName: N4-nanobody-TAIL / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2

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Supramolecule #4: IgV domain of human Nectin-4

SupramoleculeName: IgV domain of human Nectin-4 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3

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Macromolecule #1: H3-PrAC-5350A,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydrox...

MacromoleculeName: H3-PrAC-5350A,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Thermotoga maritima MSB8 (bacteria)
Strain: ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8
Molecular weightTheoretical: 36.12793 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKEIAKIVAE LLRGIARIID DIKGRDREEE VEILAKAVEK TGKPEDVRLA LEAAERGVTL DQAKAIAQIL SMPNLTDEQK RGFVQSLLD DPSVSKEILA EAKKLNEHQA AKAEEAARKM EELFKKHKIV AVLRANSVEE AIEKAVAVFA GGVHLIEITF T VPDADTVI ...String:
MKEIAKIVAE LLRGIARIID DIKGRDREEE VEILAKAVEK TGKPEDVRLA LEAAERGVTL DQAKAIAQIL SMPNLTDEQK RGFVQSLLD DPSVSKEILA EAKKLNEHQA AKAEEAARKM EELFKKHKIV AVLRANSVEE AIEKAVAVFA GGVHLIEITF T VPDADTVI KALSVLKEKG AIIGAGTVTS VEQCRKAVES GAEFIVSPHL DEEISQFCKE KGVFYMPGVM TPTELVKAMK LG HTILKLF PGEVVGPQFV KAMKGPFPNV KFVPTGGVNL DNVCEWFKAG VLAVGVGSAL VKGTPDEVRE KAKAFVEKIR GCT EAAALE HHHHHH

UniProtKB: 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase

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Macromolecule #2: N4-nanobody-TAIL

MacromoleculeName: N4-nanobody-TAIL / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 27.671258 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAEVQLQASG GGFVQPGGSL RLSCAASGRF SAFYNMGWFR QAPGKEREFV SAISWSTNSA AYYADSVKGR FTISRDNSKN TVYLQMNSL RAEDTATYYC AASWHWNPPD HSWDAGYWGQ GTLVAVVKTV EDAFLALLAL EQHLGVQPAD LAALAEKLNL S QLLELGEL ...String:
MAEVQLQASG GGFVQPGGSL RLSCAASGRF SAFYNMGWFR QAPGKEREFV SAISWSTNSA AYYADSVKGR FTISRDNSKN TVYLQMNSL RAEDTATYYC AASWHWNPPD HSWDAGYWGQ GTLVAVVKTV EDAFLALLAL EQHLGVQPAD LAALAEKLNL S QLLELGEL LKAAGHPLAP QVEALLKEKL KAASAAEAAG VIFQALVKDE ELGKKILEWA KEFGTEEAKK AIEIAEKAYE LY KKYLEHH HHHH

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Macromolecule #3: Nectin-4

MacromoleculeName: Nectin-4 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.566088 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGELETSDVV TVVLGQDAKL PCFYRGDSGE QVGQVAWARV DAGEGAQELA LLHSKYGLHV SPAYEGRVEQ PPPPRNPLDG SVLLRNAVQ ADEGEYECRV STFPAGSFQA RLRLRVLEHH HHHH

UniProtKB: Nectin-4

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.43 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 567049
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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