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- EMDB-58048: Complex of transglutaminase 2 and the 45 kDa domain of fibronectin -

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Basic information

Entry
Database: EMDB / ID: EMD-58048
TitleComplex of transglutaminase 2 and the 45 kDa domain of fibronectin
Map data
Sample
  • Complex: Complex of transglutaminase 2 and the 45 kDa fragment of fibronectin
    • Protein or peptide: Protein-glutamine gamma-glutamyltransferase 2
    • Protein or peptide: Fibronectin
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water
Keywordstransglutaminase / fibronectin / TRANSFERASE
Function / homology
Function and homology information


histone serotonyltransferase activity / histone dopaminyltransferase activity / peptide noradrenalinyltransferase activity / peptide histaminyltransferase activity / regulation of apoptotic cell clearance / negative regulation of endoplasmic reticulum calcium ion concentration / cellular response to serotonin / protein-glutamine glutaminase activity / protein-glutamine glutaminase / protein-glutamine gamma-glutamyltransferase ...histone serotonyltransferase activity / histone dopaminyltransferase activity / peptide noradrenalinyltransferase activity / peptide histaminyltransferase activity / regulation of apoptotic cell clearance / negative regulation of endoplasmic reticulum calcium ion concentration / cellular response to serotonin / protein-glutamine glutaminase activity / protein-glutamine glutaminase / protein-glutamine gamma-glutamyltransferase / positive regulation of mitochondrial calcium ion concentration / fibronectin fibril / negative regulation of monocyte activation / protein-glutamine gamma-glutamyltransferase activity / peptide cross-linking / negative regulation of transforming growth factor beta production / positive regulation of substrate-dependent cell migration, cell attachment to substrate / neural crest cell migration involved in autonomic nervous system development / fibrinogen complex / Fibronectin matrix formation / enteric nervous system development / Attachment of bacteria to epithelial cells / integrin activation / positive regulation of small GTPase mediated signal transduction / neural crest cell migration / ALK mutants bind TKIs / cellular response to dopamine / cell-substrate junction assembly / cellular response to cocaine / proteoglycan binding / positive regulation of neurogenesis / apoptotic cell clearance / Hydrolases; Acting on peptide bonds (peptidases) / Molecules associated with elastic fibres / MET activates PTK2 signaling / endodermal cell differentiation / peptidase activator activity / response to muscle activity / Syndecan interactions / extracellular matrix structural constituent / p130Cas linkage to MAPK signaling for integrins / biological process involved in interaction with symbiont / positive regulation of sprouting angiogenesis / endoplasmic reticulum-Golgi intermediate compartment / GRB2:SOS provides linkage to MAPK signaling for Integrins / regulation of protein phosphorylation / basement membrane / Non-integrin membrane-ECM interactions / blood coagulation, fibrin clot formation / ECM proteoglycans / Integrin cell surface interactions / endothelial cell migration / regulation of ERK1 and ERK2 cascade / substrate adhesion-dependent cell spreading / Degradation of the extracellular matrix / collagen binding / extracellular matrix organization / Integrin signaling / cell-matrix adhesion / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / positive regulation of cell adhesion / platelet alpha granule lumen / integrin-mediated signaling pathway / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / acute-phase response / Cell surface interactions at the vascular wall / Developmental Lineage of Pancreatic Ductal Cells / GTPase activator activity / Post-translational protein phosphorylation / bone development / response to wounding / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / protein homooligomerization / integrin binding / positive regulation of fibroblast proliferation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / phospholipase C-activating G protein-coupled receptor signaling pathway / Signaling by RAF1 mutants / heart development / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / Signaling by ALK fusions and activated point mutants / Platelet degranulation / nucleosome / peptidase activity / regulation of cell shape / heparin binding / nervous system development / GPER1 signaling / extracellular matrix / angiogenesis / protease binding / Interleukin-4 and Interleukin-13 signaling / blood microparticle / regulation of apoptotic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion
Similarity search - Function
Transglutaminase, N-terminal / Transglutaminase, C-terminal / Transglutaminase, active site / Protein-glutamine gamma-glutamyltransferase, animal / Transglutaminase, C-terminal domain superfamily / : / Transglutaminase family / Transglutaminase family, C-terminal ig like domain / Transglutaminases active site. / Transglutaminase-like superfamily ...Transglutaminase, N-terminal / Transglutaminase, C-terminal / Transglutaminase, active site / Protein-glutamine gamma-glutamyltransferase, animal / Transglutaminase, C-terminal domain superfamily / : / Transglutaminase family / Transglutaminase family, C-terminal ig like domain / Transglutaminases active site. / Transglutaminase-like superfamily / Transglutaminase/protease-like homologues / Transglutaminase-like / Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / : / Transglutaminase-like superfamily / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Kringle-like fold / Fibronectin type III domain / EGF-like domain signature 1. / Fibronectin type 3 domain / Papain-like cysteine peptidase superfamily / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin E-set / Immunoglobulin-like fold
Similarity search - Domain/homology
Fibronectin / Protein-glutamine gamma-glutamyltransferase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsHeggelund JE / Ali-Ahmad A / Sekulic N / Sollid LM
Funding support Denmark, Norway, 2 items
OrganizationGrant numberCountry
Other privateLF-OC-23-001291 Denmark
Research Council of Norway295844 Norway
CitationJournal: J Biol Chem / Year: 2026
Title: Cryo-EM structure of the complex between transglutaminase 2 and the 45 kDa domain of fibronectin.
Authors: Julie Elisabeth Heggelund / Ahmad Ali-Ahmad / Marie Kongshaug Johannesen / Nikolina Sekulić / Ludvig M Sollid /
Abstract: Fibronectin (FN) and transglutaminase 2 (TG2) engage in a high-affinity interaction. This interaction affects anchoring, migration and survival of cells, and high cellular expression of TG2 is ...Fibronectin (FN) and transglutaminase 2 (TG2) engage in a high-affinity interaction. This interaction affects anchoring, migration and survival of cells, and high cellular expression of TG2 is associated with metastasis potential of cancers. Previous work has mapped the interaction to involve the N-terminal part of TG2 and an N-terminally located 45 kDa domain of FN (FN45). In particular, the I module of FN45 is reported to be necessary and sufficient for TG2 binding. Here, we present the cryo-EM structure of a complex between human TG2 and FN45 at 2.8 Å resolution. In the structure, the distal region of the TG2 N-terminal domain binds the FN45 I module, whereas the proximal N-terminal region and adjacent catalytic core segment bind the FN45 I module and, to a lesser extent, the FN45 II module. The FN45 I and FN45 I modules have about equal buried surface areas in their interaction with TG2. A glycine residue at position 127 of TG2 is crucial for interaction with Trp553 of the FN45 I module. Mutation of this residue to isoleucine, which is carried by transglutaminase 3 that does not bind FN45, abrogates the binding of FN45 to TG2. This finding suggests that the interaction of the FN45 I module with TG2 is contingent on the FN45 I module making an interaction with TG2. Further, this finding highlights the region surrounding residue 127 of TG2 as a promising target for structure-based design of anticancer drugs aimed at disrupting the TG2-FN interaction.
History
DepositionMay 13, 2026-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_58048.png

Downloads & links

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Map

FileDownload / File: emd_58048.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
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AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 420 pix.
= 273. Å		0.65 Å/pix.
x 420 pix.
= 273. Å		0.65 Å/pix.
x 420 pix.
= 273. Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0158
Minimum - Maximum-0.21580428 - 0.3642844
Average (Standard dev.)-0.0001795696 (±0.007190498)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 273.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_58048_msk_1.map
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Half map: #2

Fileemd_58048_half_map_1.map
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Half map: #1

Fileemd_58048_half_map_2.map
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Sample components

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Entire : Complex of transglutaminase 2 and the 45 kDa fragment of fibronectin

EntireName: Complex of transglutaminase 2 and the 45 kDa fragment of fibronectin
Components
  • Complex: Complex of transglutaminase 2 and the 45 kDa fragment of fibronectin
    • Protein or peptide: Protein-glutamine gamma-glutamyltransferase 2
    • Protein or peptide: Fibronectin
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

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Supramolecule #1: Complex of transglutaminase 2 and the 45 kDa fragment of fibronectin

SupramoleculeName: Complex of transglutaminase 2 and the 45 kDa fragment of fibronectin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 125 kDa/nm

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Macromolecule #1: Protein-glutamine gamma-glutamyltransferase 2

MacromoleculeName: Protein-glutamine gamma-glutamyltransferase 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: protein-glutamine gamma-glutamyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 80.416953 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGSSHHHHHH GLNDIFEAQK IEWHEMAEEL VLERCDLELE TNGRDHHTAD LCREKLVVRR GQPFWLTLHF EGRNYEASVD SLTFSVVTG PAPSQEAGTK ARFPLRDAVE EGDWTATVVD QQDCTLSLQL TTPANAPIGL YRLSLEASTG YQGSSFVLGH F ILLFNAWC ...String:
MGSSHHHHHH GLNDIFEAQK IEWHEMAEEL VLERCDLELE TNGRDHHTAD LCREKLVVRR GQPFWLTLHF EGRNYEASVD SLTFSVVTG PAPSQEAGTK ARFPLRDAVE EGDWTATVVD QQDCTLSLQL TTPANAPIGL YRLSLEASTG YQGSSFVLGH F ILLFNAWC PADAVYLDSE EERQEYVLTQ QGFIYQGSAK FIKNIPWNFG QFEDGILDIC LILLDVNPKF LKNAGRDCSR RS SPVYVGR VVSGMVNCND DQGVLLGRWD NNYGDGVSPM SWIGSVDILR RWKNHGCQRV KYGQCWVFAA VACTVLRCLG IPT RVVTNY NSAHDQNSNL LIEYFRNEFG EIQGDKSEMI WNFHCWVESW MTRPDLQPGY EGWQALDPTP QEKSEGTYCC GPVP VRAIK EGDLSTKYDA PFVFAEVNAD VVDWIQQDDG SVHKSINRSL IVGLKISTKS VGRDEREDIT HTYKYPEGSS EEREA FTRA NHLNKLAEKE ETGMAMRIRV GQSMNMGSDF DVFAHITNNT AEEYVCRLLL CARTVSYNGI LGPECGTKYL LNLNLE PFS EKSVPLCILY EKYRDCLTES NLIKVRALLV EPVINSYLLA ERDLYLENPE IKIRILGEPK QKRKLVAEVS LQNPLPV AL EGCTFTVEGA GLTEEQKTVE IPDPVEAGEE VKVRMDLLPL HMGLHKLVVN FESDKLKAVK GFRNVIIGPA

UniProtKB: Protein-glutamine gamma-glutamyltransferase 2

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Macromolecule #2: Fibronectin

MacromoleculeName: Fibronectin / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.392973 KDa
SequenceString: AAVYQPQPHP QPPPYGHCVT DSGVVYSVGM QWLKTQGNKQ MLCTCLGNGV SCQETAVTQT YGGNSNGEPC VLPFTYNGRT FYSCTTEGR QDGHLWCSTT SNYEQDQKYS FCTDHTVLVQ TRGGNSNGAL CHFPFLYNNH NYTDCTSEGR RDNMKWCGTT Q NYDADQKF ...String:
AAVYQPQPHP QPPPYGHCVT DSGVVYSVGM QWLKTQGNKQ MLCTCLGNGV SCQETAVTQT YGGNSNGEPC VLPFTYNGRT FYSCTTEGR QDGHLWCSTT SNYEQDQKYS FCTDHTVLVQ TRGGNSNGAL CHFPFLYNNH NYTDCTSEGR RDNMKWCGTT Q NYDADQKF GFCPMAAHEE ICTTNEGVMY RIGDQWDKQH DMGHMMRCTC VGNGRGEWTC IAYSQLRDQC IVDDITYNVN DT FHKRHEE GHMLNCTCFG QGRGRWKCDP VDQCQDSETG TFYQIGDSWE KYVHGVRYQC YCYGR

UniProtKB: Fibronectin

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Macromolecule #3: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 54 / 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

BufferpH: 7.4
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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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: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 238000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: OTHER / Overall B value: 74
Output model

PDB-30uc:
Complex of transglutaminase 2 and the 45 kDa domain of fibronectin

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