[English] 日本語
Yorodumi
- PDB-30uc: Complex of transglutaminase 2 and the 45 kDa domain of fibronectin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 30uc
TitleComplex of transglutaminase 2 and the 45 kDa domain of fibronectin
Components
  • Fibronectin
  • Protein-glutamine gamma-glutamyltransferase 2
KeywordsTRANSFERASE / transglutaminase / fibronectin
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
GUANOSINE-5'-DIPHOSPHATE / Fibronectin / Protein-glutamine gamma-glutamyltransferase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsHeggelund, J.E. / Ali-Ahmad, A. / Sekulic, N. / Sollid, L.M.
Funding support Denmark, Norway, 2items
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, 2026Deposition site: PDBE / Processing site: PDBE
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: FSC / Data content type: FSC / 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: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2026Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update
Revision 1.1Jul 29, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: citation / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein-glutamine gamma-glutamyltransferase 2
B: Fibronectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,6965
Polymers114,8102
Non-polymers8863
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein Protein-glutamine gamma-glutamyltransferase 2 / Erythrocyte transglutaminase / Heart G alpha(h) / hhG alpha(h) / Isopeptidase TGM2 / Protein G ...Erythrocyte transglutaminase / Heart G alpha(h) / hhG alpha(h) / Isopeptidase TGM2 / Protein G alpha(h) / G(h) / Protein-glutamine deamidase TGM2 / Protein-glutamine dopaminyltransferase TGM2 / Protein-glutamine histaminyltransferase TGM2 / Protein-glutamine noradrenalinyltransferase TGM2 / Protein-glutamine serotonyltransferase TGM2 / Tissue transglutaminase / tTG / tTgase / Transglutaminase C / TG(C) / TGC / TGase C / Transglutaminase H / TGase H / Transglutaminase II / TGase II / Transglutaminase-2 / TG2 / TGase-2 / hTG2


Mass: 80416.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGM2 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P21980, protein-glutamine gamma-glutamyltransferase, Hydrolases; Acting on peptide bonds (peptidases), protein-glutamine glutaminase, Transferases; Acyltransferases; Transferring ...References: UniProt: P21980, protein-glutamine gamma-glutamyltransferase, Hydrolases; Acting on peptide bonds (peptidases), protein-glutamine glutaminase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Protein Fibronectin / FN / Cold-insoluble globulin / CIG


Mass: 34392.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02751
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Complex of transglutaminase 2 and the 45 kDa fragment of fibronectin
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 125 kDa/nm / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationCryogen name: ETHANE / Humidity: 100 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
12cryoSPARC3D reconstruction
13PHENIX2.0_5936model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 238000 / Symmetry type: POINT
Atomic model buildingB value: 74 / Protocol: OTHER
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 74.23 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00146615
ELECTRON MICROSCOPYf_angle_d0.38678975
ELECTRON MICROSCOPYf_chiral_restr0.0397974
ELECTRON MICROSCOPYf_plane_restr0.00231168
ELECTRON MICROSCOPYf_dihedral_angle_d3.6289935

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more