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- PDB-8tr9: Cryo-EM structure of transglutaminase 2 bound to GDP -

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Basic information

Entry
Database: PDB / ID: 8tr9
TitleCryo-EM structure of transglutaminase 2 bound to GDP
ComponentsProtein-glutamine gamma-glutamyltransferase 2
KeywordsTRANSFERASE / GDP / Complex / Signaling / G-protein / Cancer / cryo-EM
Function / homology
Function and homology information


protein deamination / histone serotonyltransferase activity / histone dopaminyltransferase activity / peptide noradrenalinyltransferase activity / peptide histaminyltransferase activity / cellular response to serotonin / regulation of apoptotic cell clearance / protein-glutamine glutaminase activity / protein-glutamine glutaminase / protein-glutamine gamma-glutamyltransferase ...protein deamination / histone serotonyltransferase activity / histone dopaminyltransferase activity / peptide noradrenalinyltransferase activity / peptide histaminyltransferase activity / cellular response to serotonin / regulation of apoptotic cell clearance / protein-glutamine glutaminase activity / protein-glutamine glutaminase / protein-glutamine gamma-glutamyltransferase / positive regulation of mitochondrial calcium ion concentration / salivary gland cavitation / protein-glutamine gamma-glutamyltransferase activity / negative regulation of endoplasmic reticulum calcium ion concentration / dopamine secretion / peptide cross-linking / branching involved in salivary gland morphogenesis / cellular response to dopamine / positive regulation of small GTPase mediated signal transduction / apoptotic cell clearance / cellular response to cocaine / Hydrolases; Acting on peptide bonds (peptidases) / positive regulation of neurogenesis / positive regulation of sprouting angiogenesis / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / positive regulation of cell adhesion / extracellular matrix / positive regulation of GTPase activity / bone development / protein homooligomerization / nucleosome / peptidase activity / phospholipase C-activating G protein-coupled receptor signaling pathway / gene expression / collagen-containing extracellular matrix / regulation of apoptotic process / positive regulation of apoptotic process / focal adhesion / calcium ion binding / chromatin / GTP binding / perinuclear region of cytoplasm / endoplasmic reticulum / mitochondrion / proteolysis / extracellular exosome / nucleus / plasma membrane / cytosol
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 / Transglutaminase-like superfamily / Papain-like cysteine peptidase superfamily / Immunoglobulin E-set / Immunoglobulin-like fold
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Protein-glutamine gamma-glutamyltransferase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsAplin, C. / Cerione, R.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA201402-09 United States
CitationJournal: To Be Published
Title: Conformational activation and inhibition of transglutaminase 2 determined by static and time resolved small-angle X-ray scattering and cryoelectron microscopy
Authors: Aplin, C. / Zielinski, K.A. / Pabit, S. / Ogunribido, D. / Katt, W.P. / Pollack, L. / Cerione, R.A. / Milano, S.K.
History
DepositionAug 9, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)77,8562
Polymers77,4131
Non-polymers4431
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, SAXS
TypeNameSymmetry operationNumber
identity operation1_5551

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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: 77412.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGM2 / Production host: Escherichia coli BL21(DE3) (bacteria)
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: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
Has ligand of interestY

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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: Transglutaminase 2 bound to GDP / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 51.1 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 136297 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 99.32 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0035568
ELECTRON MICROSCOPYf_angle_d0.48367564
ELECTRON MICROSCOPYf_chiral_restr0.0418832
ELECTRON MICROSCOPYf_plane_restr0.0027985
ELECTRON MICROSCOPYf_dihedral_angle_d4.3699757

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