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- EMDB-42356: Cryo-EM map of transglutaminase 2 bound to calcium -

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Basic information

Entry
Database: EMDB / ID: EMD-42356
TitleCryo-EM map of transglutaminase 2 bound to calcium
Map data
Sample
  • Complex: Transglutaminase 2 bound to calcium
    • Protein or peptide: Protein-glutamine gamma-glutamyltransferase 2
KeywordsGDP / Complex / Signaling / G-protein / Cancer / cryo-EM / TRANSFERASE
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 / negative regulation of endoplasmic reticulum calcium ion concentration / salivary gland cavitation / protein-glutamine gamma-glutamyltransferase activity / dopamine secretion / branching involved in salivary gland morphogenesis / peptide cross-linking / cellular response to dopamine / positive regulation of small GTPase mediated signal transduction / apoptotic cell clearance / Hydrolases; Acting on peptide bonds (peptidases) / cellular response to cocaine / 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
Protein-glutamine gamma-glutamyltransferase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.44 Å
AuthorsAplin C / Cerione RA
Funding support United States, 1 items
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 KA / Pabit S / Ogunribido D / Katt WP / Pollack L / Cerione RA / Milano SK
History
DepositionOct 16, 2023-
Header (metadata) releaseJul 31, 2024-
Map releaseJul 31, 2024-
UpdateJul 31, 2024-
Current statusJul 31, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42356.png

Downloads & links

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Map

FileDownload / File: emd_42356.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 256 pix.
= 264.704 Å		1.03 Å/pix.
x 256 pix.
= 264.704 Å		1.03 Å/pix.
x 256 pix.
= 264.704 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.034 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.131
Minimum - Maximum-0.22558609 - 0.45721272
Average (Standard dev.)-0.00009402438 (±0.007958753)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 264.704 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_42356_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_42356_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Transglutaminase 2 bound to calcium

EntireName: Transglutaminase 2 bound to calcium
Components
  • Complex: Transglutaminase 2 bound to calcium
    • Protein or peptide: Protein-glutamine gamma-glutamyltransferase 2

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Supramolecule #1: Transglutaminase 2 bound to calcium

SupramoleculeName: Transglutaminase 2 bound to calcium / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Protein-glutamine gamma-glutamyltransferase 2

MacromoleculeName: Protein-glutamine gamma-glutamyltransferase 2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: protein-glutamine gamma-glutamyltransferase
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAEELVLERC DLELETNGRD HHTADLCREK LVVRRGQPFW LTLHFEGRNY EASVDSLTFS VVTGPAPSQ EAGTKARFPL RDAVEEGDWT ATVVDQQDCT LSLQLTTPAN APIGLYRLSL E ASTGYQGS SFVLGHFILL FNAWCPADAV YLDSEEERQE YVLTQQGFIY ...String:
MAEELVLERC DLELETNGRD HHTADLCREK LVVRRGQPFW LTLHFEGRNY EASVDSLTFS VVTGPAPSQ EAGTKARFPL RDAVEEGDWT ATVVDQQDCT LSLQLTTPAN APIGLYRLSL E ASTGYQGS SFVLGHFILL FNAWCPADAV YLDSEEERQE YVLTQQGFIY QGSAKFIKNI PW NFGQFED GILDICLILL DVNPKFLKNA GRDCSRRSSP VYVGRVVSGM VNCNDDQGVL LGR WDNNYG DGVSPMSWIG SVDILRRWKN HGCQRVKYGQ CWVFAAVACT VLRCLGIPTR VVTN YNSAH DQNSNLLIEY FRNEFGEIQG DKSEMIWNFH CWVESWMTRP DLQPGYEGWQ ALDPT PQEK SEGTYCCGPV PVRAIKEGDL STKYDAPFVF AEVNADVVDW IQQDDGSVHK SINRSL IVG LKISTKSVGR DEREDITHTY KYPEGSSEER EAFTRANHLN KLAEKEETGM AMRIRVG QS MNMGSDFDVF AHITNNTAEE YVCRLLLCAR TVSYNGILGP ECGTKYLLNL NLEPFSEK S VPLCILYEKY RDCLTESNLI KVRALLVEPV INSYLLAERD LYLENPEIKI RILGEPKQK RKLVAEVSLQ NPLPVALEGC TFTVEGAGLT EEQKTVEIPD PVEAGEEVKV RMDLLPLHMG LHKLVVNFE SDKLKAVKGF RNVIIGPA

UniProtKB: Protein-glutamine gamma-glutamyltransferase 2

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 51.1 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 68975
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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