+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41574 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of transglutaminase 2 bound to GDP | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | GDP / Complex / Signaling / G-protein / Cancer / cryo-EM / TRANSFERASE | |||||||||
Function / homology | Function and homology information histone serotonyltransferase activity / histone dopaminyltransferase activity / peptide noradrenalinyltransferase activity / peptide histaminyltransferase activity / cellular response to serotonin / regulation of apoptotic cell clearance / protein deamination / protein-glutamine glutaminase activity / protein-glutamine glutaminase / protein-glutamine gamma-glutamyltransferase ...histone serotonyltransferase activity / histone dopaminyltransferase activity / peptide noradrenalinyltransferase activity / peptide histaminyltransferase activity / cellular response to serotonin / regulation of apoptotic cell clearance / protein deamination / 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 / 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 / bone development / extracellular matrix / positive regulation of GTPase activity / 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 / GTP binding / chromatin / perinuclear region of cytoplasm / endoplasmic reticulum / mitochondrion / proteolysis / extracellular exosome / nucleus / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Aplin C / Cerione RA | |||||||||
Funding support | United States, 1 items
| |||||||||
Citation | Journal: 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 |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_41574.map.gz | 448.7 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-41574-v30.xml emd-41574.xml | 13.9 KB 13.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41574_fsc.xml | 17.1 KB | Display | FSC data file |
Images | emd_41574.png | 45.1 KB | ||
Filedesc metadata | emd-41574.cif.gz | 5.8 KB | ||
Others | emd_41574_half_map_1.map.gz emd_41574_half_map_2.map.gz | 475.1 MB 475.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41574 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41574 | HTTPS FTP |
-Validation report
Summary document | emd_41574_validation.pdf.gz | 970.6 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_41574_full_validation.pdf.gz | 970.2 KB | Display | |
Data in XML | emd_41574_validation.xml.gz | 26.6 KB | Display | |
Data in CIF | emd_41574_validation.cif.gz | 34.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41574 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41574 | HTTPS FTP |
-Related structure data
Related structure data | 8tr9MC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_41574.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.517 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: #2
File | emd_41574_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_41574_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Transglutaminase 2 bound to GDP
Entire | Name: Transglutaminase 2 bound to GDP |
---|---|
Components |
|
-Supramolecule #1: Transglutaminase 2 bound to GDP
Supramolecule | Name: Transglutaminase 2 bound to GDP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Protein-glutamine gamma-glutamyltransferase 2
Macromolecule | Name: 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 weight | Theoretical: 77.41268 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MAEELVLERC DLELETNGRD HHTADLCREK LVVRRGQPFW LTLHFEGRNY EASVDSLTFS VVTGPAPSQE AGTKARFPLR DAVEEGDWT ATVVDQQDCT LSLQLTTPAN APIGLYRLSL EASTGYQGSS FVLGHFILLF NAWCPADAVY LDSEEERQEY V LTQQGFIY ...String: MAEELVLERC DLELETNGRD HHTADLCREK LVVRRGQPFW LTLHFEGRNY EASVDSLTFS VVTGPAPSQE AGTKARFPLR DAVEEGDWT ATVVDQQDCT LSLQLTTPAN APIGLYRLSL EASTGYQGSS FVLGHFILLF NAWCPADAVY LDSEEERQEY V LTQQGFIY QGSAKFIKNI PWNFGQFEDG ILDICLILLD VNPKFLKNAG RDCSRRSSPV YVGRVVSGMV NCNDDQGVLL GR WDNNYGD GVSPMSWIGS VDILRRWKNH GCQRVKYGQC WVFAAVACTV LRCLGIPTRV VTNYNSAHDQ NSNLLIEYFR NEF GEIQGD KSEMIWNFHC WVESWMTRPD LQPGYEGWQA LDPTPQEKSE GTYCCGPVPV RAIKEGDLST KYDAPFVFAE VNAD VVDWI QQDDGSVHKS INRSLIVGLK ISTKSVGRDE REDITHTYKY PEGSSEEREA FTRANHLNKL AEKEETGMAM RIRVG QSMN MGSDFDVFAH ITNNTAEEYV CRLLLCARTV SYNGILGPEC GTKYLLNLNL EPFSEKSVPL CILYEKYRDC LTESNL IKV RALLVEPVIN SYLLAERDLY LENPEIKIRI LGEPKQKRKL VAEVSLQNPL PVALEGCTFT VEGAGLTEEQ KTVEIPD PV EAGEEVKVRM DLLPLHMGLH KLVVNFESDK LKAVKGFRNV IIGPA UniProtKB: Protein-glutamine gamma-glutamyltransferase 2 |
-Macromolecule #2: GUANOSINE-5'-DIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: GDP |
---|---|
Molecular weight | Theoretical: 443.201 Da |
Chemical component information | ChemComp-GDP: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 200 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
---|---|
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 51.1 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |