+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11015 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | CryoEM Structure of CtBP2 Confirms Tetrameric Architecture | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Function / homology | Function and homology information positive regulation of retinoic acid receptor signaling pathway / Signaling by TCF7L2 mutants / Repression of WNT target genes / Sensory processing of sound by inner hair cells of the cochlea / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / white fat cell differentiation / transcription repressor complex / viral genome replication / transcription corepressor binding / transcription coregulator binding ...positive regulation of retinoic acid receptor signaling pathway / Signaling by TCF7L2 mutants / Repression of WNT target genes / Sensory processing of sound by inner hair cells of the cochlea / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / white fat cell differentiation / transcription repressor complex / viral genome replication / transcription corepressor binding / transcription coregulator binding / transcription corepressor activity / NAD binding / DNA-binding transcription factor binding / transcription coactivator activity / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / synapse / protein-containing complex binding / regulation of transcription by RNA polymerase II / protein kinase binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.0 Å | |||||||||
Authors | Jecrois AM | |||||||||
Funding support | United States, 1 items
| |||||||||
Citation | Journal: Structure / Year: 2021 Title: Cryo-EM structure of CtBP2 confirms tetrameric architecture. Authors: Anne M Jecrois / M Michael Dcona / Xiaoyan Deng / Dipankar Bandyopadhyay / Steven R Grossman / Celia A Schiffer / William E Royer / Abstract: C-terminal binding proteins 1 and 2 (CtBP1 and CtBP2) are transcriptional regulators that activate or repress many genes involved in cellular development, apoptosis, and metastasis. NADH-dependent ...C-terminal binding proteins 1 and 2 (CtBP1 and CtBP2) are transcriptional regulators that activate or repress many genes involved in cellular development, apoptosis, and metastasis. NADH-dependent CtBP activation has been implicated in multiple types of cancer and poor patient prognosis. Central to understanding activation of CtBP in oncogenesis is uncovering how NADH triggers protein assembly, what level of assembly occurs, and if oncogenic activity depends upon such assembly. Here, we present the cryoelectron microscopic structures of two different constructs of CtBP2 corroborating that the native state of CtBP2 in the presence of NADH is tetrameric. The physiological relevance of the observed tetramer was demonstrated in cell culture, showing that CtBP tetramer-destabilizing mutants are defective for cell migration, transcriptional repression of E-cadherin, and activation of TIAM1. Together with our cryoelectron microscopy studies, these results highlight the tetramer as the functional oligomeric form of CtBP2. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11015.map.gz | 93.3 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-11015-v30.xml emd-11015.xml | 15.9 KB 15.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11015_fsc.xml | 13.6 KB | Display | FSC data file |
Images | emd_11015.png | 91.1 KB | ||
Others | emd_11015_half_map_1.map.gz emd_11015_half_map_2.map.gz | 30 MB 29.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11015 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11015 | HTTPS FTP |
-Validation report
Summary document | emd_11015_validation.pdf.gz | 280.9 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_11015_full_validation.pdf.gz | 280 KB | Display | |
Data in XML | emd_11015_validation.xml.gz | 6.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11015 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11015 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_11015.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.87 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Half map: #2
File | emd_11015_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_11015_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : EM map of CtBP2(31-445)
Entire | Name: EM map of CtBP2(31-445) |
---|---|
Components |
|
-Supramolecule #1: EM map of CtBP2(31-445)
Supramolecule | Name: EM map of CtBP2(31-445) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Molecular weight | Experimental: 190 KDa |
-Macromolecule #1: CtBP2(31-364)
Macromolecule | Name: CtBP2(31-364) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: HPRPLVALLD GRDCTVEMPI LKDLATVAFC DAQSTQEIH EKVLNEAVGA MMYHTITLTR EDLEKFKALR VIVRIGSGYD NVDIKAAGEL G IAVCNIPS AAVEETADST ICHILNLYRR NTWLYQALRE GTRVQSVEQI REVASGAARI RG ETLGLIG FGRTGQAVAV ...String: HPRPLVALLD GRDCTVEMPI LKDLATVAFC DAQSTQEIH EKVLNEAVGA MMYHTITLTR EDLEKFKALR VIVRIGSGYD NVDIKAAGEL G IAVCNIPS AAVEETADST ICHILNLYRR NTWLYQALRE GTRVQSVEQI REVASGAARI RG ETLGLIG FGRTGQAVAV RAKAFGFSVI FYDPYLQDGI ERSLGVQRVY TLQDLLYQSD CVS LHCNLN EHNHHLINDF TIKQMRQGAF LVNAARGGLV DEKALAQALK EGRIRGAALD VHES EPFSF AQGPLKDAPN LICTPHTAWY SEQASLEMRE AAATEIRRAI TGRIPESLRN CVNKE FFVT SAPWSVIDQQ AIHPELNGAT YRYPPGIVGV APGGLPAAME GIIPGGIPVT HNLPTV AHP SQAPSPNQPT KHGDNREHPN EQ |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Grid | Model: C-flat-1.2/1.3 / Material: COPPER Details: Grid washed in Ethyl acetate before glow discharge treatment. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: Blotting time: 3s Blotting force: 8 Waiting time: 0. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 3000 / Average exposure time: 1.5 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |