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Yorodumi- EMDB-21811: EM structure of CtBP2 with a minimal dehydrogenase domain of CtBP2 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21811 | |||||||||
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Title | EM structure of CtBP2 with a minimal dehydrogenase domain of CtBP2 | |||||||||
Map data | CryoEM map of CtBP2 with the minimal dehydrogenase domain, CtBP31-364 | |||||||||
Sample |
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Keywords | Transcriptional corepression / Cancer / Gene repression / metabolic sensor / GENE REGULATION | |||||||||
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: 3.6 Å | |||||||||
Authors | Jecrois AM | |||||||||
Funding support | United States, 1 items
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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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_21811.map.gz | 59.8 MB | EMDB map data format | |
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Header (meta data) | emd-21811-v30.xml emd-21811.xml | 17.2 KB 17.2 KB | Display Display | EMDB header |
Images | emd_21811.png | 114.4 KB | ||
Filedesc metadata | emd-21811.cif.gz | 6 KB | ||
Others | emd_21811_half_map_1.map.gz emd_21811_half_map_2.map.gz | 3.8 MB 3.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21811 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21811 | HTTPS FTP |
-Validation report
Summary document | emd_21811_validation.pdf.gz | 659.9 KB | Display | EMDB validaton report |
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Full document | emd_21811_full_validation.pdf.gz | 659.4 KB | Display | |
Data in XML | emd_21811_validation.xml.gz | 12 KB | Display | |
Data in CIF | emd_21811_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21811 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21811 | HTTPS FTP |
-Related structure data
Related structure data | 6wkwMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_21811.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | CryoEM map of CtBP2 with the minimal dehydrogenase domain, CtBP31-364 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.87 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: EM structure of CtBP2 Half map
File | emd_21811_half_map_1.map | ||||||||||||
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Annotation | EM structure of CtBP2 Half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: EM structure of CtBP2 Half map
File | emd_21811_half_map_2.map | ||||||||||||
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Annotation | EM structure of CtBP2 Half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of CtBP2 with four NADH molecules
Entire | Name: Complex of CtBP2 with four NADH molecules |
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Components |
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-Supramolecule #1: Complex of CtBP2 with four NADH molecules
Supramolecule | Name: Complex of CtBP2 with four NADH molecules / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 190 KDa |
-Macromolecule #1: C-terminal-binding protein 2
Macromolecule | Name: C-terminal-binding protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 36.620715 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: RPLVALLDGR DCTVEMPILK DLATVAFCDA QSTQEIHEKV LNEAVGAMMY HTITLTREDL EKFKALRVIV RIGSGYDNVD IKAAGELGI AVCNIPSAAV EETADSTICH ILNLYRRNTW LYQALREGTR VQSVEQIREV ASGAARIRGE TLGLIGFGRT G QAVAVRAK ...String: RPLVALLDGR DCTVEMPILK DLATVAFCDA QSTQEIHEKV LNEAVGAMMY HTITLTREDL EKFKALRVIV RIGSGYDNVD IKAAGELGI AVCNIPSAAV EETADSTICH ILNLYRRNTW LYQALREGTR VQSVEQIREV ASGAARIRGE TLGLIGFGRT G QAVAVRAK AFGFSVIFYD PYLQDGIERS LGVQRVYTLQ DLLYQSDCVS LHCNLNEHNH HLINDFTIKQ MRQGAFLVNA AR GGLVDEK ALAQALKEGR IRGAALDVHE SEPFSFAQGP LKDAPNLICT PHTAWYSEQA SLEMREAAAT EIRRAITGRI PES LRNCVN KEFF UniProtKB: C-terminal-binding protein 2 |
-Macromolecule #2: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Macromolecule | Name: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 4 / Formula: NAD |
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Molecular weight | Theoretical: 663.425 Da |
Chemical component information | ChemComp-NAD: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.25 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. Details: Grid was washed in Ethyl acetate prior to glow-discharge. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 278.15 K / Instrument: FEI VITROBOT MARK IV / Details: Blotting time: 4s Blotting force: 8 Wait time: 0. |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 3405 / Average exposure time: 1.7 sec. / Average electron dose: 37.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 50000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |