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Yorodumi- EMDB-6400: Electron microscopy of BRCA1(5832insC) mutant-RNAP II transcripti... -
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-Basic information
Entry | Database: EMDB / ID: EMD-6400 | |||||||||
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Title | Electron microscopy of BRCA1(5832insC) mutant-RNAP II transcriptional complex | |||||||||
Map data | Reconstruction of BRCA1-RNAP II mutant complex | |||||||||
Sample |
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Keywords | transcription / DNA damage repair / breast cancer / protein | |||||||||
Function / homology | Function and homology information negative regulation of mRNA 3'-end processing / Defective DNA double strand break response due to BRCA1 loss of function / Defective DNA double strand break response due to BARD1 loss of function / microfibril binding / BRCA1-BARD1 complex / BRCA1-C complex / BRCA1-B complex / BRCA1-A complex / random inactivation of X chromosome / negative regulation of centriole replication ...negative regulation of mRNA 3'-end processing / Defective DNA double strand break response due to BRCA1 loss of function / Defective DNA double strand break response due to BARD1 loss of function / microfibril binding / BRCA1-BARD1 complex / BRCA1-C complex / BRCA1-B complex / BRCA1-A complex / random inactivation of X chromosome / negative regulation of centriole replication / sex-chromosome dosage compensation / negative regulation of intracellular estrogen receptor signaling pathway / gamma-tubulin ring complex / nuclear ubiquitin ligase complex / chordate embryonic development / cellular response to indole-3-methanol / negative regulation of fatty acid biosynthetic process / lateral element / homologous recombination / DNA strand resection involved in replication fork processing / tissue homeostasis / protein K6-linked ubiquitination / regulation of DNA damage checkpoint / regulation of phosphorylation / Impaired BRCA2 binding to PALB2 / XY body / mitotic G2/M transition checkpoint / negative regulation of protein export from nucleus / postreplication repair / Abortive elongation of HIV-1 transcript in the absence of Tat / DNA repair complex / RNA polymerase binding / centrosome cycle / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / MicroRNA (miRNA) biogenesis / FGFR2 alternative splicing / Resolution of D-loop Structures through Holliday Junction Intermediates / Viral Messenger RNA Synthesis / intracellular non-membrane-bounded organelle / HDR through Single Strand Annealing (SSA) / Signaling by FGFR2 IIIa TM / negative regulation of gene expression via chromosomal CpG island methylation / Impaired BRCA2 binding to RAD51 / DNA-binding transcription activator activity / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / response to ionizing radiation / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / PIWI-interacting RNA (piRNA) biogenesis / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / mRNA Splicing - Minor Pathway / Transcriptional Regulation by E2F6 / mitotic G2 DNA damage checkpoint signaling / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / Presynaptic phase of homologous DNA pairing and strand exchange / Processing of Capped Intron-Containing Pre-mRNA / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / negative regulation of cell cycle / RNA polymerase II activity / positive regulation of vascular endothelial growth factor production / negative regulation of reactive oxygen species metabolic process / Tat-mediated elongation of the HIV-1 transcript / positive regulation of DNA repair / Formation of HIV-1 elongation complex containing HIV-1 Tat / protein autoubiquitination / Formation of HIV elongation complex in the absence of HIV Tat / male germ cell nucleus / RNA polymerase II, core complex / SUMOylation of DNA damage response and repair proteins / regulation of DNA repair / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / ubiquitin ligase complex / Meiotic synapsis / Inhibition of DNA recombination at telomere / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / RNA Polymerase II Pre-transcription Events Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 26.0 Å | |||||||||
Authors | Winton CE / Gilmore BL / Demmert AC / Tanner JR / Bowman S / Karageorge V / Patel K / Sheng Z / Kelly DF | |||||||||
Citation | Journal: Nat Struct Biol / Year: 2001 Title: Crystal structure of the BRCT repeat region from the breast cancer-associated protein BRCA1. Authors: R S Williams / R Green / J N Glover / Abstract: The C-terminal BRCT region of BRCA1 is essential for its DNA repair, transcriptional regulation and tumor suppressor functions. Here we determine the crystal structure of the BRCT domain of human ...The C-terminal BRCT region of BRCA1 is essential for its DNA repair, transcriptional regulation and tumor suppressor functions. Here we determine the crystal structure of the BRCT domain of human BRCA1 at 2.5 A resolution. The domain contains two BRCT repeats that adopt similar structures and are packed together in a head-to-tail arrangement. Cancer-causing missense mutations occur at the interface between the two repeats and destabilize the structure. The manner by which the two BRCT repeats interact in BRCA1 may represent a general mode of interaction between homologous domains within proteins that interact to regulate the cellular response to DNA damage. The structure provides a basis to predict the structural consequences of uncharacterized BRCA1 mutations. #3: Journal: NAT.STRUCT.BIOL. / Year: 2001 Title: Structure of a BRCA1-BARD1 heterodimeric RING-RING complex Authors: Brzovic PS / Rajagopal P / Hoyt DW / King MC / Klevit RE #4: Journal: J.MOL.BIOL. / Year: 1987 Title: Structure of ubiquitin refined at 1.8 A resolution Authors: Vijay-Kumar S / Bugg CE / Cook WJ | |||||||||
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_6400.map.gz | 6.2 MB | EMDB map data format | |
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Header (meta data) | emd-6400-v30.xml emd-6400.xml | 21.7 KB 21.7 KB | Display Display | EMDB header |
Images | 400_6400.gif 80_6400.gif | 61.5 KB 14.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6400 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6400 | HTTPS FTP |
-Validation report
Summary document | emd_6400_validation.pdf.gz | 78.8 KB | Display | EMDB validaton report |
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Full document | emd_6400_full_validation.pdf.gz | 77.9 KB | Display | |
Data in XML | emd_6400_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6400 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6400 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_6400.map.gz / Format: CCP4 / Size: 12.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of BRCA1-RNAP II mutant complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Mutant BRCA1(5382insC)-RNAP II transcriptional assemblies isolate...
Entire | Name: Mutant BRCA1(5382insC)-RNAP II transcriptional assemblies isolated from hereditary breast cancer cells |
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Components |
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-Supramolecule #1000: Mutant BRCA1(5382insC)-RNAP II transcriptional assemblies isolate...
Supramolecule | Name: Mutant BRCA1(5382insC)-RNAP II transcriptional assemblies isolated from hereditary breast cancer cells type: sample / ID: 1000 Oligomeric state: one mutant BRCA1(5382insC) molecule binds to one polymerase complex Number unique components: 4 |
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Molecular weight | Theoretical: 800 KDa |
-Macromolecule #1: RNA Polyermase II core
Macromolecule | Name: RNA Polyermase II core / type: protein_or_peptide / ID: 1 / Name.synonym: Pol2 / Number of copies: 1 / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Homo sapiens (human) / synonym: human / Tissue: breast / Cell: tumor / Organelle: nucleus |
Molecular weight | Theoretical: 500 KDa |
Sequence | UniProtKB: DNA-directed RNA polymerase II subunit RPB1 |
-Macromolecule #2: BRCA1
Macromolecule | Name: BRCA1 / type: protein_or_peptide / ID: 2 Details: Mutated BRCA1 was attached to tunable microchips using antibodies against the BRCA1 C-terminal domain. Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Homo sapiens (human) / synonym: human / Tissue: breast / Cell: tumor / Organelle: nucleus |
Molecular weight | Theoretical: 200 KDa |
Sequence | UniProtKB: Breast cancer type 1 susceptibility protein |
-Macromolecule #3: BARD1
Macromolecule | Name: BARD1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Homo sapiens (human) / synonym: human / Tissue: breast / Cell: tumor / Organelle: nucleus |
Molecular weight | Theoretical: 87 KDa |
Sequence | UniProtKB: BRCA1-associated RING domain protein 1 |
-Macromolecule #4: Ubiquitin
Macromolecule | Name: Ubiquitin / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Oligomeric state: monomer / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Homo sapiens (human) / synonym: human / Tissue: breast / Cell: tumor / Organelle: nucleus |
Molecular weight | Theoretical: 8 KDa |
Sequence | UniProtKB: Polyubiquitin-C |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 / Details: 50 mM HEPES, 150 mM NaCl, 10 mM MgCl2, 10 mM CaCl2 |
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Staining | Type: NEGATIVE Details: Protein complexes were adsorbed to antibody-decorated microchips for 2 minutes and stained with 1% uranyl formate for 1 minute. |
Grid | Details: SiN microchips with TEM windows coated with 25% Ni-NTA functionalized lipid monolayers |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI SPIRIT |
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Temperature | Min: 83 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at high magnification. |
Details | low-dose illumination |
Date | Mar 23, 2015 |
Image recording | Category: CCD / Film or detector model: FEI EAGLE (2k x 2k) / Digitization - Sampling interval: 30 µm / Number real images: 129 / Average electron dose: 5 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Calibrated magnification: 75000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: -3.0 µm / Nominal defocus min: -1.0 µm / Nominal magnification: 68000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai Spirit / Image courtesy: FEI Company |
-Image processing
Details | The particles were selected using an automatic selection program. |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 26.0 Å / Resolution method: OTHER / Software - Name: RELION / Number images used: 3000 |
Final two d classification | Number classes: 1 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D / Chain - #4 - Chain ID: E / Chain - #5 - Chain ID: F / Chain - #6 - Chain ID: G / Chain - #7 - Chain ID: H / Chain - #8 - Chain ID: I / Chain - #9 - Chain ID: J / Chain - #10 - Chain ID: K / Chain - #11 - Chain ID: L |
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Software | Name: Chimera |
Details | The domains were separately fitted by manual docking using the Chimera software package. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
-Atomic model buiding 2
Initial model | PDB ID: Chain - Chain ID: A |
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Software | Name: Chimera |
Details | The domains were separately fitted by manual docking using the Chimera software package. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
-Atomic model buiding 3
Initial model | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B |
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Software | Name: Chimera |
Details | The domains were separately fitted by manual docking using the Chimera software package. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
-Atomic model buiding 4
Initial model | PDB ID: Chain - Chain ID: A |
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Software | Name: Chimera |
Details | This domain was used to generate a homology based model using the program SWISS-MODEL. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |