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- EMDB-6400: Electron microscopy of BRCA1(5832insC) mutant-RNAP II transcripti... -
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Open data
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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 | |||||||||
![]() | Reconstruction of BRCA1-RNAP II mutant complex | |||||||||
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![]() | transcription / DNA damage repair / breast cancer / protein | |||||||||
Function / homology | ![]() 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 / DNA strand resection involved in replication fork processing / chordate embryonic development / cellular response to indole-3-methanol / negative regulation of fatty acid biosynthetic process / homologous recombination / lateral element / 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 / negative regulation of gene expression via chromosomal CpG island methylation / intracellular non-membrane-bounded organelle / HDR through Single Strand Annealing (SSA) / Signaling by FGFR2 IIIa TM / Impaired BRCA2 binding to RAD51 / DNA-binding transcription activator activity / response to ionizing radiation / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / 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 / positive regulation of vascular endothelial growth factor production / negative regulation of reactive oxygen species metabolic process / localization / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / protein autoubiquitination / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase II, core complex / regulation of DNA repair / SUMOylation of DNA damage response and repair proteins / RNA Polymerase II Transcription Elongation / RNA polymerase II activity / Formation of RNA Pol II elongation complex / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / ubiquitin ligase complex / 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 / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 26.0 Å | |||||||||
![]() | Winton CE / Gilmore BL / Demmert AC / Tanner JR / Bowman S / Karageorge V / Patel K / Sheng Z / Kelly DF | |||||||||
![]() | ![]() 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: ![]() Title: Structure of a BRCA1-BARD1 heterodimeric RING-RING complex Authors: Brzovic PS / Rajagopal P / Hoyt DW / King MC / Klevit RE #4: ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 6.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 21.7 KB 21.7 KB | Display Display | ![]() |
Images | ![]() ![]() | 61.5 KB 14.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 78.8 KB | Display | ![]() |
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Full document | ![]() | 77.9 KB | Display | |
Data in XML | ![]() | 494 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of BRCA1-RNAP II mutant complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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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: ![]() |
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: ![]() |
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: ![]() |
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: ![]() |
Molecular weight | Theoretical: 8 KDa |
Sequence | UniProtKB: Polyubiquitin-C |
-Experimental details
-Structure determination
Method | negative staining |
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![]() | single particle reconstruction |
Aggregation state | particle |
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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 |
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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 |
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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: ![]() |
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: ![]() |
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: ![]() |
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: ![]() |
Details | This domain was used to generate a homology based model using the program SWISS-MODEL. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |