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Open data
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Basic information
Entry | Database: PDB / ID: 6kea | ||||||
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Title | crystal structure of MBP-tagged REV7-IpaB complex | ||||||
![]() | Maltose-binding periplasmic protein,LINKER,hREV7,LINKER,Invasin IpaB,hREV3 | ||||||
![]() | CELL CYCLE / REV7 / MAD2B / MAD2L2 / Shigella Invasin IpaB | ||||||
Function / homology | ![]() somatic diversification of immunoglobulins involved in immune response / DNA damage response, signal transduction resulting in transcription / telomere maintenance in response to DNA damage / negative regulation of transcription regulatory region DNA binding / zeta DNA polymerase complex / positive regulation of isotype switching / positive regulation of extracellular matrix assembly / negative regulation of transcription by competitive promoter binding / negative regulation of cell-cell adhesion mediated by cadherin / JUN kinase binding ...somatic diversification of immunoglobulins involved in immune response / DNA damage response, signal transduction resulting in transcription / telomere maintenance in response to DNA damage / negative regulation of transcription regulatory region DNA binding / zeta DNA polymerase complex / positive regulation of isotype switching / positive regulation of extracellular matrix assembly / negative regulation of transcription by competitive promoter binding / negative regulation of cell-cell adhesion mediated by cadherin / JUN kinase binding / negative regulation of epithelial to mesenchymal transition / negative regulation of ubiquitin protein ligase activity / detection of maltose stimulus / maltose transport complex / mitotic spindle assembly checkpoint signaling / positive regulation of double-strand break repair via nonhomologous end joining / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / host cell membrane / maltodextrin transmembrane transport / negative regulation of double-strand break repair via homologous recombination / error-prone translesion synthesis / positive regulation of epithelial to mesenchymal transition / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / cell chemotaxis / regulation of cell growth / actin filament organization / double-strand break repair via homologous recombination / negative regulation of canonical Wnt signaling pathway / negative regulation of protein catabolic process / negative regulation of DNA-binding transcription factor activity / DNA-templated DNA replication / spindle / host cell / double-strand break repair / positive regulation of peptidyl-serine phosphorylation / chromosome / site of double-strand break / 4 iron, 4 sulfur cluster binding / outer membrane-bounded periplasmic space / RNA polymerase II-specific DNA-binding transcription factor binding / periplasmic space / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / cell division / nucleotide binding / DNA damage response / host cell nucleus / chromatin / nucleolus / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / extracellular region / nucleoplasm / membrane / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, X. / Pernicone, N. / Pertz, L. / Hua, D.P. / Zhang, T.Q. / Listovsky, T. / Xie, W. | ||||||
Funding support | ![]()
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![]() | ![]() Title: REV7 has a dynamic adaptor region to accommodate small GTPase RAN/ShigellaIpaB ligands, and its activity is regulated by the RanGTP/GDP switch. Authors: Wang, X. / Pernicone, N. / Pertz, L. / Hua, D. / Zhang, T. / Listovsky, T. / Xie, W. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 447.9 KB | Display | ![]() |
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PDB format | ![]() | 369 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 464.8 KB | Display | ![]() |
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Full document | ![]() | 489.5 KB | Display | |
Data in XML | ![]() | 78.3 KB | Display | |
Data in CIF | ![]() | 108.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6nifC ![]() 3abdS ![]() 3vd8S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 68963.570 Da / Num. of mol.: 4 / Mutation: D83A/K84A/E173A/N174A/K240A/R485A Source method: isolated from a genetically manipulated source Details: MBP-tagged human REV7 and Shigella Invasin IpaB fusion protein Source: (gene. exp.) ![]() ![]() ![]() ![]() Strain: K12 / Production host: ![]() ![]() References: UniProt: P0AEX9, UniProt: Q9UI95, UniProt: P18011, UniProt: O60673 #2: Water | ChemComp-HOH / | Sequence details | residues 360-373 and 573-596 are LINKER | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 100 mM Bistris, pH 5.6, 25% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→29.91 Å / Num. obs: 98435 / % possible obs: 97.5 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.1366 / Net I/σ(I): 14.22 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.8728 / % possible all: 97.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3VD8, 3ABD Resolution: 2.35→29.91 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.35→29.91 Å
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LS refinement shell | Resolution: 2.35→2.434 Å
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