- PDB-3sr2: Crystal Structure of Human XLF-XRCC4 Complex -
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ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3sr2
Title
Crystal Structure of Human XLF-XRCC4 Complex
Components
DNA repair protein XRCC4
Non-homologous end-joining factor 1
Keywords
DNA BINDING PROTEIN/PROTEIN BINDING / XRCC4 / XLF / NHEJ / DNA Repair / DNA / DNA Ligases / DNA-Binding Proteins / Dimerization / Humans / Protein Structure / Quaternary / Complex / Non-Homologous End Joining (NHEJ) / DNA ligase IV / Ku / XLF-XRCC4 / Protein DNA-interaction / DNA BINDING PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information
FHA domain binding / positive regulation of ligase activity / DNA ligase IV complex / DNA ligation involved in DNA repair / DNA end binding / DNA-dependent protein kinase-DNA ligase 4 complex / immunoglobulin V(D)J recombination / nonhomologous end joining complex / protein localization to site of double-strand break / response to ionizing radiation ...FHA domain binding / positive regulation of ligase activity / DNA ligase IV complex / DNA ligation involved in DNA repair / DNA end binding / DNA-dependent protein kinase-DNA ligase 4 complex / immunoglobulin V(D)J recombination / nonhomologous end joining complex / protein localization to site of double-strand break / response to ionizing radiation / cellular response to lithium ion / 2-LTR circle formation / T cell differentiation / response to X-ray / SUMOylation of DNA damage response and repair proteins / DNA polymerase binding / B cell differentiation / central nervous system development / Nonhomologous End-Joining (NHEJ) / fibrillar center / double-strand break repair via nonhomologous end joining / double-strand break repair / site of double-strand break / nucleoplasm / identical protein binding / nucleus / cytosol Similarity search - Function
Helix hairpin bin / DNA double-strand break repair and VJ recombination XRCC4, N-terminal / Dna Repair Protein Xrcc4; Chain: A, domain 1 / XLF, N-terminal / XLF N-terminal domain / XRCC4, N-terminal domain superfamily / DNA repair protein XRCC4 / XRCC4 N-terminal domain / XRCC4-like, N-terminal domain superfamily / DNA repair protein XRCC4-like, C-terminal ...Helix hairpin bin / DNA double-strand break repair and VJ recombination XRCC4, N-terminal / Dna Repair Protein Xrcc4; Chain: A, domain 1 / XLF, N-terminal / XLF N-terminal domain / XRCC4, N-terminal domain superfamily / DNA repair protein XRCC4 / XRCC4 N-terminal domain / XRCC4-like, N-terminal domain superfamily / DNA repair protein XRCC4-like, C-terminal / Beta Complex / Helix Hairpins / Orthogonal Bundle / Mainly Beta / Mainly Alpha Similarity search - Domain/homology
A: DNA repair protein XRCC4 B: DNA repair protein XRCC4 C: Non-homologous end-joining factor 1 D: Non-homologous end-joining factor 1 E: DNA repair protein XRCC4 F: DNA repair protein XRCC4 G: Non-homologous end-joining factor 1 H: Non-homologous end-joining factor 1
DNArepairproteinXRCC4 / X-ray repair cross-complementing protein 4
Mass: 16256.343 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC4 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) pLysS / References: UniProt: Q13426
#2: Protein
Non-homologousend-joiningfactor1 / Protein cernunnos / XRCC4-like factor
Mass: 25868.922 Da / Num. of mol.: 4 / Fragment: UNP Residues 1-224 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NHEJ1, XLF / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) pLysS / References: UniProt: Q9H9Q4
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 3.96 Å3/Da / Density % sol: 68.93 %
Crystal grow
Temperature: 303.15 K / Method: vapor diffusion / pH: 7 Details: protein combined with equal volumes of 100 mM HEPES, pH 7.8, 13% (w/v) PEG 3350, 300 mM NaCl, 2 mM ADP, 7 mM NaF and 3 mM BeCl) and then dehydrated over 1000 ul of 19% PEG 3350, 300 mM NaCl, ...Details: protein combined with equal volumes of 100 mM HEPES, pH 7.8, 13% (w/v) PEG 3350, 300 mM NaCl, 2 mM ADP, 7 mM NaF and 3 mM BeCl) and then dehydrated over 1000 ul of 19% PEG 3350, 300 mM NaCl, 100 mM HEPES, pH7.8 under argon., vapor diffusion, temperature 303.15K
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Data collection
Diffraction
Mean temperature: 90 K
Diffraction source
Source: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.116 Å
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