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Yorodumi- EMDB-44537: Human DNA polymerase theta helicase domain dimer bound to DNA in ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-44537 | |||||||||
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Title | Human DNA polymerase theta helicase domain dimer bound to DNA in the microhomology aligning conformation | |||||||||
Map data | Map locally filtered by resolution | |||||||||
Sample |
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Keywords | DNA repair / TMEJ / MMEJ / DNA binding protein | |||||||||
Function / homology | Function and homology information single-stranded DNA endodeoxyribonuclease activity / HDR through MMEJ (alt-NHEJ) / single-stranded DNA helicase activity / double-strand break repair via alternative nonhomologous end joining / replication fork processing / site of DNA damage / 5'-deoxyribose-5-phosphate lyase activity / somatic hypermutation of immunoglobulin genes / negative regulation of double-strand break repair via homologous recombination / error-prone translesion synthesis ...single-stranded DNA endodeoxyribonuclease activity / HDR through MMEJ (alt-NHEJ) / single-stranded DNA helicase activity / double-strand break repair via alternative nonhomologous end joining / replication fork processing / site of DNA damage / 5'-deoxyribose-5-phosphate lyase activity / somatic hypermutation of immunoglobulin genes / negative regulation of double-strand break repair via homologous recombination / error-prone translesion synthesis / DNA helicase activity / base-excision repair / protein homooligomerization / RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / double-strand break repair / site of double-strand break / DNA helicase / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / DNA damage response / chromatin binding / Golgi apparatus / magnesium ion binding / ATP hydrolysis activity / nucleoplasm / ATP binding / identical protein binding / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Zerio CJ / Lander GC | |||||||||
Funding support | United States, 2 items
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Citation | Journal: To Be Published Title: Human polymerase theta helicase positions DNA microhomologies for double-strand break repair Authors: Zerio CJ / Bai Y / Sosa-Alvarado BA / Guzi T / Lander GC | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_44537.map.gz | 5.7 MB | EMDB map data format | |
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Header (meta data) | emd-44537-v30.xml emd-44537.xml | 25.4 KB 25.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_44537_fsc.xml | 12.2 KB | Display | FSC data file |
Images | emd_44537.png | 95.2 KB | ||
Masks | emd_44537_msk_1.map | 129.7 MB | Mask map | |
Filedesc metadata | emd-44537.cif.gz | 7.7 KB | ||
Others | emd_44537_additional_1.map.gz emd_44537_half_map_1.map.gz emd_44537_half_map_2.map.gz | 122.5 MB 120.5 MB 120.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-44537 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-44537 | HTTPS FTP |
-Validation report
Summary document | emd_44537_validation.pdf.gz | 835.8 KB | Display | EMDB validaton report |
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Full document | emd_44537_full_validation.pdf.gz | 835.4 KB | Display | |
Data in XML | emd_44537_validation.xml.gz | 19 KB | Display | |
Data in CIF | emd_44537_validation.cif.gz | 24.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-44537 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-44537 | HTTPS FTP |
-Related structure data
Related structure data | 9bh9MC 9bh6C 9bh7C 9bh8C 9bhaC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_44537.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Map locally filtered by resolution | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.833 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_44537_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Sharp map
File | emd_44537_additional_1.map | ||||||||||||
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Annotation | Sharp map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A
File | emd_44537_half_map_1.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B
File | emd_44537_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human DNA polymerase theta helicase domain bound to stem-loop DNA...
Entire | Name: Human DNA polymerase theta helicase domain bound to stem-loop DNA with microhomology in the 3' overhang |
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Components |
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-Supramolecule #1: Human DNA polymerase theta helicase domain bound to stem-loop DNA...
Supramolecule | Name: Human DNA polymerase theta helicase domain bound to stem-loop DNA with microhomology in the 3' overhang type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 20 KDa |
-Supramolecule #2: Human DNA polymerase theta helicase domain
Supramolecule | Name: Human DNA polymerase theta helicase domain / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: Stem-loop DNA with microhomology in the 3' overhang
Supramolecule | Name: Stem-loop DNA with microhomology in the 3' overhang / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: DNA polymerase theta
Macromolecule | Name: DNA polymerase theta / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA helicase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 99.671344 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: NLLRRSGKRR RSESGSDSFS GSGGDSSASP QFLSGSVLSP PPGLGRCLKA AAAGECKPTV PDYERDKLLL ANWGLPKAVL EKYHSFGVK KMFEWQAECL LLGQVLEGKN LVYSAPTSAG KTLVAELLIL KRVLEMRKKA LFILPFVSVA KEKKYYLQSL F QEVGIKVD ...String: NLLRRSGKRR RSESGSDSFS GSGGDSSASP QFLSGSVLSP PPGLGRCLKA AAAGECKPTV PDYERDKLLL ANWGLPKAVL EKYHSFGVK KMFEWQAECL LLGQVLEGKN LVYSAPTSAG KTLVAELLIL KRVLEMRKKA LFILPFVSVA KEKKYYLQSL F QEVGIKVD GYMGSTSPSR HFSSLDIAVC TIERANGLIN RLIEENKMDL LGMVVVDELH MLGDSHRGYL LELLLTKICY IT RKSASCQ ADLASSLSNA VQIVGMSATL PNLELVASWL NAELYHTDFR PVPLLESVKV GNSIYDSSMK LVREFEPMLQ VKG DEDHVV SLCYETICDN HSVLLFCPSK KWCEKLADII AREFYNLHHQ AEGLVKPSEC PPVILEQKEL LEVMDQLRRL PSGL DSVLQ KTVPWGVAFH HAGLTFEERD IIEGAFRQGL IRVLAATSTL SSGVNLPARR VIIRTPIFGG RPLDILTYKQ MVGRA GRKG VDTVGESILI CKNSEKSKGI ALLQGSLKPV RSCLQRREGE EVTGSMIRAI LEIIVGGVAS TSQDMHTYAA CTFLAA SMK EGKQGIQRNQ ESVQLGAIEA CVMWLLENEF IQSTEASDGT EGKVYHPTHL GSATLSSSLS PADTLDIFAD LQRAMKG FV LENDLHILYL VTPMFEDWTT IDWYRFFCLW EKLPTSMKRV AELVGVEEGF LARCVKGKVV ARTERQHRQM AIHKRFFT S LVLLDLISEV PLREINQKYG CNRGQIQSLQ QSAAVYAGMI TVFSNRLGWH NMELLLSQFQ KRLTFGIQRE LCDLVRVSL LNAQRARVLY ASGFHTVADL ARANIVEVEV ILKNAVPFKS ARKAVDEEEE AVEERRNMRT IWVTGRKGLT EREAAALIVE EARMILQQD LVEM UniProtKB: DNA polymerase theta |
-Macromolecule #2: Stem-loop DNA with microhomology in the 3' overhang
Macromolecule | Name: Stem-loop DNA with microhomology in the 3' overhang / type: dna / ID: 2 / Number of copies: 2 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 17.264012 KDa |
Sequence | String: (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DC)(DA)(DC)(DT) (DG)(DT)(DG)(DA)(DG)(DC)(DT)(DT)(DA) (DG)(DC)(DG)(DT)(DT)(DA)(DG)(DA)(DG)(DT) (DA) (DG)(DG)(DT)(DT)(DT)(DT) ...String: (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DC)(DA)(DC)(DT) (DG)(DT)(DG)(DA)(DG)(DC)(DT)(DT)(DA) (DG)(DC)(DG)(DT)(DT)(DA)(DG)(DA)(DG)(DT) (DA) (DG)(DG)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DG)(DC)(DC)(DC)(DG)(DG)(DG) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.25 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. Details: Grids were glow discharged under vacuum for 30 s at 15 mA in a Pelco easiGlow 91000 Glow Discharge Cleaning System. | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: HOMEMADE PLUNGER Details: 3 microliters of sample was applied to the surface of the grid, blotted for 2 seconds after the liquid spot on the filter paper stopped spreading, and the grid was plunged into a liquid ...Details: 3 microliters of sample was applied to the surface of the grid, blotted for 2 seconds after the liquid spot on the filter paper stopped spreading, and the grid was plunged into a liquid ethane bath cooled by liquid nitrogen.. | ||||||||||||
Details | We added 2X pre-annealed DNA to the protein, lowered the NaCl concentration to 100 mM, and purified the DNA-bound complex by SEC. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 70.0 K / Max: 77.0 K |
Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 12440 / Average exposure time: 1.4 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 150.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 0.3 µm / Calibrated magnification: 60024 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
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Details | We modeled DNA bases into sharpened density when possible. We modeled the DNA backbone into locally filtered density in low resolution areas. | |||||||||
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 67.19 / Target criteria: Cross-correlation coefficient | |||||||||
Output model | PDB-9bh9: |