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- EMDB-6803: Cryo-EM structure of Human DNA-PK Holoenzyme -

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Basic information

Entry
Database: EMDB / ID: 6803
TitleCryo-EM structure of Human DNA-PK Holoenzyme
Map data
SamplePRKDC-Helix
  • (X-ray repair cross-complementing protein ...) x 2
  • (nucleic-acidNucleic acid) x 2
  • DNA-dependent protein kinase catalytic subunit
Function / homologySPOC-like, C-terminal domain superfamily / Ku70/Ku80 beta-barrel domain / Ku70/Ku80, N-terminal alpha/beta / Ku70/Ku80 C-terminal arm / Phosphatidylinositol 3- and 4-kinases signature 1. / FATC domain / Ku C terminal domain like / PIK-related kinase, FAT / SAP domain / von Willebrand factor, type A ...SPOC-like, C-terminal domain superfamily / Ku70/Ku80 beta-barrel domain / Ku70/Ku80, N-terminal alpha/beta / Ku70/Ku80 C-terminal arm / Phosphatidylinositol 3- and 4-kinases signature 1. / FATC domain / Ku C terminal domain like / PIK-related kinase, FAT / SAP domain / von Willebrand factor, type A / Phosphatidylinositol 3-/4-kinase, catalytic domain / Ku70/Ku80 N-terminal alpha/beta domain / Ku70/Ku80 C-terminal arm / FATC domain / Phosphatidylinositol 3- and 4-kinases signature 2. / FAT domain / SAP domain / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinase / DNA-dependent protein kinase catalytic subunit, catalytic domain / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Ku, C-terminal domain superfamily / von Willebrand factor A-like domain superfamily / SAP domain superfamily / Ku70, bridge and pillars domain superfamily / Ku80 / Ku70/Ku80 beta-barrel domain / NUC194 domain / Phosphatidylinositol 3- and 4-kinases family profile. / IRF3-mediated induction of type I IFN / PIK-related kinase / E3 ubiquitin ligases ubiquitinate target proteins / Neutrophil degranulation / Ku, C-terminal / Armadillo-type fold / Nonhomologous End-Joining (NHEJ) / Protein kinase-like domain superfamily / NUC194 / Cytosolic sensors of pathogen-associated DNA / 2-LTR circle formation / FATC domain profile. / FAT domain profile. / Ku70 / SAP motif profile. / signal transduction involved in mitotic G1 DNA damage checkpoint / negative regulation of response to gamma radiation / negative regulation of immunoglobulin production / Ku70:Ku80 complex / DNA-dependent protein kinase activity / double-strand break repair via classical nonhomologous end joining / double-strand break repair via alternative nonhomologous end joining / negative regulation of t-circle formation / T cell receptor V(D)J recombination / immunoglobulin V(D)J recombination / pro-B cell differentiation / DNA-dependent protein kinase-DNA ligase 4 complex / T cell lineage commitment / cellular response to X-ray / nonhomologous end joining complex / DNA ligation / regulation of smooth muscle cell proliferation / positive regulation of developmental growth / B cell lineage commitment / positive regulation of neurogenesis / hematopoietic stem cell differentiation / nuclear telomere cap complex / 5'-deoxyribose-5-phosphate lyase activity / ectopic germ cell programmed cell death / somitogenesis / cellular hyperosmotic salinity response / regulation of telomere maintenance / ec:3.6.4.-: / ATP-dependent DNA helicase activity / activation of innate immune response / negative regulation of cellular senescence / cellular response to fatty acid / protein localization to chromosome, telomeric region / telomeric DNA binding / telomere capping / positive regulation of catalytic activity / positive regulation of type I interferon production / Other Carbon-Oxygen Lyases / cellular response to leukemia inhibitory factor / positive regulation of protein kinase activity / regulation of circadian rhythm / telomere maintenance / positive regulation of telomere maintenance via telomerase / cyclin binding / cellular protein modification process / double-strand break repair / negative regulation of protein phosphorylation / response to activity / positive regulation of telomerase activity / thymus development / double-strand break repair via nonhomologous end joining / spleen development / ribonucleoprotein complex / protein destabilization / enzyme activator activity / cellular response to gamma radiation
Function and homology information
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 6.6 Å resolution
AuthorsYin X / Liu M
CitationJournal: Cell Res. / Year: 2017
Title: Cryo-EM structure of human DNA-PK holoenzyme.
Authors: Xiaotong Yin / Mengjie Liu / Yuan Tian / Jiawei Wang / Yanhui Xu
Validation ReportPDB-ID: 5y3r

SummaryFull reportAbout validation report
DateDeposition: Jul 29, 2017 / Header (metadata) release: Sep 6, 2017 / Map release: Sep 6, 2017 / Last update: Jun 13, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5y3r
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_6803.map.gz (map file in CCP4 format, 108001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
300 pix
1.3 Å/pix.
= 390. Å
300 pix
1.3 Å/pix.
= 390. Å
300 pix
1.3 Å/pix.
= 390. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density
Contour Level:0.03 (by author), 0.03 (movie #1):
Minimum - Maximum-0.052921083 - 0.13899168
Average (Standard dev.)0.0004368765 (0.00405337)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions300300300
Origin000
Limit299299299
Spacing300300300
CellA=B=C: 390.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z390.000390.000390.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0530.1390.000

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Supplemental data

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Sample components

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Entire PRKDC-Helix

EntireName: PRKDC-Helix / Number of components: 7

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Component #1: protein, PRKDC-Helix

ProteinName: PRKDC-Helix / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #2: protein, X-ray repair cross-complementing protein 6

ProteinName: X-ray repair cross-complementing protein 6 / Recombinant expression: No
MassTheoretical: 57.619352 kDa
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, X-ray repair cross-complementing protein 5

ProteinName: X-ray repair cross-complementing protein 5 / Recombinant expression: No
MassTheoretical: 60.972969 kDa
Source (engineered)Expression System: Homo sapiens (human)

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Component #4: protein, PRKDC-Helix

ProteinName: PRKDC-Helix / Recombinant expression: No
MassTheoretical: 1.084182 kDa
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: nucleic-acid, DNA (34-MER)

Nucleic-acidName: DNA (34-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DT)(DA)(DA)(DA)(DA)(DA)(DC)(DT)(DA)(DT) (DT)(DA)(DT)(DT)(DA)(DT)(DG)(DG)(DT)(DA) (DT)(DT)(DA)(DT)(DG)(DG)(DC)(DC)(DT)(DT) (DG)(DG)(DG)(DC)
MassTheoretical: 10.502785 kDa

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Component #6: nucleic-acid, DNA (36-MER)

Nucleic-acidName: DNA (36-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DC)(DA)(DG)(DC)(DT)(DA)(DA)(DT)(DG)(DG) (DC)(DC)(DA)(DT)(DA)(DA)(DT)(DA)(DC)(DC) (DA)(DT)(DA)(DA)(DT)(DA)(DA)(DT)(DA)(DG) (DT)(DT)(DT)(DT)(DT)(DA)
MassTheoretical: 11.042164 kDa

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Component #7: protein, DNA-dependent protein kinase catalytic subunit

ProteinName: DNA-dependent protein kinase catalytic subunit / Recombinant expression: No
MassTheoretical: 468.885344 kDa
Source (engineered)Expression System: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.6 mg/ml / pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 283 K / Humidity: 1 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 5 e/Å2 / Illumination mode: OTHER
LensMagnification: 18000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1700.0 - 4700.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 3496

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 53451
3D reconstructionSoftware: RELION / Resolution: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Output model

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